Package ‘plotrix’

October 3, 2018
Version 3.7-4
Date 2018-10-03
Title Various Plotting Functions
Author Jim Lemon, Ben Bolker, Sander Oom,
Eduardo Klein, Barry Rowlingson,
Hadley Wickham, Anupam Tyagi,
Olivier Eterradossi, Gabor Grothendieck,
Michael Toews, John Kane, Rolf Turner,
Carl Witthoft, Julian Stander, Thomas Petzoldt,
Remko Duursma, Elisa Biancotto, Ofir Levy,
Christophe Dutang, Peter Solymos, Robby Engelmann,
Michael Hecker, Felix Steinbeck, Hans Borchers,
Henrik Singmann, Ted Toal, Derek Ogle, Darshan Baral,
Ulrike Groemping
Maintainer Jim Lemon <drjimlemon@gmail.com>
Imports grDevices, graphics, stats, utils
Description Lots of plots, various labeling, axis and color scaling functions.
License GPL (>= 2)
NeedsCompilation no
Repository CRAN
Date/Publication 2018-10-03 10:40:03 UTC

R topics documented:
plotrix-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
ablineclip . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
add.ps . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7
addtable2plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9
arctext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
axis.break . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
axis.mult . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
barlabels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15

1
2 R topics documented:

barNest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
barp . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
battleship.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
bin.wind.records . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24
binciW . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25
binciWl . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
binciWu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27
box.heresy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28
boxed.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
brkdn.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31
brkdnNest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33
bumpchart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
categoryReshape . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36
centipede.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37
clean.args . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
clock24.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
clplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
cluster.overplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 42
clustered.dotplots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
color.axis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
color.gradient . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
color.id . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 46
color.legend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 47
color.scale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 48
color.scale.lines . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 50
color2D.matplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
corner.label . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
count.overplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 55
cylindrect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
death_reg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
dendroPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
diamondplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59
dispersion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
do.first . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
dotplot.mtb . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
draw.arc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
draw.circle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
draw.ellipse . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 66
draw.radial.line . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
draw.tilted.sector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
drawNestedBars . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69
drawSectorAnnulus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 71
ehplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
election . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
emptyspace . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 74
fan.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
feather.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 77
fill.corner . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
R topics documented: 3

floating.pie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 79
fullaxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 80
furc . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
gantt.chart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
gap.barplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 85
gap.boxplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
gap.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 88
get.breaks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
get.gantt.info . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
get.segs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 92
get.soil.texture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
get.tablepos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
get.triprop . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
getFigCtr . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
getIntersectList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
getMarginWidth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
getYmult . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
get_axispos3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99
gradient.rect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
hexagon . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
histStack . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
intersectDiagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
jiggle . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
joyPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 107
kiteChart . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
labbePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 111
ladderplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
legendg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
lengthKey . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
listDepth . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
makeDendrite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
makeIntersectList . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
maxEmptyRect . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
mtext3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
multhist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 121
multivari . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
multsymbolbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125
oz.windrose . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
oz.windrose.legend . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
p2p_arrows . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
panes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
pasteCols . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 131
paxis3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 132
perspx . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 133
pie.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 134
pie3D . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 135
pie3D.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 137
placeLabels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
4 R topics documented:

plot.dendrite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 139
plotCI . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 140
plotH . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 142
plot_bg . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 144
polar.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 145
polygon.shadow . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
print.brklist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 147
propbrk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 148
psegments3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 149
ptext3d . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
pyramid.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 150
radial.grid . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 153
radial.pie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 154
radial.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 156
radial.plot.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 159
radialtext . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 161
raw.means.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 162
rectFill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 168
rescale . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 169
revaxis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 170
ruginv . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 171
seats . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 172
sizeplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 173
sizetree . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 174
size_n_color . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 176
sliceArray . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
smoothColors . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
soil.texture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 180
soil.texture.uk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 182
soils . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
spread.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 184
spreadout . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 186
stackpoly . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 187
staircase.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 189
staircasePlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 191
starPie . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 193
staxlab . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 194
std.error . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 195
sumbrk . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 196
sumDendrite . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 197
symbolbarplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 198
symbolbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 199
tab.title . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 200
taylor.diagram . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 201
textbox . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 203
thigmophobe . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 205
thigmophobe.labels . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 206
triax.abline . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
plotrix-package 5

triax.fill . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 208
triax.frame . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 209
triax.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 211
triax.points . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 213
tsxpos . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
twoord.plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 215
twoord.stackplot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 218
valid.n . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220
vectorField . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 221
violin_plot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 222
weighted.hist . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 224
zoomInPlot . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 225

Index 227

plotrix-package Specialized plots and plotting accessories

Description
A large number of specialized plots and accessory functions like color scaling, text placement and
legends.

Details

Package: plotrix
Version: 3.7-4
Date: 2018-10-03
License: GPL (>=2)
Packaged: 2018-10-03 7:47:00 UTC; root
Built: R 3.5.0; ; 2018-10-03 7:47:00 UTC; linux

The plotrix package is intended to provide a method for getting many sorts of specialized plots
quickly, yet allow easy customization of those plots without learning a great deal of specialized
syntax. There are three major aims that can be represented as follows:
Fast foods
Think of plotrix as a graphics vending machine or fast graphics cafe. You walk in, make your choice
and get your lunch. It may not be exactly the lunch you want, but you do get a pretty good lunch,
fast. You can get junk food or health food, you make the choice.
Hot rods
You can customize plotrix as much as you want. Like the ageing machinery that is usually bolted
into hot rods, the base graphics package is fairly easy to understand. plotrix is modular. You can
create a frame for your plot, then you can add whatever bits you like to it instead of just taking the
default plot that is available. You can have wide wheels and chromed exhaust pipes if you want.
6 ablineclip

No black boxes
If you want to go from pushing the fast food button to hot rodding, it’s not hard. The source code
in the functions is written to be understood. If something goes wrong, you can usually find where
it happened right away and work on it. This means that you can learn about how the functions do
what they do rather than just what they do. So that’s how to write recursive functions in R!
Because plotrix encourages users to learn how it works, you usually begin to do so pretty quickly.
Users often decide to write their own versions of plotrix functions and sometimes they contribute
the results back into plotrix. You may find that you like other graphics systems like grid or lattice
better. That’s great, because one idea behind plotrix is that if you get into R and can get things done
quickly and easily, you’ll stick with it and soon want to get things done your way.

Author(s)

Jim Lemon <drjimlemon@gmail.com>, and many others

Maintainer: Jim Lemon <drjimlemon@gmail.com>

ablineclip Add a straight line to a plot

Description

As ‘abline’, but has arguments ‘x1,x2,y1,y2’ as in ‘clip’.

Usage

ablineclip(a=NULL,b=NULL,h=NULL,v=NULL,reg=NULL,coef=NULL,untf=FALSE,
x1=NULL,x2=NULL,y1=NULL,y2=NULL,...)

Arguments

a Intercept.
b Slope.
h the x-value(s) for vertical line(s).
v the y-value(s) for horizontal line(s).
reg Fitted lm object.
coef Coefficients, typically intercept and slope.
untf How to plot on log coordinates, see ‘abline’.
x1,x2,y1,y2 Clipping limits, see ‘clip’.
... Further arguments passed to ‘abline’.
add.ps 7

Details

‘ablineclip’ sets a new clipping region and then calls ‘abline’. If any of the four clipping limits
is NULL, the values from ‘par("usr")’ are substituted. After the call to ‘abline’, the old clipping
region is restored. In order to make ‘clip’ work, there is a call to ‘abline’ that draws a line off the
plot.
Multiple lines of the same type can be drawn in a single call, but the clipping region must be the
same for each group of lines. Thanks to Berry Boessenkool for pointing this out.

Value

None. Adds to the current plot.

Author(s)

Remko Duursma

See Also

abline, clip

Examples
x <- rnorm(100)
y <- x + rnorm(100)
lmfit <- lm(y~x)
plot(x, y, xlim=c(-3.5, 3.5))
ablineclip(lmfit, x1 = -2, x2 = 2, lty = 2)
ablineclip(h = 0, x1 = -2,x2 = 2,lty = 3, col = "red")
ablineclip(v = 0, y1 = -2.5, y2 = 1.5, lty=4, col = "green")

add.ps add p-values from t-tests

Description

Adds p-values comparing the different cells at each x-axis position with a reference cell. Uses a
syntax similar to ‘raw.means.plot2’.

Usage

add.ps(data, col.id, col.offset, col.x, col.value, fun.aggregate = "mean",

ref.offset = 1, prefixes,alternative = c("two.sided", "less", "greater"),
mu = 0, paired = FALSE, var.equal = FALSE, lty = 0, ...)
8 add.ps

Arguments
data A ‘data.frame’
col.id ‘character’ vector specifying the id column.
col.offset ‘character’ vector specifying the offset column.
col.x ‘character’ vector specifying the x-axis column.
col.value ‘character’ vector specifying the data column.
fun.aggregate Function or function name used for aggregating the results. Default is ‘"mean"’.
ref.offset Scalar ‘numeric’ indicating the reference level to be tested against. The default
is 1 corresponding to ‘levels(factor(d[,col.offset]))[1]’.
prefixes ‘character’ vector of the indices for the p-values. If missing corresponds to
‘levels(factor(d.new[,col.offset]))[-ref.offset]’.
alternative same as in t.test
mu same as in t.test
paired same as in t.test
var.equal same as in t.test
lty line type of axis, Default is 0 (i.e., no line).
... further arguments passed to axis.

Details
This function computes t-tests comparing the values at each x-axis position for each condition
against the reference condition at and adds the p-values to the axis.
This functions uses the same syntax as raw.means.plot2 and should be used in addition to it. Note
that values are ordered according to the ‘col.id’ so ‘paired = TRUE’ should be fine.

Value
axis is plotted.

Author(s)
Henrik Singmann

See Also
raw.means.plot as the accompanying main functions.

Examples
## Not run:
#The examples uses the OBrienKaiser dataset from car and needs reshape.
# This extends the examples from raw.means.plot
require(reshape)
require(car)
data(OBrienKaiser)
addtable2plot 9

OBKnew <- cbind(factor(1:nrow(OBrienKaiser)), OBrienKaiser)

colnames(OBKnew)[1] <- "id"
OBK.long <- melt(OBKnew)
OBK.long[, c("measurement", "time")] <-
t(vapply(strsplit(as.character(OBK.long$variable), "\\."), "[", c("", "")))

# For this example the position at each x-axis are within-subject comparisons!
raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")
add.ps(OBK.long, "id", "measurement", "gender", "value", paired = TRUE)
#reference is "fup"

raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")

add.ps(OBK.long, "id", "measurement", "gender", "value", ref.offset = 2,
paired = TRUE) #reference is "post"

# Use R's standard (i.e., Welch test)

raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")
add.ps(OBK.long, "id", "treatment", "gender", "value",
prefixes = c("p(control vs. A)", "p(control vs. B)"))

# Use standard t-test

raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")
add.ps(OBK.long, "id", "treatment", "gender", "value", var.equal = TRUE,
prefixes = c("p(control vs. A)", "p(control vs. B)"))

## End(Not run)

addtable2plot Add a table of values to a plot

Description
Displays a table of values at a user-specified position on an existing plot

Usage
addtable2plot(x,y=NULL,table,lwd=par("lwd"),bty="n",bg=par("bg"),
cex=1,xjust=0,yjust=1,xpad=0.1,ypad=0.5,box.col=par("fg"),text.col=par("fg"),
display.colnames=TRUE,display.rownames=FALSE,hlines=FALSE,vlines=FALSE,
title=NULL)

Arguments
x,y Either x and y coordinates to locate the table or an ‘xy.coords’ object.
table A data frame, matrix or similar object that will be displayed.
lwd The line width for the box and horizontal dividers.
bty Whether to draw a box around the table ("o") or not ("n").
10 addtable2plot

bg The background color for the table.

cex Character expansion for the table.
xjust,yjust Positioning for the table relative to ‘x,y’.
xpad,ypad The amount of padding around text in the cells as a proportion of the maximum
width and height of the strings in each column.
box.col The color for the box and lines.
text.col The color for the text.
display.colnames
Whether to display the column names in the table.
display.rownames
Whether to display the row names in the table.
hlines Whether to draw horizontal lines between each row of the table.
vlines Whether to draw vertical lines between each column of the table.
title Optional title placed over the table.

Details
‘addtable2plot’ displays the values in ‘table’ at a position in user coordinates specified by ‘x,y’.
The two justification arguments, ‘xjust’ and ‘yjust’ are the same as in the ‘legend’ function, and
‘addtable2plot’ has been programmed to be as similar to ‘legend’ as possible. The function now
accepts the positional arguments such as "topright" if passed as ‘x’. The defaults are those that were
most popular in scientific journals at the time of programming.
If ‘bg’ is a matrix of colors of the same dimensions as ‘x’, those colors will be the backgrounds of
the cells. The default is no background color.

Value
nil

Author(s)
Original by John Kane, mods by Jim Lemon and Brian Diggs. Thanks to Andrija Djurovic for
asking for the individual cell colors and Gabor Grothendieck for alerting me to the problem of
widely varying column widths.

See Also
legend

Examples
testdf <- data.frame(Before = c(10, 7, 5, 9), During = c(8, 6, 2, 5),
After = c(5, 3, 4, 3))
rownames(testdf) <- c("Red", "Green", "Blue", "Lightblue")
barp(testdf, main = "Test addtable2plot", ylab = "Value",
names.arg = colnames(testdf), col = 2:5)
# show most of the options including the christmas tree colors
arctext 11

abg <- matrix(c(2, 3, 5, 6, 7, 8), nrow=4, ncol=3)

addtable2plot(2, 8, testdf, bty = "o", display.rownames = TRUE, hlines = TRUE,
vlines = TRUE, title = "The table", bg = abg)

arctext Display text on a circular arc

Description
Displays a character string on the circumference of an imaginary circle on an existing plot.

Usage
arctext(x,center=c(0,0),radius=1,start=NA,middle=pi/2,end=NA,stretch=1,
clockwise=TRUE,cex=NA,...)

Arguments
x A character string.
center The center of the circular arc in x/y user units.
radius The radius of the arc in user units.
start The starting position of the string in radians.
middle The middle position of the string in radians.
end The end position of the string in radians.
stretch How much to stretch the string for appearance.
clockwise Whether to print the string in the clockwise direction.
cex The character expansion factor.
... additional arguments passed to ‘text’.

Details
‘arctext’ displays a string along a circular arc, rotating each letter. This may not work on all
devices, as not all graphic devices can rotate text to arbitrary angles. The output looks best on a
Postscript or similar device that can rotate text without distortion. Rotated text often looks very
ragged on small bitmaps.
If the user passes a value for ‘start’, this will override any value passed to ‘middle’. If the plot
area is not square, see ‘par(pty="s")’, the arc will be somewhat elliptical.
If the ‘clockwise’ argument is TRUE, the string will be displayed in a clockwise direction and
the orientation of the characters will be rotated ‘pi’ radians (180 degrees). This is useful when the
string is to be displayed on the bottom of the circumference.

Value
nil
12 axis.break

Author(s)
Jim Lemon - Thanks to Suhas Parandekar for the idea, Ted Toal for greatly improving the placement
of the text and Andy South for providing the initial code for the clockwise argument.

See Also
text

Examples
plot(0, xlim = c(1, 5),ylim = c(1, 5),main = "Test of arctext", xlab = "",
ylab = "", type = "n")
arctext("bendy like spaghetti", center = c(3,3), col = "blue")
arctext("bendy like spaghetti", center = c(3,3), radius = 1.5, start = pi,
cex = 2)
arctext("bendy like spaghetti", center = c(3, 3),radius = 0.5,
start = pi/2, stretch = 1.2)
arctext("bendy like spaghetti", center = c(3, 3), radius = 1.7,
start = 4 * pi / 3, cex = 1.3, clockwise = FALSE)

axis.break Place a "break" mark on an axis

Description
Places a "break" mark on an axis on an existing plot.

Usage
axis.break(axis=1,breakpos=NULL,pos=NA,bgcol="white",breakcol="black",
style="slash",brw=0.02)

Arguments
axis which axis to break
breakpos where to place the break in user units
pos position of the axis (see axis).
bgcol the color of the plot background
breakcol the color of the "break" marker
style Either ‘gap’, ‘slash’ or ‘zigzag’
brw break width relative to plot width

Details
The ‘pos’ argument is not needed unless the user has specified a different position from the default
for the axis to be broken.
axis.mult 13

Value

nil

Note

There is some controversy about the propriety of using discontinuous coordinates for plotting, and
thus axis breaks. Discontinuous coordinates allow widely separated groups of values or outliers to
appear without devoting too much of the plot to empty space. The major objection seems to be that
the reader will be misled by assuming continuous coordinates. The ‘gap’ style that clearly separates
the two sections of the plot is probably best for avoiding this.

Author(s)

Jim Lemon and Ben Bolker

See Also

gap.plot

Examples
plot(3:10, main = "Axis break test")
# put a break at the default axis and position
axis.break()
axis.break(2, 2.9, style = "zigzag")
twogrp <- c(rnorm(10) + 4, rnorm(10) + 20)
gap.plot(twogrp,gap = c(8,16), xlab = "Index", ylab = "Group values",
main = "Two separated groups with gap axis break",
col = c(rep(2, 10), rep(3, 10)), ytics = c(3, 5, 18, 20))
legend(12, 6, c("Low group", "High group"), pch = 1, col = 2:3)

axis.mult Display an axis with values having a multiplier

Description

An axis is displayed on an existing plot where the tick values are divided by a multiplier and the
multiplier is displayed next to the axis.

Usage

axis.mult(side=1,at=NULL,labels,mult=1,mult.label,mult.line,
mult.labelpos=NULL,...)
14 axis.mult

Arguments
side which side to display
at where to place the tick marks - defaults to ‘axTicks()’
labels tick labels - defaults to at/mult
mult the multiplier factor
mult.label the label to show the multiplier - defaults to "x mult"
mult.line the margin line upon which to show the multiplier
mult.labelpos where to place ‘mult.label’ - defaults to centered and outside the axis tick
labels
... additional arguments passed to ‘axis’.

Details
‘axis.mult’ automates the process of displaying an axis with a multiplier applied to the tick values.
By default it will divide the default axis tick labels by ‘mult’ and place ‘mult.label’ where ‘xlab’
or ‘ylab’ would normally appear. Thus the plot call should set the relevant label to an empty string
in such cases. It is simplest to call ‘plot’ with ‘axes=FALSE’ and then display the box and any
standard axes before calling ‘axis.mult’.

Value
nil

Note
While ‘axis.mult’ will try to display an axis on any side, the top and right margins will require
adjustment using ‘par’ for ‘axis.mult’ to display properly.

Author(s)
Jim Lemon

See Also
axis, mtext

Examples
plot(1:10 * 0.001, 1:10 * 100,axes = FALSE, xlab = "", ylab = "",
main = "Axis multipliers")
box()
axis.mult(1, mult = 0.001)
axis.mult(2, mult = 100)
barlabels 15

barlabels Label the bars on a barplot

Description

Displays labels on a plot, usually a bar plot.

Usage

barlabels(xpos,ypos,labels=NULL,cex=1,prop=0.5,miny=0,offset=0,...)

Arguments

xpos A vector, matrix or data frame of x positions for the labels.

ypos A vector, matrix or data frame of y positions for the labels.
labels The labels to display. Defaults to the values of y.
cex Relative size of the labels. See ‘text’.
prop The proportion of ‘ypos’ at which to place the labels. Defaults to 0.5 (the mid-
dle).
miny The minimum value at which to display labels.
offset Amount to horizontally offset successive labels in case of vertical overlaps.
... Extra arguments passed to ‘boxed.labels’.

Details

‘barlabels’ places labels on a plot at horizontal positions ‘xpos’ and vertical positions ‘ypos’ *
‘pos’. The typical use of this function is to place labels on bars, by default in the middle of the bars.
To put labels just over the tops of the bars, set ‘prop’ to 1 and add a constant amount to ‘ypos’.

Value

nil

Author(s)

Jim Lemon

See Also

boxed.labels
16 barNest

Examples
heights<-c(14,20,9,31,17)
barpos<-barplot(heights,main="A redundant bar plot")
# show the usual value labels on the bars
barlabels(barpos,heights)
# now with stacked bars and offsets
heights<-matrix(sample(c(1,2,10,15),20,TRUE),ncol=4)
barpos<-barplot(heights,main="Another redundant bar plot")
barlabels(barpos,heights,offset=0.1)
# finally use barp for the plot
barpos<-barp(heights,main="A third and final bar plot",col=2:6,
names.arg=paste("Day",1:4))
barlabels(barpos$x,barpos$y,matrix(LETTERS[1:5],nrow=5,ncol=4))

barNest Display a nested breakdown of numeric values

Description
Breaks down the elements of a data frame by one or more categorical elements and displays the
breakdown as a bar plot.

Usage
barNest(formula=NULL,data=NULL,FUN=c("mean","sd","sd","valid.n"),ylim=NULL,
main="",xlab="",ylab="",shrink=0.1,errbars=FALSE,col=NA,
labelcex=1,lineht=NA,showall=TRUE,Nwidths=FALSE,barlabels=NULL,
showlabels=TRUE,mar=NULL,arrow.cap=NA,trueval=TRUE)

Arguments
formula A formula with a numeric element of a data frame on the left and one or more
categorical elements on the right.
data A data frame containing the elements in ‘formula’.
FUN The functions to apply to x.
ylim Optional y limits for the plot, usually necessary for counts.
main Title for the plot.
xlab,ylab Axis labels for the plot. The x axis label is typically blank
shrink The proportion to shrink the width of the bars at each level.
errbars Whether to display error bars on the lowest level of breakdown.
col The colors to use to fill the bars. See Details.
labelcex Character size for the group labels.
lineht The height of a line of text in the lower margin of the plot in user units. This
will be calculated by the function if a value is not passed.
barNest 17

showall Whether to display bars for the entire breakdown.

Nwidths Whether to scale the widths of the bars to the number of observations.
barlabels Optional group labels that may be useful if the factors used to break down the
numeric variable are fairly long strings.
showlabels Whether to display the labels below the bars.
mar If not NULL, a four element vector to set the plot margins. If new margins are
set, the user must reset the margins after the function exits.
arrow.cap The width of the "cap" on error bars in user units, calculated on the basis of the
number of bars in the final breakdown if NA.
trueval If this is not NA, the call to ‘brkdnNest’ will return the proportions of the re-
sponse variable that are equal to ‘trueval’. See Details.

Details

‘barNest’ displays a bar plot illustrating the hierarchic breakdown of the elements of a data frame.
The breakdown is performed by ‘brkdnNest’ and the actual display is performed by ‘drawNestedBars’.
The heights of the bars will be proportional to the values returned by the first function in ‘FUN’. If
‘showall’ is TRUE, the entire nested breakdown will be displayed. This can be useful in visualizing
the relationship between groups and subgroups in a compact format.
‘barNest’ assumes that there will be four breakdowns in the list returned by ‘brkdnNest’ in the
order summary measure, upper dispersion value, lower dispersion value and number of valid obser-
vations. If ‘Nwidths=FALSE’, it may work with only three and if ‘errbars=FALSE’ as well, it may
work with only one.
If ‘Nwidths=TRUE’, the bar widths will be scaled to the relative number of observations per group.
When the numbers of observations are very different, the labels for those bars with small numbers
of observations will probably overlap.
A number of functions can be passed in the ‘FUN’ argument. Three functions, ‘propbrk’, ‘sumbrk’
and ‘valid.n’ will work as summary measures, giving proportions or sums of particular values
of a discrete variable and counts in each group and subgroup respectively. Binomial confidence
limits can be added to the proportions returned by ‘propbrk’ with ‘binciWl’ and ‘binciWu’ as in
the second last example. If ‘valid.n’ is the first element of ‘FUN’, the "overall" bar and label will
be suppressed, as they are not informative. It is up to the user to decide whether any "error bars"
displayed are meaningful.
The colors of the bars are determined by ‘col’. If ‘showall’ is FALSE, the user only need pass a
vector of colors, usually the same length as the number of categories in the final (last on the right
side) element in the formula. If ‘showall’ is TRUE and the user wants to color all of the bars, a list
with as many elements as there are levels in the breakdown should be passed. Each element should
be a vector of colors, again usually the same length as the number of categories. As the categorical
variables are likely to be factors, it is important to remember that the colors must be in the correct
order for the levels of the factors. When the levels are not in the default alphanumeric order, it is
quite easy to get this wrong. As a ‘barNest’ plot with more than a few factors and levels in each
factor is quite dense, easily distinguished colors for each level of the breakdown may be preferable.
As with some other plots, trying to cram too much information into a single illustration may not
work well.
18 barNest

Value
The summary list produced by brkdnNest.

Author(s)
Jim Lemon and Ofir Levy

References
Lemon, J. & Levy, O. (2011) barNest: Illustrating nested summary measures. Statistical Computing
and Graphics Newsletter of the American Statistical Association, 21(2): 5-10.

See Also
brkdnNest, drawNestedBars, superbarplot(UsingR)

Examples
# recreate the Titanic data frame and show the three way breakdown
titanic<-data.frame(
class=c(rep("1st",325),rep("2nd",285),rep("3rd",706),rep("Crew",885)),
age=c(rep("Adult",319),rep("Child",6),rep("Adult",261),rep("Child",24),
rep("Adult",627),rep("Child",79),rep("Adult",885)),
sex=c(rep("M",175),rep("F",144),rep("M",5),rep("F",1),
rep("M",168),rep("F",93),rep("M",11),rep("F",13),
rep("M",462),rep("F",165),rep("M",48),rep("F",31),
rep("M",862),rep("F",23)),
survived=c(rep("Yes",57),rep("No",118),rep("Yes",140),rep("No",4),rep("Yes",6),
rep("Yes",14),rep("No",154),rep("Yes",80),rep("No",13),rep("Yes",24),
rep("Yes",75),rep("No",387),rep("Yes",76),rep("No",89),
rep("Yes",13),rep("No",35),rep("Yes",14),rep("No",17),
rep("Yes",192),rep("No",670),rep("Yes",20),rep("No",3)))
require(plotrix)
titanic.colors<-list("gray90",c("#0000ff","#7700ee","#aa00cc","#dd00aa"),
c("#ddcc00","#ee9900"),c("pink","lightblue"))
barNest(survived~class+age+sex,titanic,col=titanic.colors,showall=TRUE,
main="Titanic survival by class, age and sex",ylab="Proportion surviving",
FUN=c("propbrk","binciWu","binciWl","valid.n"),shrink=0.15,trueval="Yes")
barNest(survived~class+age+sex,titanic,col=titanic.colors,showall=TRUE,
main="Titanic survival by class, age and sex (scaled bar widths)",
ylab="Proportion surviving",FUN=c("propbrk","binciWu","binciWl","valid.n"),
shrink=0.15,trueval="Yes",Nwidths=TRUE)
# now show the actual numbers of passengers
barNest(survived~class+age+sex,titanic,col=titanic.colors,showall=TRUE,
main="Titanic passengers and crew by class, age and sex",
ylab="Number",FUN="valid.n",shrink=0.15)
# to see this properly displayed, start a wide plot window
# x11(width=10)
test.df<-data.frame(Age=rnorm(100,35,10),
Sex=sample(c("Male","Female"),100,TRUE),
Marital=sample(c("Div","Mar","Sing","Wid"),100,TRUE),
Employ=sample(c("FT","PT","Un"),100,TRUE))
barp 19

test.col<-list(Overall="gray",Sex=c("pink","lightblue"),
Marital=c("mediumpurple","orange","tan","lightgreen"),
Employ=c("#1affd8","#caeecc","#ff90d0"))
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Mean age (years)",
main="Mean age by subgroups",errbars=TRUE,col=test.col)
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Mean age (years)",
main="Mean age by subgroups (widths scaled to Ns)",errbars=TRUE,col=test.col,
Nwidths=TRUE)
# set up functions for 20th and 80th percentiles
q20<-function(x,na.rm=TRUE) return(quantile(x,probs=0.2,na.rm=TRUE))
q80<-function(x,na.rm=TRUE) return(quantile(x,probs=0.8,na.rm=TRUE))
# show the asymmetric dispersion measures
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Mean age (years)",
main="Use median and quantiles for dispersion",
FUN=c("median","q80","q20","valid.n"),
errbars=TRUE,col=test.col)
barNest(formula=Employ~Sex+Marital,data=test.df,ylab="Proportion unemployed",
main="Proportion unemployed by sex and marital status",
FUN=c("propbrk","binciWu","binciWl","valid.n"),
errbars=TRUE,col=test.col,trueval="Un")
barNest(formula=Employ~Sex+Marital,data=test.df,ylab="Proportion unemployed",
main="Proportion unemployed by sex and marital status (scaled bar widths)",
FUN=c("propbrk","binciWu","binciWl","valid.n"),
errbars=TRUE,col=test.col,trueval="Un",Nwidths=TRUE)
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Counts",
main="Show the counts in subgroups (final level only)",FUN="valid.n",
col=test.col,showall=FALSE,ylim=c(0,10))
barNest(formula=Age~Sex+Marital+Employ,data=test.df,ylab="Counts",
main="Show all the counts in subgroups",FUN="valid.n",mar=c(5,5,4,2),
col=test.col)

barp A bar plotting routine

Description

Display a bar plot

Usage

barp(height,width=0.4,names.arg=NULL,legend.lab=NULL,legend.pos=NULL,
col=NULL,border=par("fg"),main=NULL,xlab="",ylab="",xlim=NULL,ylim=NULL,
x=NULL,staxx=FALSE,staxy=FALSE, height.at=NULL,height.lab=NULL,
cex.axis=par("cex.axis"),pch=NULL,cylindrical=FALSE,shadow=FALSE,
do.first=NULL,ylog=FALSE,srt=NA)
20 barp

Arguments
height A numeric vector, matrix or data frame that will be represented as the heights of
bars.
width Half the width of a single bar or group of bars in X axis units.
names.arg The labels for the bars or groups of bars.
legend.lab Labels for an optional legend. If NULL, no legend is displayed.
legend.pos Optional position for the legend as a list with ‘x’ and ‘y’ components. If this is
NULL, ‘locator’ will be called.
col The fill colors for the bars. The default is no fill.
border The border for the bars.
main The title at the top of the plot.
xlab,ylab The labels for the X and Y axes respectively.
xlim,ylim Optional horizontal and vertical limits for the plot.
x Optional horizontal positions for the bars. Defaults to 1:length(height).
staxx,staxy Whether to use staxlab to stagger the X or Y axis tick labels.
height.at Optional positions of the tick marks on the Y axis.
height.lab Optional tick labels for the Y axis.
cex.axis Character expansion for the axis labels.
pch Symbol(s) to fill the bars. See Details.
cylindrical Whether to give the bars a cylindrical appearance by shading them.
shadow Whether to place a shadow behind the bars.
do.first An optional string that will be evaluated before anything else is displayed on the
plot. Useful for background colors or lines.
ylog Logical for whether a log scale is to be used. see details.
srt Rotation of axis labels if staxx or staxy is TRUE (see ‘staxlab’).

Details
‘barp’ displays a bar plot similar to ‘barplot’ but with axes and horizontal bar positions more like
‘plot’. Bars or groups of bars are centered on integral X values by default, and so both the width
and spacing of the bars are controlled by a single number. If the user passes explicit ‘x’ values, those
values will determine the spacing. If ‘height’ is a vector, single bars representing each value will
be displayed centered at ‘1:length(height)’ unless the user has specified ‘x’ values. If ‘height’
is a matrix, 2D array, or data frame, a group of bars will be drawn for each column, with the values
of the group taken from the rows of that column. Explicit x values cannot be used with a matrix,
however, by adjusting the values of x, grouped bars can be displayed.
The values from ‘freq’ or ‘brkdn’ in the prettyR package can be used as the ‘height’ argument.
The value from ‘table’ can also be passed as ‘height’, as can a 2D array returned from the ‘by’
function.
Bars are empty by default but fill colors can be defined in several ways. If a single color is passed,
all bars will be the same color. If ‘height’ is a vector, colors will be recycled or some will be
barp 21

ignored if the length of ‘col’ is not equal to that of ‘height’. If ‘height’ is a matrix or data frame,
the user may pass a vector of colors equal to the number of rows in ‘height’ or a matrix of colors
of the same dimensions as ‘height’. Other sequences of color will probably not result in an easy
to interpret plot.
‘barp’ is intended to simplify illustrating categorical data for which both the variable designations
and the categories are names, as on many multiple choice questions. ‘height.at’ and ‘height.lab’
allow the user to place labels on the vertical axis, usually representing the options. If ‘staxx’ or
‘staxy’ are TRUE, the labels on the horizontal or vertical axes respectively will be staggered, al-
lowing the user to use many or lengthy variable or value labels. If ‘srt’ is not NA, these labels will
be rotated counterclockwise by that value as angles in degrees instead of staggered.
‘barp’ allows two enhancements that may be useful in those areas where fancy plots are appreciated.
One is to give the bars a cylindrical look by shading the color. The other is to place an apparent
shadow behind each bar. Both of these effects appear as though the light is coming from the upper
left, and this is hard coded. You can add error bars by calling ‘dispersion’, but many advise
against this.
If ‘legend.lab’ is not NULL, a legend will be displayed. If ‘legend.pos’ is NA, ‘locator’ is
called to place the legend. On Windows, the alert may not appear on the console, and the function
will appear to hang unless the user clicks on the console window or the plot.
The ‘ylog’ argument produces a log scale on the y axis. Currently, neither ‘pretty’ nor ‘axTicks’
seems to produce a nice set of axis ticks, so it is best to pass the positions of these in ‘height.at’.
If the ‘pch’ argument is not NULL, barp will display white bars filled with the symbols specified
in ‘pch’. With grouped bars, this must be a matrix with the same form as the ‘col’ argument. This
option allows a black and white bar plot to be produced.

Value
A list containing two components of the same form as ‘height’:

x The centers of the bars displayed.

y The heights of the bars.

Author(s)
Jim Lemon

See Also
staxlab, barplot, cylindrect, gradient.rect

Examples
# get some extra room on the left
par(mar=c(5,5,4,2))
# make up some happiness data, as so many seem to do
happyday<-data.frame(Monday=c(2.3,3.4),Tuesday=c(2.8,3.3),Wednesday=c(3.2,3.1),
Thursday=c(3.6,2.8),Friday=c(4.2,2.6),Saturday=c(4.5,2.9),Sunday=c(4.1,2.8))
happylabels<-c("Utterly dashed","Rather mopey","Indifferent","Somewhat elated",
"Euphoric")
22 battleship.plot

barp(happyday,names.arg=names(happyday),legend.lab=c("Slaves","Unemployed"),
legend.pos=list(x=2,y=4.5),col=c("#ee7700","#3333ff"),main="9AM happiness by weekday",
xlab="Day of week",ylab="Happiness rating",ylim=c(1,5),staxx=TRUE,staxy=TRUE,
height.at=1:5,height.lab=happylabels,cex.axis=0.9,cylindrical=TRUE,
shadow=TRUE)
# now do a plot with colors scaled to the sex ratio (real data!)
sexratio<-c(0.24,0.35,0.09,0.59,0.63,0.34,0.7,0.6)
# the fun ratings are once again a pack of lies
funrating<-c(3.2,3.5,1.5,5.4,4.5,2.7,6.8,4.9)
funstudy<-c("Astronomy","Chemistry","Economics","Anthropology","Linguistics",
"Math/Stats","Psychology","Sociology")
funlabels<-c("Torture","Agony","Boredom","Neutral","Entertaining","Exhilarating",
"Maniacal")
# xrange is used to get the colors to match the 0-100% scale
barp(funrating,names.arg=funstudy,main="Fun ratings for various areas of study",
col=color.scale(sexratio,c(0.2,1),c(0.2,0.4),c(1,0.4),xrange=c(0,1)),
xlab="Study",ylab="Rating",height.at=1:7,height.lab=funlabels,ylim=c(1,7),
staxx=TRUE,staxy=TRUE,cex.axis=0.9)
# here we want the full scale from zero to one
color.legend(2,6,4,6.4,legend=c("100% guys","100% girls"),
rect.col=color.scale(seq(0,1,by=0.25),c(0.2,1),c(0.2,0.4),c(1,0.4)))
par(mar=c(5,4,4,2))
# use barp to display a multiple histogram with a shaded background
# notice how the expression uses local variables inside the barp function
gradbg<-"gradient.rect(xlim[1],ylim[1],xlim[2],ylim[2],
c(1,0.5,1),c(1,0.5,1),c(1,0.5,1),gradient=\"y\",nslices=100)"
h1<-table(cut(rnorm(100,4),breaks=seq(0,8,by=2)))
h2<-table(cut(rnorm(100,4),breaks=seq(0,8,by=2)))
h3<-table(cut(rnorm(100,4),breaks=seq(0,8,by=2)))
hmat<-matrix(c(h1,h2,h3),nrow=3,byrow=TRUE)
barp(hmat,names.arg=names(h1),width=0.45,col=2:4,do.first=gradbg,
main="Multiple histogram using barp",xlab="Bins",ylab="Frequency")
legend(3.8,50,c("h1","h2","h3"),fill=2:4)
# now display a positive/negative plot
barp(c(2,-3,4,-5,6,-7,8),main="Positive/negative plot",
xlab="Alternating colors",ylab="For alternating values",
col=2+(c(2,-3,4,-5,6,-7,8)>0))

battleship.plot Display a matrix of values as the widths of stacked rectangles

Description

‘battleship.plot’ displays a matrix of rectangles, with widths proportional to the values in ‘x’.
The values are scaled so that half the width of the largest rectangle is equal to ‘maxxspan’ in user
units. This prevents the rectangles from overlapping. The user can adjust the spacing of the stacks of
rectangles by changing ‘maxxspan’. Similarly, maxyspan controls the spacing between rectangles
in the vertical direction.
battleship.plot 23

The labels for each stack of plots (the columns of x) are displayed at the top of the plot, angled at
45 degrees. The labels for each row of rectangles in the stacks (the rows of x) are displayed at the
left. Long labels for either may require adjusting the ‘mar’ argument.
The function will try to extract the labels ‘xaxlab’ and ‘yaxlab’ from the matrix column and row
names respectively if none are passed.

Usage
battleship.plot(x,mar=c(2,5,5,1),col="white",border="black",
main="",xlab="",ylab="",xaxlab=NA,yaxlab=NA,cex.labels=1,
maxxspan=0.45,maxyspan=0.45)

Arguments
x A matrix or data frame containing numeric values. See the example.
mar Margins for the plot.
col The fill colors for the rectangles.
border The border colors for the rectangles.
main The title for the plot (i.e. ‘main’).
xlab,ylab The x and y axis labels.
xaxlab,yaxlab Optional labels for the rows and columns.
cex.labels Character expansion for the row and column labels.
maxxspan,maxyspan
Scaling factor for the widths and heights of the rectangles so that they don’t
overlap.

Value
nil

Author(s)
Jim Lemon - thanks to Adam Maltese for the suggestion

See Also
plot, staxlab

Examples
x<-matrix(sample(10:50,100,TRUE),10)
xaxlab=c("One","Two","Three","Four","Five","Six","Seven","Eight","Nine","Ten")
yaxlab=c("First","Second","Third","Fourth","Fifth","Sixth","Seventh",
"Eighth","Ninth","Tenth")
battleship.plot(x,xlab="The battle has just begun",main="Battleship1",
xaxlab=xaxlab,yaxlab=yaxlab)
24 bin.wind.records

bin.wind.records Classify wind direction and speed records

Description
Classifies wind direction and speed records into a matrix of percentages of observations in speed
and direction bins.

Usage
bin.wind.records(winddir,windspeed,ndir=8,radians=FALSE,
speed.breaks=c(0,10,20,30))

Arguments
winddir A vector of wind directions.
windspeed A vector of wind speeds corresponding to the above directions.
ndir Number of direction bins in a compass circle.
radians Whether wind directions are in radians.
speed.breaks Minimum wind speed for each speed bin.

Details
‘bin.wind.records’ bins a number of wind direction and speed records into a matrix of percent-
ages of observations that can be used to display a cumulative wind rose with ‘oz.windrose’ The
defaults are those used by the Australian Bureau of Meteorology.

Value
A matrix of percentages in which the rows represent wind speed categories and the columns repre-
sent wind direction categories.

Author(s)
Jim Lemon

See Also
oz.windrose

Examples
winddir<-sample(0:360,100,TRUE)
windspeed<-sample(0:40,100,TRUE)
bin.wind.records(winddir,windspeed)
binciW 25

binciW Binomial confidence limits

Description

Calculates binomial confidence limits using the Wilson approximation.

Usage

binciW(x,n,alpha=0.05,cc=FALSE)

Arguments

x The number of successes or failures for which the CI is to be calculated.

n The number of trials as above.
alpha The desired coverage - 0.05 produces 95 percent coverage
cc Whether to apply a continuity correction

Details

‘binciW’ calculates binomial confidence limits for the given number of successes and trials. It is
mainly to allow binomial confidence limits to be calculated in the ‘brkdnNest’ function, which is
why the upper and lower CIs are called separately.

Value

The lower and upper binomial confidence limits

Author(s)

Jim Lemon

See Also

binciWl, binciWu

Examples
binciW(5,42)
26 binciWl

binciWl Lower binomial confidence limit

Description

Returns the lower binomial confidence limit using the Wilson approximation.

Usage

binciWl(x,n,alpha=0.05,trueval=TRUE,na.rm=TRUE)

Arguments

x The number of successes or failures for which the CI is to be calculated.

n The number of trials as above.
alpha The desired coverage - 0.05 produces 95 percent coverage
trueval The value representing the outcome of interest for the CI.
na.rm Argument needed to make this work

Details

‘binciWl’ now calls ‘binciW’ and returns the lower limit.

Value

The lower binomial confidence limit

Author(s)

Jim Lemon

See Also

binciWu

Examples
binciWl(c(rep(5,TRUE),rep(37,FALSE)))
binciWu 27

binciWu Upper binomial confidence limit

Description

Returns the upper binomial confidence limit using the Wilson approximation.

Usage

binciWu(x,n,alpha=0.05,trueval=TRUE,na.rm=TRUE)

Arguments

x The number of successes or failures for which the CI is to be calculated.

n The number of trials as above.
alpha The desired coverage - 0.05 produces 95 percent coverage
trueval The value representing the outcome of interest for the CI.
na.rm Argument needed to make this work

Details

‘binciWu’ now calls ‘binciW’ and returns the upper limit.

Value

The upper binomial confidence interval

Author(s)

Jim Lemon

See Also

binciWl

Examples
binciWl(c(rep(5,TRUE),rep(37,FALSE)))
28 box.heresy

box.heresy Display a sort of box plot

Description
‘box.heresy’ displays a box plot in which a symbol represents a measure of central tendency, a
surrounding box that represents an "inner" measure of dispersion (e.g. standard error) and whiskers
represent an "outer" measure of dispersion (e.g. standard deviation). The function is pretty basic at
this time and will probably change a bit.
The argument "intervals" is particularly important, and can wreak havoc on the resulting plot. The
default of FALSE means that the values passed to the inner and outer measures of dispersion are
absolute, not intervals away from the measure of central tendency. Mixing absolute and relative
values will always lead to errors and typically a very strange looking plot. It is probably easiest to
calculate the absolute values before calling box.heresy. The first and second examples show how
intervals=FALSE and intervals=TRUE can be used.
One of the first changes is to allow varying box widths. The user can specify the box widths as a
vector of numeric values at least as long as the number of boxes to be displayed. The usual reason
for doing this is to display widths that are proportional to the number of observations. A useful start
is to pass ‘boxwidth’ as the number of observations and let the function work it out.

Usage
box.heresy(x,y,uinner,linner,ulim,llim,boxwidth=NA,
intervals=FALSE,arrow.cap=NA,pch=22,main="",xlab="",ylab="",
xaxlab=NA,col="white",do.first=NULL,...)

Arguments
x,y Vectors of numeric values representing measures of central tendency.
uinner,linner Vectors of numeric values representing "inner" measures of dispersion.
ulim,llim Vectors of numeric values representing "outer" measures of dispersion.
boxwidth Optional widths for the boxes.
intervals Whether the values for dispersion are intervals (TRUE) or absolute limits (FALSE).
arrow.cap The width of the cap on the "whiskers" relative to the width of the plot. Defaults
to the same width as the outer box.
pch The symbol to be used to represent the measure(s) of central tendency in the
box.
main The title for the plot (i.e. ‘main’).
xlab,ylab The x and y axis labels.
xaxlab Optional labels for the boxes.
col The fill colors for the "inner" rectangles.
do.first An expression that will be evaluated before anything is displayed.
... additional arguments passed to the ‘dispersion’ function.
boxed.labels 29

Value
nil

Author(s)
Jim Lemon - thanks to Gianni Lavaredo for the suggestion

See Also
plot, boxplot

Examples
y1<-runif(20,2,10)
y2<-rnorm(30,6,2)
y3<-sample(0:20,40,TRUE)
Ns<-c(20,30,40)
ymean<-c(mean(y1),mean(y2),mean(y3))
y1inner<-quantile(y1,probs=c(.16,.84))
y2inner<-c(ymean[2]+sd(y2),ymean[2]-sd(y2))
y3inner<-quantile(y3,probs=c(.16,.84))
uinner<-c(y1inner[1],y2inner[1],y3inner[1])
linner<-c(y1inner[2],y2inner[2],y3inner[2])
ulim<-c(max(y1),max(y2),max(y3))
llim<-c(min(y1),min(y2),min(y3))
box.heresy(ymean,uinner=uinner,linner=linner,ulim=ulim,llim=llim,boxwidth=Ns,
main="Boxplot of means, central spread and range",xlab="Distribution",
xaxlab=c("Uniform","Normal","Sample"))
y1outer<-
y<-runif(5)
ulim<-runif(5)
llim<-runif(5)
uinner<-ulim/2
linner<-llim/2
box.heresy(y,uinner=uinner,linner=linner,ulim=ulim,llim=llim,
intervals=TRUE,main="The heretical boxplot",
xlab="Number of observations",ylab="Value")

boxed.labels Place labels in boxes

Description
Places labels in boxes on an existing plot

Usage
boxed.labels(x,y=NA,labels,
bg=ifelse(match(par("bg"),"transparent",0),"white",par("bg")),
border=TRUE,xpad=1.2,ypad=1.2,srt=0,cex=1,adj=0.5,xlog=FALSE,ylog=FALSE,...)
30 boxed.labels

Arguments

x,y x and y position of the centers of the labels. ‘x’ can be an xy.coords list.
bg The fill color of the rectangles on which the labels are displayed (see Details).
labels Text strings
border Whether to draw borders around the rectangles.
xpad,ypad The proportion of the rectangles to the extent of the text within.
srt Rotation of the labels. If 90 or 270 degrees, the box will be rotated 90 degrees.
cex Character expansion. See ‘text’.
adj left/right adjustment. If this is set outside the function, the box will not be
aligned properly.
xlog Whether the X axis is a log axis
ylog Whether the Y axis is a log axis
... additional arguments passed to ‘text’.

Details

The label(s) are displayed on a rectangular background. This may be useful for visibility and is the
reason that "transparent" background is not available. With the default ‘textcol=NA’, the function
tries to work out whether white or black text will be more easily read based on the background color
and displays the text accordingly. If the user specifies text colors in the additional arguments, these
colors will override the automatic white/black above - see the last example.
Only right angle rotations are allowed in ‘boxed.labels’. Important change: ‘xpad’ and ‘ypad’
are now the full proportion of the box to text, not half. The user can now call ‘cylindrect’ or
‘gradient.rect’ for the background rectangle.

Value

nil

Note

This function is best for regularly spaced labels where overlapping is not a problem. See thigmo-
phobe.labels for placing labels where overlap is likely.

Author(s)

Jim Lemon - thanks to Thorn Thaler for the code allowing user-specified text colors and Flemming
Skjoth for the log axis correction

See Also

spread.labels, thigmophobe.labels
brkdn.plot 31

Examples
x<-rnorm(10)
y<-rnorm(10)
plot(x,y,type="p")
nums<-c("one","two","three","four","five","six","seven","eight","nine","ten")
boxed.labels(x,y-0.1,nums)
# now label a barplot
xpos<-barp(c(1,3,2,4))
boxed.labels(xpos$x,0.5,nums[1:4])
# and add labels below the x axis ticks
boxed.labels(xpos$x,-0.4,c("First","Second","Third","Fourth"))
# perform a PCA on the "swiss" dataset and plot the first two components
data(swiss)
swiss.pca<-prcomp(swiss)
plot(swiss.pca$rotation[,1:2],xlim=c(-1,0.2),main="PCA of swiss dataset",
type="n")
boxed.labels(swiss.pca$rotation[1:6],swiss.pca$rotation[7:12],ypad=1.5,
colnames(swiss),bg=c("red","purple","blue","blue","darkgreen","red"),
col="yellow")

brkdn.plot A point/line plotting routine

Description
Display a point/line plot of breakdowns of one or more variables.

Usage
brkdn.plot(vars,groups=NA,obs=NA,data,mct="mean",md="std.error",stagger=NA,
dispbar=TRUE,main="Breakdown plot",xlab=NA,ylab=NA,xaxlab=NA,
ylim=NA,type="b",pch=1,lty=1,col=par("fg"),staxx=FALSE,yat=NA,...)

Arguments
vars The names or indices of one or more columns in a data frame. The columns
must contain numeric data. If only one variable is to be broken down, vars can
be a formula.
groups The name or index of a column in a data frame that classifies the values in ‘vars’
into different, usually fixed effect, levels.
obs The name or index of a column in a data frame that classifies the values in ‘vars’
into different, usually random effect, levels.
data The data frame.
mct The measure of central tendency to calculate for each group.
md The measure of dispersion to calculate, NA for none.
32 brkdn.plot

stagger The amount to offset the successive values at each horizontal position as a pro-
portion of the width of the plot. The calculated default is usually adequate. Pass
zero for none.
dispbar Whether to display the measures of dispersion as bars.
main The title at the top of the plot.
xlab,ylab The labels for the X and Y axes respectively. There are defaults, but they are
basic.
xaxlab Optional labels for the horizontal axis ticks.
ylim Optional vertical limits for the plot.
type Whether to plot symbols, lines or both (as in ‘plot’).
pch Symbol(s) to plot.
lty Line type(s) to plot.
col Color(s) for the symbols and lines.
staxx Whether to call staxlab to display the X axis labels.
yat Optional y axis tick positions.
... additional arguments passed to ‘plot’.

Details
‘brkdn.plot’ displays a plot useful for visualizing the breakdown of a response measure by two
factors, or more than one response measure by either a factor representing something like levels of
treatment (‘groups’) or something like repeated observations (‘obs’). For example, if observations
are made at different times on data objects that receive different treatments, the ‘groups’ factor will
display the measures of central tendency as points/lines with the same color, symbol and line type,
while the ‘obs’ factor will be represented as horizontal positions on the plot. If ‘obs’ is numeric,
its unique values will be used as the positions, if not, 1 to the number of unique values. This is a
common way of representing changes over time intervals for experimental groups.
If only one numeric variable is to be broken down, ‘vars’ may be a formula like ‘var~groups+obs’.
The position of the two factors to break down the variable is fixed - the second term will be inter-
preted as "groups" and the third, if present, will be interpreted as "obs".

Value
A list of two matrices of dimension ‘length(levels(groups))’ by ‘length(levels(obs))’. The
first contains the measures of central tendency calculated and its name is the name of the function
passed as ‘mct’. The second contains the measures of dispersion and its name is the name of the
function passed as ‘md’.
If both ‘groups’ and ‘obs’ are not NA, the rows of each matrix will be the ‘groups’ and the columns
the ‘obs’. If ‘obs’ is NA, the rows will be the ‘groups’ and the columns the ‘vars’. If ‘groups’
is NA, the rows will be the ‘vars’ and the columns the ‘obs’. That is, if ‘vars’ has more than one
element, if ‘obs’ is NA, the elements of ‘vars’ will be considered to represent observations, while
if ‘groups’ is NA, they will be considered to represent groups. At least one of ‘groups’ and ‘obs’
must be not NA or there is no point in using ‘brkdn.plot’.
brkdnNest 33

Author(s)

Jim Lemon

See Also

dispersion

Examples
test.df<-data.frame(a=rnorm(80)+4,b=rnorm(80)+4,c=rep(LETTERS[1:4],each=20),
d=rep(rep(letters[1:4],each=4),5))
# first use the default values
brkdn.plot("a","c","d",test.df,pch=1:4,col=1:4)
# now jazz it up a bit using medians and median absolute deviations
# and some enhancements
bp<-brkdn.plot(a~c+d,data=test.df,main="Test of the breakdown plot",
mct="median",md="mad",xlab="Temperature range", ylab="Cognition",
xaxlab=c("10-15","16-20","21-25","25-30"),pch=1:4,lty=1:4,col=1:4)
es<-emptyspace(bp)
legend(es,legend=c("Sydney","Gosford","Karuah","Brisbane"),pch=1:4,
col=1:4,lty=1:4,xjust=0.5,yjust=0.5)

brkdnNest Perform a nested breakdown of numeric values

Description

Breaks down a numeric or categorical element of a data frame by one or more categorical elements.

Usage

brkdnNest(formula,data,FUN=c("mean","sd","sd","valid.n"),label1="Overall",
trueval=TRUE)

Arguments

formula A formula with a numeric element of a data frame on the left and one or more
categorical elements on the right.
data A data frame containing the elements in ‘formula’.
FUN The functions to be applied to successive breakdowns.
label1 The label to use for the overall value of the first function.
trueval The value to use in calculating proportions or sums of a categorical response
variable. See Details.
34 brkdnNest

Details

‘brkdnNest’ performs a nested breakdown of an element of a data frame by one or more categorical
elements. For each category and optional subcategories, the variable on the left of the formula is
summarized as specified by the functions named in ‘FUN’.
If ‘trueval’ is not NA, brkdnNest will calculate the proportion of ‘trueval’ values in the response
variable out of the total valid responses. If the function ‘valid.n’ is the first function in ‘FUN’, the
counts of the groups and subgroups will be returned.
Two specialized summary functions are defined within ‘brkdnNest’. ‘sumbrk’ returns the count
of values in a factor equal to ‘trueval’, and ‘propbrk’ returns the proportion of values equal to
‘trueval’. Be aware that if a categorical variable is specified on the left of the formula, functions
which expect numeric data such as ‘mean’ should not be included in ‘FUN’.
The user should take care when specifying different summary functions. ‘barNest’ expects a sum-
mary measure as the first component of the list and measures of dispersion as the second and third.
If two different measures of dispersion are passed, the first must calculate the upper and the second
the lower measure.

Value

A list with as many elements as there are functions in ‘FUN’. It is probably best to always specify
four functions (summary measure, upper dispersion measure, lower dispersion measure and number
of valid observations) even if this is redundant as in the default.
This function is similar to ‘brkdn’ in the prettyR package, but is structured to be used with the
‘barNest’ function. It produces one or more measures for the overall data, then the subsets of the
data defined by the first variable to the right of the tilde, then the subsets defined by the first and
second variable, and so on.

Author(s)

Jim Lemon

See Also

by

Examples
brkdntest<-data.frame(Age=rnorm(100,25,10),
Sex=factor(sample(c("M","F"),100,TRUE)),
Marital=sample(c("M","X","S","W"),100,TRUE),
Employ=sample(c("FT","PT","NO"),100,TRUE))
brkdnNest(formula=Age~Sex+Marital+Employ,data=brkdntest)
# show the proportion of unemployed with binomial confidence intervals
brkdnNest(formula=Employ~Sex+Marital,data=brkdntest,
FUN=c("propbrk","binciWu","binciWl"),trueval="NO")
bumpchart 35

bumpchart Display a "bumps" chart

Description
Display a chart with two of more columns of points in order of ascending values with lines connect-
ing the points in a row.

Usage
bumpchart(y,top.labels=colnames(y),labels=rep(rownames(y),2),rank=TRUE,
mar=c(2,8,5,8),pch=19,col=par("fg"),lty=1,lwd=1,arrows=FALSE,...)

Arguments
y A numeric matrix or data frame which may contain NAs.
top.labels The strings that will appear at the top of each column of points on the plot.
labels The strings that will appear next to the outer columns of points.
rank Whether to rank the values in ‘y’ before plotting.
mar The margins to use for the bumps chart. Alter to your taste.
pch The symbols to use when plotting the points.
col The colors to use.
lty The line types to use.
lwd The line widths to use.
arrows Whether to join the points with lines (FALSE) or arrows (TRUE).
... Additional arguments passed to ‘matplot’ or ‘arrows’.

Details
‘bumpchart’ calls ‘matplot’ to plot the values in the transposed ‘y’ matrix or data frame, joining
the points with lines. At the left and right edges of the plot, the labels identifying each row of points
are displayed. These labels may now be different for each side of the plot, for example if the values
of ‘y’ are to be included. Remember that due to the transposition of the values for plotting, the
labels on the right have to precede those on the left - see the second example.
This type of plot is often used to show the changing positions of entities over time, like the ranking
in surveys in different years. For a similar, but more flexible plot, see ladderplot.
Because of the way ‘matplot’ plots the values, the order of everything is reversed. As the typical
display of ranks is with rank 1 at the top, the actual rank positions are used to plot the values. This
places the lowest scores at the bottom of the plot and the highest at the top.
Any arguments that are included in ‘...’ will be passed to ‘matplot’ if the ‘arrows’ argument is
FALSE, and to the ‘arrows’ function if the ‘arrows’ argument is TRUE as in the first example.
36 categoryReshape

Value
nil

Author(s)
Jim Lemon

See Also
matplot

Examples
# percentage of those over 25 years having completed high school
# in 10 cities in the USA in 1990 and 2000
educattn<-matrix(c(90.4,90.3,75.7,78.9,66,71.8,70.5,70.4,68.4,67.9,
67.2,76.1,68.1,74.7,68.5,72.4,64.3,71.2,73.1,77.8),ncol=2,byrow=TRUE)
rownames(educattn)<-c("Anchorage AK","Boston MA","Chicago IL",
"Houston TX","Los Angeles CA","Louisville KY","New Orleans LA",
"New York NY","Philadelphia PA","Washington DC")
colnames(educattn)<-c(1990,2000)
bumpchart(educattn,main="Rank for high school completion by over 25s",
arrows=TRUE,length=0.2)
vallab<-c(paste(educattn[,2],rownames(educattn),sep="-"),
paste(rownames(educattn),educattn[,1],sep="-"))
# now show the raw percentages and add central ticks
bumpchart(educattn,rank=FALSE,labels=vallab,
main="Percentage high school completion by over 25s",
lty=1:10,lwd=1,col=rainbow(10))
# margins have been reset, so use
par(xpd=TRUE)
boxed.labels(1.5,seq(65,90,by=5),seq(65,90,by=5))
par(xpd=FALSE)

categoryReshape Convert object label/attribute label coding.

Description
Convert object label/attribute label coding to an object by attribute data frame.

Usage
categoryReshape(x)

Arguments
x A matrix or data frame with at least two columns.
centipede.plot 37

Details

‘categoryReshape’ attempts to convert the first two columns of its input into a data frame in which
rows represent objects and columns attributes. For each object, a value of 1 indicates that the object
has that attribute, and a value of 0 that it does not. In set membership terms, a 1 indicates that the
object is a member of that set and a 0 that it is not.

Value

A data frame (see Details).

Author(s)

Jim Lemon

See Also

makeIntersectList

Examples

ns<-sample(1:8,20,TRUE)
objects<-0
for(i in 1:length(ns)) objects<-c(objects,rep(i,ns[i]))
attributes<-"Z"
for(i in 1:length(ns)) attributes<-c(attributes,sample(LETTERS[1:8],ns[i]))
setdf<-data.frame(objects[-1],attributes[-1])
categoryReshape(setdf)

centipede.plot Display a centipede plot

Description

Displays a centipede plot on the current graphics device.

Usage

centipede.plot(segs,mct="mean",lower.limit="std.error",
upper.limit=lower.limit,left.labels=NULL,right.labels=NULL,sort.segs=TRUE,
main="",xlab=NA,pch=21,vgrid=NA,hgrid=NA,gridcol="lightgray",mar=NA,col=par("fg"),
bg="green",...)
38 centipede.plot

Arguments
segs a matrix of midpoints and limits calculated by get.segs OR a ‘dstat’ object
returned by ‘brkdn’.
mct The function to use in calculating the midpoint of each segment.
lower.limit The functions to use in calculating the lower limits for each subset of the data.
upper.limit The functions to use in calculating the upper limits.
left.labels The variable or subset labels to place at the left margin of the plot. Default
values are provided.
right.labels The variable or subset labels to place at the right margin of the plot.
sort.segs Whether to sort the segments in ascending order.
main Optional title for the plot.
xlab Optional x axis label for the plot. The default NA displays a text label showing
the midpoint and limit functions.
pch The symbols to use when plotting midpoints.
vgrid Optional vertical line(s) to display on the plot. Defaults to NA (none).
hgrid Optional horizontal grid lines to display on the plot. Defaults to NA (none).
gridcol The color for the vgrid and hgrid lines.
mar Margin widths for the plot. Defaults to c(4,5,1,4) or c(4,5,3,4) if there is a title.
col The color(s) of the limit lines and borders of the midpoint markers.
bg The color(s) to fill the midpoint markers.
... additional arguments passed to ‘plot’.

Details
‘centipede.plot’ displays one or more midpoints and limits as filled circles with horizontal error
bars. It places labels on the left and right sides of the plot. If these labels are long, it may be
necessary to pass explicit values to the ‘mar’ argument to leave enough room.
The ‘vgrid’ argument is usually used to display an average value for all of the midpoints. If one
or more values are passed in this argument, they will be displayed as vertical lines spanning the
plot. The ‘hgrid’ argument acts like the ‘grid’ function, drawing dashed horizontal lines across
the plot. If ‘hgrid=NULL’, these lines will be drawn under the values displayed, which will be 1
to the number of values on the vertical axis. The user can pass explicit values if desired. With
horizontal and optionally vertical grid lines, the centipede plot is practically equivalent to a dotplot
with error bars.
Similarly, centipede plots typically have a large number of subsets, and it may be necessary to
start the graphics device with an aspect ratio that will prevent crowding of the labels when over 30
segments are displayed.
The matrix ‘segs’ may be entered manually or read from a file. The first row specifies midpoints,
the second and third rows the lower and upper limits respectively and the fourth row the number of
valid observations. If there are no values for number of valid observations, just pass vector of blank
strings with the ‘right.labels’ argument. If a ‘dstat’ object is passed as ‘segs’, the function
will calculate the lower and upper values according to the relevant arguments. This type of plot is
also known as a caterpillar plot or a league table.
clean.args 39

Value
nil.

Author(s)
Jim Lemon

See Also
get.segs

Examples
testcp<-list("",40)
for(i in 1:40) testcp[[i]]<-rnorm(sample(1:8,1)*50)
segs<-get.segs(testcp)
centipede.plot(segs,main="Test centipede plot",vgrid=0)
# now leave out the number of valid observations, pass x labels and no right labels
centipede.plot(segs[1:3,],main="Test centipede plot",vgrid=0,mar=c(4,5,3,2),
left.labels=paste("X",1:40,sep=""),right.labels=rep("",40))

clean.args Remove inappropriate arguments from an argument list

Description
Takes a list of arguments and eliminates those that are not appropriate for passing to a particular
function (and hence would produce an error if passed).

Usage
clean.args(argstr,fn,exclude.repeats=FALSE,exclude.other=NULL,dots.ok=TRUE)
remove.args(argstr,fn)

Arguments
argstr a named list of arguments, e.g. from ‘...’
fn a function
exclude.repeats
(logical) remove repeated arguments?
exclude.other a character vector of names of additional arguments to remove
dots.ok should "..." be allowed in the argument list?

Value
‘clean.args’ returns a list which is a copy of ‘argstr’ with arguments inappropriate for ‘fn’
removed; ‘remove.args’ removes the arguments for ‘fn’ from the list.
40 clock24.plot

Author(s)
Ben Bolker

Examples
tststr <- list(n=2,mean=0,sd=1,foo=4,bar=6)
clean.args(tststr,rnorm)
try(do.call("rnorm",tststr))
do.call("rnorm",clean.args(tststr,rnorm))
remove.args(tststr,rnorm)
## add example of combining arg. lists?

clock24.plot Plot values on a 24 hour "clockface"

Description
‘clock24.plot’ displays a plot of radial lines, symbols or a polygon centered at the midpoint of
the plot frame on a 24 hour ’clockface’. In contrast to the default behavior of ‘radial.plot’, the
positions are interpreted as beginning at vertical (000) and moving clockwise.
If ‘add=TRUE’ is passed as one of the additional arguments, the values will be added to the current
plot. If a ‘radial.lim’ argument was passed on the initial plot, it must be passed again to add
values or the values will be displayed incorrectly.

Usage
clock24.plot(lengths,clock.pos,labels=0:23,minutes=FALSE,
label.pos=NULL,rp.type="r",...)

Arguments
lengths numeric data vector. Magnitudes will be represented as line lengths, or symbol
or polygon vertex positions.
clock.pos numeric vector of positions on the ’clockface’. These must be in decimal hours
and will be rescaled to radians.
labels Labels to place at the circumference.
minutes Whether to add minutes (".00") to the labels.
label.pos Radial positions of the labels.
rp.type Whether to plot radial lines, symbols or a polygon.
... additional arguments are passed to ‘radial.plot’ and then to ‘plot’.

Value
A list of the parameters altered by radial.plot.
clplot 41

Author(s)
Jim Lemon

See Also
polar.plot,radial.plot

Examples
testlen<-rnorm(24)*2+5
testpos<-0:23+rnorm(24)/4
clock24.plot(testlen,testpos,main="Test Clock24 (lines)",show.grid=FALSE,
line.col="green",lwd=3)
if(dev.interactive()) par(ask=TRUE)
# now do a 'daylight' plot
oldpar<-clock24.plot(testlen[7:19],testpos[7:19],
main="Test Clock24 daytime (symbols)",
point.col="blue",rp.type="s",lwd=3)
# reset everything
par(oldpar)

clplot Plot lines with colors determined by values.

Description
‘clplot’ displays a plot of lines for which the colors are dependent upon the x and y values.
‘clplot’ is similar to ‘color.scale.lines’ except that while the latter calculates a color for each
unique value, ‘clplot’ assigns colors to groups of values within the cutpoints defined by ‘levels’.

Usage
clplot(x,y,ylab=deparse(substitute(y)),xlab=deparse(substitute(x)),
levels=seq(min(y)+(max(y)-min(y))/5,max(y)-(max(y)-min(y))/5,length.out=4),
cols=c("black","blue","green","orange","red"),lty=1,showcuts=FALSE,...)

Arguments
x,y numeric data vectors.
ylab,xlab Labels for the X and Y axes.
levels Cut points to assign colors to the values of ‘x’ and ‘y’.
cols The colors to be assigned.
lty The line type.
showcuts Whether to show the positions of the cut points.
... additional arguments passed to ‘plot’ or ‘lines’.
42 cluster.overplot

Value
nil

Author(s)
Carl Witthoft

See Also
plot

Examples
x<-seq(1,100)
y<-sin(x/5)+x/20
clplot(x,y,main="Test of clplot")

cluster.overplot Shift overlying points into clusters

Description
‘cluster.overplot’ checks for overlying points in the x and y coordinates passed. Those points
that are overlying are moved to form a small cluster of up to nine points. For large numbers of
overlying points, see count.overplot or sizeplot. If you are unsure of the number of overplots in
your data, run ‘count.overplot’ first to see if there are any potential clusters larger than nine.

Usage
cluster.overplot(x,y,away=NULL,tol=NULL,...)

Arguments
x,y Numeric data vectors or the first two columns of a matrix or data frame. Typi-
cally the x/y coordinates of points to be plotted.
away How far to move overlying points in user units. Defaults to the width of a lower
case "o" in the x direction and 5/8 of the height of a lower case "o" in the y
direction. Must have both values.
tol The largest distance between points that will be considered to be overlying. De-
faults to 1/2 of the width of a lower case "o" in the x direction and 1/2 of the
height of a lower case "o" in the y direction.
... additional arguments returned as they are passed.

Value
A list with two components. For unique x-y pairs the elements will be the same as in the original.
For overlying points up to eight additional points will be generated that will create a cluster of points
instead of one.
clustered.dotplots 43

Author(s)
Jim Lemon - thanks to Markus Elze for the test for a current graphics device

See Also
count.overplot,sizeplot

Examples
xy.mat<-cbind(sample(1:10,200,TRUE),sample(1:10,200,TRUE))
clusteredpoints<-
cluster.overplot(xy.mat,col=rep(c("red","green"),each=100),
away=rep(0.2,2))
plot(clusteredpoints,col=clusteredpoints$col,
main="Cluster overplot test")

clustered.dotplots Display the frequencies of two categories

Description
‘clustered.dotplots’ displays a contingency table as clusters of symbols on a plot. It expects
‘xgroup’ and ‘ygroup’ to contain all or some of the combinations of their unique values. It also
expects ‘freq’ to contain the number of instances of each combination.

Usage
clustered.dotplots(xgroup, ygroup, freq, type = "circles",
main="",xlab="",ylab="",x_las=1,y_las=1,axes=TRUE,size=1,...)

Arguments
xgroup,ygroup Vectors that specify the two groupings to be displayed (see Details).
freq The frequencies in the two groupings.
type The type of symbols to use as "dots".
main,xlab,ylab As in plot.
x_las,y_las Orientation of the axis tick labels.
axes Whether to display axes.
size Spacing for the clusters.
... additional arguments passed to "points".

Value
nil
44 color.axis

Author(s)
Darshan Baral

See Also
cluster.overplot

Examples
df <- structure(list(set = c("09t0101 TJ", "09t0102 MW", "09t0201 EH",
"09t0202 NH", "09t0101 TJ", "09t0102 MW", "09t0201 EH", "09t0202 NH",
"09t0101 TJ", "09t0102 MW", "09t0201 EH", "09t0202 NH", "09t0101 TJ",
"09t0102 MW", "09t0201 EH", "09t0202 NH", "09t0202 NH"), grade = c("1",
"1", "1", "1", "2", "2", "2", "2", "3", "3", "3", "3", "4", "4",
"4", "4", "5"), freq = c(7, 8, 2, 3, 11, 4, 11, 3, 3, 8, 3, 8,
3, 9, 3, 2, 5)), .Names = c("set", "grade", "freq"), row.names = c(NA,
17L), class = "data.frame")
clustered.dotplots(xgroup = df$set, ygroup = df$grade, freq = df$freq)
clustered.dotplots(xgroup = df$set, ygroup = df$grade, freq = df$freq,
col = "gray")
clustered.dotplots(xgroup = df$set, ygroup = df$grade, freq = df$freq,
type = "points")
clustered.dotplots(xgroup = df$set, ygroup = df$grade, freq = df$freq,
type = "points", pch = 19, col = "red")
# this will cause an error
# clustered.dotplots(xgroup = mtcars$cyl, ygroup = mtcars$gear,
# freq = mtcars$carb)
# how to fix it
cumcars<-by(mtcars$carb,list(mtcars$cyl,mtcars$gear),valid.n)
mtcars2<-data.frame(cyl=NA,gear=NA,carb=NA)
rownum<-1
for(cyl in dimnames(cumcars)[[1]]) {
for(gear in dimnames(cumcars)[[2]]) {
if(!is.na(cumcars[cyl,gear])) {
mtcars2[rownum,]<-c(as.numeric(cyl),as.numeric(gear),cumcars[cyl,gear])
rownum<-rownum+1
}
}
}
clustered.dotplots(xgroup = mtcars2$cyl, ygroup = mtcars2$gear,
freq = mtcars2$carb,main="Cars by number of cylinders and gears",
xlab="Number of cylinders",ylab="Number of gears",type="points",pch=5)

color.axis Display an axis in a specified color

Description
‘color.axis’ displays an axis in the specified color.
color.gradient 45

Usage
color.axis(side=1,at=NULL,labels=TRUE,axlab=NA,axlab.at=NA,
col=par("fg"),cex.axis=par("cex.axis"),cex=par("cex"))

Arguments
side Which axis - see axis.
at Positions for the tick labels.
labels Tick labels.
axlab Optional axis label.
axlab.at Where to position the axis label - defaults to centered.
col Color for the axis.
cex.axis Character expansion for the tick labels.
cex Character expansion for the axis label.

Value
nil

Author(s)
Jim Lemon

color.gradient Calculate an arbitrary sequence of colors

Description
‘color.gradient’ is now just a call to ‘color.scale’ with a vector of equally spaced integers
(1:nslices). The function is kept for backward compatibility.

Usage
color.gradient(reds,greens,blues,nslices=50)

Arguments
reds,greens,blues
vectors of the values of the color components as 0 to 1.
nslices The number of color "slices".

Value
A vector of hexadecimal color values as used by ‘col’.
46 color.id

Note
The function is mainly useful for defining a set of colors to represent a known number of gradations.
Such a set can be used to assign a grade to a small number of values (e.g. points on a scatterplot
- but see ‘color.scale’ for large numbers) and display a color bar using ‘gradient.rect’ as a
legend.

Author(s)
Jim Lemon

See Also
rescale,approx,color.scale

Examples
# try it with red and blue endpoints and green midpoints.
color.gradient(c(0,1),c(1,0.6,0.4,0.3,0),c(0.1,0.6))

color.id Identify closest match to a color

Description
Given a color specified as a hex string, find the closest match in the table of known (named) colors

Usage
color.id(col)

Arguments
col a color specified as a hex string

Details
finds the color with the minimum squared distance in RGB space

Value
the name of the closest match

Author(s)
Ben Bolker

See Also
col2rgb,colors
color.legend 47

Examples
color.id("#cc00cc")

color.legend Legend matching categories or values to colors

Description
Display a color legend on a plot

Usage
color.legend(xl,yb,xr,yt,legend,rect.col,cex=1,align="lt",gradient="x",...)

Arguments
xl,yb,xr,yt The lower left and upper right coordinates of the rectange of colors in user co-
ordinates.
legend The labels that will appear next to some or all of the colors.
rect.col The colors that will fill the rectangle.
cex Character expansion factor for the labels.
align How to align the labels relative to the color rectangle.
gradient Whether to have a horizontal (x) or vertical (y) color gradient.
... Additional arguments passed to ‘text’.

Details
‘color.legend’ displays a rectangle defined by the first four arguments filled with smaller rectan-
gles of color defined by the ‘rect.col’ argument. Labels, defined by the ‘legend’ argument, are
placed next to the color rectangle. The position of the labels is determined by whether the color
rectangle is horizontal or vertical and the ‘align’ argument. The default value of ‘lt’ places the
labels at the left of a vertical rectangle or the top of a horizontal one. ‘rb’ puts them on the other
side. To have the labels in the same color as the rectangles, include a ‘col’ argument that will be
passed to ‘text’ as in the example.
There can be fewer labels than colors. The labels will be evenly spaced along the rectangle in this
case. It is possible to use empty labels to get uneven spacing. The user can pass more labels than
colors, but the labels will almost certainly be crowded and I have only found one use for this. If
the user wants the labels at the intersection of the boxes rather than in the center, see the alternative
specification for the labels in the example (thanks Claudia Tebaldi). To have complete control over
the labels, see gradient.rect and text or mtext.
‘colorlegend’ in the shape package offers a different approach, creating a large number of colors
from a color generating function (a bit like ‘color.gradient’) and then allowing the user to specify
tick marks at arbitrary points along the color bar.
48 color.scale

Value
nil

Author(s)
Jim Lemon

See Also
color.gradient, gradient.rect

Examples
# get some extra room
par(mar=c(7,4,4,6))
testcol<-color.gradient(c(0,1),0,c(1,0),nslices=5)
col.labels<-c("Cold","Warm","Hot")
# this will put the labels at the intersections
# col.labels<-c("","Cold","","Warm","","Warmer","","Hot","")
color2D.matplot(matrix(rnorm(100),nrow=10),c(1,0),0,c(0,1),
main="Test color legends")
color.legend(11,6,11.8,9,col.labels,testcol,gradient="y")
color.legend(10.2,2,11,5,col.labels,testcol,align="rb",gradient="y")
color.legend(0.5,-2,3.5,-1.2,col.labels,testcol)
color.legend(7,-1.8,10,-1,col.labels,testcol,align="rb",col=testcol[c(1,3,5)])
par(mar=c(5,4,4,2))

color.scale Turn values into colors.

Description
Transform numeric values into colors using RGB, HSV or HCL

Usage
color.scale(x,cs1=c(0,1),cs2=c(0,1),cs3=c(0,1),alpha=1,
extremes=NA,na.color=NA,xrange=NULL,color.spec="rgb")

Arguments
x a numeric vector, matrix or data frame
cs1,cs2,cs3 color parameters for scaling ‘x’
alpha Value for transparency in colors.
extremes The colors for the extreme values of ‘x’ (RGB only).
na.color The color to use for NA values of ‘x’.
xrange An explicit range to use in the transformation.
color.spec The color specification to use in the transformation. Anything other than "rgb",
"hsv" or "hcl" will almost certainly fail.
color.scale 49

Details
‘color.scale’ calculates a sequence of colors by a linear transformation of the numeric values
supplied into the ranges for the three color parameters. If only one number is supplied for a color
range, that color remains constant for all values of ‘x’. If more than two values are supplied, the ‘x’
values will be split into equal ranges (one less than the number of colors) and the transformation
carried out on each range. Values for a color range must be between 0 and 1 for the RGB or HSV
specifications, and between 0 and 360 (cs1) and 0 to 100 (cs2 and cs3) for the HCL specifications.
IMPORTANT: If ‘x’ has fewer values than the number of values in the color parameters, it will
usually return incorrect colors. This is usually only a problem when using ‘color.legend’ with a
small number of rectangles in the legend as ‘color.legend’ calls ‘color.scale’ to calculate the
color rectangles.
If ‘extremes’ is not NA, the ranges will be calculated from its values using ‘col2rgb’, even if
ranges are also supplied. ‘extremes’ allows the user to just pass the extreme color values in any
format that ‘col2rgb’ will accept. Note that this forces the color specification to RGB.
If the user wants to specify a range of values with ‘xrange’, it must at least include the range of x
values. This can be useful when there is a notional range like 0-100% that the values do not cover,
or when several series of values with different ranges are to be assigned the same color scale.
The user may not want the color scheme to be continuous across some critical point, often zero.
In this case, color scale can be called separately for the values below and above zero. I may
get around to adding an argument to do this in one shot. Until then, see the second example for
‘color2D.matplot’ and also the ‘diverge.hcl’ and ‘diverge.hsv’ functions in the colorspace
package.

Value
A vector or matrix of hexadecimal color values.

Note
The function is useful for highlighting a numeric dimension or adding an extra "dimension" to a
plot.
There are quite a few R functions that transform numeric values into colors or produce colors that
can be used to represent values. Two packages that might be of interest are RColorBrewer and
colourschemes.

Author(s)
Jim Lemon

See Also
rescale, col2rgb, smoothColors

Examples
# go from green through yellow to red with no blue
x<-rnorm(20)
y<-rnorm(20)
50 color.scale.lines

# use y for the color scale

plot(x,y,col=color.scale(y,c(0,1,1),c(1,1,0),0),main="Color scale plot",
pch=16,cex=2)
plot(1:10,rep(1:3,length.out=10),axes=FALSE,type="n",xlim=c(0,11),ylim=c(0,4),
main="Test of RGB, HSV and HCL",xlab="",ylab="Color specification")
axis(2,at=1:3,labels=c("HCL","HSV","RGB"))
points(1:10,rep(1,10),pch=19,cex=8,col=color.scale(1:10,c(0,300),35,85,
color.spec="hcl"))
points(1:10,rep(2,10),pch=19,cex=8,col=color.scale(1:10,c(0,1),
0.8,1,color.spec="hsv"))
points(1:10,rep(3,10),pch=19,cex=8,col=color.scale(1:10,c(1,0.5,0),
c(0,0.5,0),c(0,0,1),color.spec="rgb"))

color.scale.lines Line segments with scaled colors

Description
Display line segments with colors scaled to numeric values.

Usage
color.scale.lines(x,y,reds,greens,blues,col=NA,colvar=NA,...)

Arguments
x,y Numeric vectors or a list with at least two components, the first two of which
must be named x and y.
reds,greens,blues
Color ranges into which to scale the numeric values.
col One or more colors to use for the resultant lines. Will be recycled if necessary.
colvar A numeric vector from which to scale the colors.
... Additional arguments passed to ‘segments’.

Details
‘color.scale.lines’ displays line segments that can be individually colored according to a variety
of methods. In order of precedence, if ‘col’ is not NA, the color values passed will be used. If
‘colvar’ is not NA, the function will call ‘color.scale’ with the three color range arguments to
determine the line colors. If ‘colvar’ is the same length as ‘length(x)-1’, exactly enough colors
for the number of lines displayed will be calculated. If shorter, some colors will be recycled and if
longer, some colors will not be used. Finally, the values in ‘y’ will be color-scaled if both of the
above arguments are NA. Thus the user can pass predetermined colors, use colors scaled from an
arbitrary vector of numerical values or use the ‘y’ values. See ‘color.scale’ for an explanation of
specifying color ranges.
color2D.matplot 51

Value
nil

Note
The function is useful for highlighting a numeric dimension or adding an extra "dimension" to a
plot.

Author(s)
Jim Lemon

See Also
color.scale

Examples
# color a random walk "hot" (red) to "cold" (blue) on its distance
# from the starting point
x<-c(0,cumsum(rnorm(99)))
y<-c(0,cumsum(rnorm(99)))
xydist<-sqrt(x*x+y*y)
plot(x,y,main="Random walk plot",xlab="X",ylab="Y",type="n")
color.scale.lines(x,y,c(1,1,0),0,c(0,1,1),colvar=xydist,lwd=2)
boxed.labels(x,y,labels=1:100,border=FALSE,cex=0.5)
# now color the lines to show whether each step went away from
# or toward the starting position
color.scale.lines(x,y,col=2+(diff(xydist)>0))
boxed.labels(x,y,labels=1:100,border=FALSE,cex=0.5)

color2D.matplot Display a numeric matrix as color matrix

Description
Display the values of a numeric 2D matrix or data frame as colored rectangles or hexagons.

Usage
color2D.matplot(x,cs1=c(0,1),cs2=c(0,1),cs3=c(0,1),
extremes=NA,cellcolors=NA,show.legend=FALSE,nslices=10,xlab="Column",
ylab="Row",do.hex=FALSE,axes=TRUE,show.values=FALSE,vcol=NA,vcex=1,
border="black",na.color=NA,xrange=NULL,color.spec="rgb",yrev=TRUE,
xat=NULL,yat=NULL,Hinton=FALSE,...)
52 color2D.matplot

Arguments
x data values
cs1,cs2,cs3 the color parameters that will be scaled to represent the range of numeric values.
(see ‘color.scale’)
extremes The colors for the extreme values of ‘x’. Takes precedence over the color ranges.
cellcolors A precalculated matrix of cell colors. This must have the same number of rows
and columns as the matrix or it will be uninformative. It can be a vector, but be
careTakes precedence over both ‘extremes’ and color ranges.
show.legend whether to display a color legend with the extreme numeric values in the lower
left corner of the plot. This will force the color specification to "rgb", so if this is
different from the color specification requested, call ‘color.legend’ separately.
nslices The number of color "slices" in the legend.
xlab,ylab axis labels for the plot.
do.hex plot packed hexagons instead of rectangles.
axes Whether to suppress the default axis labelling.
show.values Whether to display the numeric values of ‘x’. This also controls the number of
decimal places displayed.
vcol The color for the value display. If NA, the values are displayed in black or white
depending upon the darkness of the cell color.
vcex The character expansion for the value display.
border The color(s) for the borders of the cells. Pass NA if no border is wanted.
na.color The color to use for NA values of ‘x’.
xrange An explicit range for the transformation of colors. see ‘color.scale’
color.spec The color specification system to use.
yrev Whether to reverse the order of the y-axis to display the cells in "reading" order
(left to right and top to bottom) if TRUE, or in the order of a typical plot (left to
right and bottom to top) if FALSE.
xat,yat Values at which to place tick marks to override ‘pretty’.
Hinton Whether to display a Hinton diagram in which the magnitude of cell values is
proportional to the size of the squares and the sign is indicated by the color of
the squares.
... arguments passed to ‘plot’.

Details
Displays a plot with the same number of rectangular or hexagonal cells as there are numeric values
in the matrix or data frame. Each rectangle is colored to represent its corresponding value. The
rectangles are arranged in the conventional display of a 2D matrix with rows beginning at the top
and columns at the left. To get the rows beginning at the bottom, use ‘yrev=FALSE’. The color scale
defaults to black for the minimum value and white for the maximum.
The user will have to adjust the plot device dimensions to get regular squares or hexagons, especially
when the matrix is not square. As the margins are not equivalent for all display devices, this is
currently a matter of trial and error. Drawing hexagons is quite slow.
color2D.matplot 53

‘show.values’ and ‘show.legend’ are also used to control the number of decimal places displayed
if the values or legend are shown. ‘TRUE’ will give one decimal place, ‘2’ two, and so on.
if ‘Hinton’ is TRUE, a Hinton diagram in which the sizes of the squares are proportional to the ab-
solute value of ‘x’ and the colors of the squares indicate the sign of the ‘x’ values will be displayed.
This only works with squares.

Value
nil

Note
The function image performs almost the same when passed a matrix of values without grid positions,
except that it assigns values to a specified list of colors rather than calculating a color for each
distinct value.

Author(s)
Jim Lemon (thanks to Ashoka Polpitiya for ‘axes’)

See Also
color.scale, fill.corner, image

Examples
x<-matrix(rnorm(1024),nrow=32)
# simulate a correlation matrix with values -0.5 to 0.5
x<-rescale(x,c(-0.5,0.5))
# add a column with the extreme values (-1,1) to calculate
# the colors, then drop the extra column in the result
cellcol<-color.scale(cbind(x,c(-1,rep(1,31))),c(0,1),0,c(1,0))[,1:32]
color2D.matplot(x,cellcolors=cellcol,main="Blue to red correlations")
# do the legend call separately to get the full range
color.legend(0,-4,10,-3,legend=c(-1,-0.5,0,0.5,1),
rect.col=color.scale(c(-1,-0.5,0,0.5,1),c(0,1),0,c(1,0)),align="rb")
x<-matrix(rnorm(100),nrow=10)
# generate colors that show negative values in red to brown
# and positive in blue-green to green
cellcol<-matrix(rep("#000000",100),nrow=10)
cellcol[x<0]<-color.scale(x[x<0],c(1,0.8),c(0,0.8),0)
cellcol[x>0]<-color.scale(x[x>0],0,c(0.8,1),c(0.8,0))
# now do hexagons without borders
color2D.matplot(x,cellcolors=cellcol,xlab="Columns",ylab="Rows",
do.hex=TRUE,main="2D matrix plot (hexagons)",border=NA)
# for this one, we have to do the color legend separately
# because of the two part color scaling
legval<-seq(min(x),max(x),length.out=6)
legcol<-rep("#000000",6)
legcol[legval<0]<-color.scale(legval[legval<0],c(1,0.8),c(0,0.8),0)
legcol[legval>0]<-color.scale(legval[legval>0],0,c(0.8,1),c(0.8,0))
54 corner.label

color.legend(0,-1.8,3,-1.4,round(c(min(x),0,max(x)),1),rect.col=legcol)
# do a color only association plot
xt<-table(sample(1:10,100,TRUE),sample(1:10,100,TRUE))
observed<-xt[,rev(1:dim(xt)[2])]
expected<-outer(rowSums(observed),colSums(observed),"*")/sum(xt)
deviates<-(observed-expected)/sqrt(expected)
cellcol<-matrix(rep("#000000",100),nrow=10)
cellcol[deviates<0]<-
color.scale(deviates[deviates<0],c(1,0.8),c(0,0.5),0)
cellcol[deviates>0]<-
color.scale(deviates[deviates>0],0,c(0.7,0.8),c(0.5,0))
color2D.matplot(x=round(deviates,2),cellcolors=cellcol,
show.values=TRUE,main="Association plot")
# Hinton diagram
border.col<-color.scale(x,extremes=2:3)
color2D.matplot(x,extremes=c(2,3),main="Hinton diagram (green +, red -)",
Hinton=TRUE,border=border.col)
# waffle plot of percentages with two contributing elements
waffle.col<-fill.corner(c(rep("red",18),rep("blue",45)),10,10)
color2D.matplot(matrix(1:100,nrow=10),cellcolors=waffle.col,yrev=FALSE,
border="lightgray",xlab="",ylab="",main="Waffle plot",axes=FALSE)

corner.label Find corner locations and optionally display a label

Description
Finds the coordinates in user parameters of a specified corner of the figure region and optionally
displays a label there

Usage
corner.label(label=NULL,x=-1,y=1,xoff=NA,yoff=NA,figcorner=FALSE,...)

Arguments
label Text to display. The default is to display nothing.
x an integer value: -1 for the left side of the plot, 1 for the right side
y an integer value: -1 for the bottom side of the plot, 1 for the top side
xoff,yoff Horizontal and vertical text offsets. Defaults to one half of the width and height
of "m" respectively.
figcorner Whether to find/display at the corner of the plot or figure.
... further arguments to the ‘text’ command for the label

Details
‘corner.label’ finds the specified corner of the plot or figure and if ‘label’ is not NULL, displays
it there. The text justification is specified so that the label will be justified away from the corner. To
get the label squeezed right into a corner, set ‘xoff’ and ‘yoff’ to zero.
count.overplot 55

Value
A list of the x and y positions of the corner adjusted for the offsets.

Author(s)
Ben Bolker

Examples
plot(1:10,1:10)
corner.label("A")
corner.label(x=1,y=1)
corner.label("B",y=-1,x=1,figcorner=TRUE,col="red")

count.overplot Show overlying points as counts

Description
‘count.overplot’ checks for overlying points defined as points separated by a maximum of ‘tol’,
a two element numeric vector of the x and y tolerance. Defaults to 1/2 of the width of a lower case
"o" in the x direction and 1/2 of the height of a lower case "o" in the y direction.

Usage
count.overplot(x,y,tol=NULL,col=par("fg"),pch="1",...)

Arguments
x,y Two numeric data vectors or the first two columns of a matrix or data frame.
Typically the x/y coordinates of points to be plotted.
tol The largest distance between points that will be considered to be overlying.
col Color(s) for the points (not the numbers).
pch Symbol(s) to display.
... additional arguments passed to ‘plot’.

Value
nil

Author(s)
Jim Lemon

See Also
cluster.overplot,sizeplot
56 cylindrect

Examples
xy.mat<-cbind(sample(1:10,200,TRUE),sample(1:10,200,TRUE))
count.overplot(xy.mat,main="count.overplot",
xlab="X values",ylab="Y values")

cylindrect Display an apparent cylinder

Description
Display rectangles shaded to appear like cylinders.

Usage
cylindrect(xleft,ybottom,xright,ytop,col,border=NA,gradient="x",nslices=50)

Arguments
xleft The position of the left side of the rectangle(s).
ybottom The position of the bottom of the rectangle(s).
xright The position of the right side of the rectangle(s).
ytop The position of the top side of the rectangle(s).
col The base color(s) of the rectangles.
border Whether to draw a border and what color.
gradient Whether to vary the shading horizontally ("x" - the default) or vertically (any-
thing but "x").
nslices The number of "slices" of color for shading.

Details
‘cylindrect’ displays a rectangle filled with "slices" of color that simulate the appearance of a
cylinder. The slices are calculated so that the base color appears at the right or bottom edge of the
rectangle, becomes progressively lighter to a "highlight" at two thirds of the width or height and
then darkens toward the base color again.
The appearance is of a cylinder lit from above and to the left of the viewer. The position of the
apparent light source is hard coded into the function.

Value
The base color(s) of the rectangle(s).

Author(s)
Jim Lemon
death_reg 57

See Also
gradient.rect

Examples
plot(0,xlim=c(0,5),ylim=c(0,5),main="Examples of pseudocylindrical rectangles",
xlab="",ylab="",axes=FALSE,type="n")
cylindrect(0,0,1,5,"red")
cylindrect(rep(1,3),c(0,2,4),rep(4,3),c(1,3,5),"green",gradient="y")
cylindrect(4,0,5,5,"#8844aa")

death_reg Death registrations from 1996 to 2010

Description
Death registrations for underlying cause of death as ICD-10 chapters for 1996 to 2010.

Usage
data(death_reg)

dendroPlot Display distributions as dendrites

Description
Display the distributions of one or more sets of points as branching (dendritic) clusters.

Usage
dendroPlot(x,breaks=list(10,10,10),pch=1,col=par("fg"),cex=1,nudge=NA,
setlabels=NA,...)

Arguments
x A list or data frame of numeric or factor or character columns.
breaks A list of cutpoints to transform numeric values into factors (see cut). Must be at
least one number >= 2.
pch Symbol(s) to use in plotting the values.
col Color(s) for the symbols.
cex Size of the symbol(s) to use in plotting.
nudge The amount to set each consecutive value in a category away from the center of
the dendrite.
setlabels Labels to place along the abcissa to identify the sets.
... Other arguments passed to plot.
58 dendroPlot

Details

‘dendroPlot’ displays the distributions of categorical values as stacks of "branches". The lengths of
the branches show the number of values in each category, rather like the opposed bars in a pyramid
plot, except that there is no separation of groups. The distribution of numeric values can also be
displayed by passing a set of breakpoints to categorize the values. The breakpoints will usually be
equidistant, but unevenly spaced breakpoints can be passed. If an element of ‘x’ is numeric, the
values of the corresponding ‘x’ element will be used to place the points, but the branches will be
defined as the categories formed by applying the breaks to those numeric values.
Note that in the first example, the breakpoints for the first and third elements are used to define
the ten branches for each. The second element of ‘x’ is already categorical, so the breakpoints are
ignored. When comparing distributions with very different ranges it may be necessary to adjust the
breakpoints to get a satisfactory result.
Each successive point in a category is ‘nudge’d away from the center of the dendrite. If ‘nudge’
has more than one value, the points will be nudged up and down for categorical variables to enable
closer packing. The second value of ‘nudge’ is ignored for numeric variables. The aspect ratio of
the plot, the character expansion and the nudging will have to be adjusted to give the best point
spacing for most dendroPlots.

Value

nil

Note

The ‘ehplot’ function is a much more versatile instantiation of this type of plot. ‘dendroPlot’ has
been retained as there are currently a few differences that some users may find valuable. However,
it is not impossible that ‘dendroPlot’ will disappear in the future. Another very useful version of
this type of plot is ‘beeswarm’ in the beeswarm package.

Author(s)

Jim Lemon

See Also

ehplot

Examples
x<-list(runif(90,1,3),factor(sample(LETTERS[1:10],100,TRUE)),rnorm(80,mean=5))
dendroPlot(x,xlab="Groups",ylab="Value of x",main="Test dendroPlot I")
# now apply a nudge factor and different breaks
dendroPlot(x,breaks=list(8,10,10),nudge=c(0.05,0.1),
xlab="Groups",ylab="Value of x",main="Test dendroPlot II")
diamondplot 59

diamondplot Plot multiple variables as polygons on a radial grid

Description

‘diamondplot’ displays a plot of polygons on a radial grid representing the relationships between
one or more attributes of data objects. For a slightly different style of plot, see the "spiderweb plot"
example in ‘radial.plot’.

Usage

diamondplot(x, bg=gray(0.6), col=rainbow,name="", ...)

Arguments

x A data frame containing numeric values that represent attributes (possibly re-
peated observations) of data objects. See the example.
bg The background color for the plot.
col The colors for the polygons.
name The title for the plot (i.e. ‘main’).
... additional arguments passed to ‘plot’.

Value

nil

Author(s)

Elisa Biancotto

See Also

plot, radial.plot

Examples
data(mtcars)
mysubset<-mtcars[substr(dimnames(mtcars)[[1]],1,1)=="M",c("mpg","hp","wt","disp")]
diamondplot(mysubset)
60 dispersion

dispersion Display a measure of dispersion.

Description
Display lines or capped bars at specified points on a plot representing measures of dispersion.

Usage
dispersion(x,y,ulim,llim=ulim,intervals=TRUE,arrow.cap=0.01,arrow.gap=NA,
type="a",fill=NA,lty=NA,pch=NA,border=NA,col=par("fg"),display.na=TRUE,
...)

Arguments
x,y x and y position of the centers of the bars
ulim,llim The extent of the dispersion measures.
arrow.cap The width of the cap at the outer end of each bar as a proportion of the width of
the plot.
arrow.gap The gap to leave at the inner end of each bar. Defaults to two thirds of the height
of a capital "O".
intervals Whether the limits are intervals (TRUE) or absolute values (FALSE).
type What type of display to use.
fill Color to fill between the lines if ‘type’ is not NULL and ‘fill’ is not NA.
lty Line type for redrawing the lines if necessary.
pch Symbol for redrawing the points if necessary.
border Line type for drawing a border on the confidence band.
col Color for the lines or capped bars.
display.na Whether to display NA values as lines going off the plot.
... additional arguments passed to ‘arrows’ or ‘lines’ depending upon ‘type’.

Details
‘dispersion’ displays a measure of dispersion on an existing plot. Currently it will display either
vertical lines with caps (error bars) or lines that form a "confidence band" around a line of central
tendency. If ‘fill’ is not NA and ‘type’ is ‘"l"’, a polygon will be drawn between the confidence
lines. Remember that any points or lines within the confidence band will be obscured, so pass point
and/or line types as in the second example.
The default behavior is to display an undefined dispersion (e.g. a variance with only one obser-
vation) as a line going off the plot. If ‘display.na’ is FALSE, NA values will not be displayed,
allowing the user to show only upper or lower dispersion limits.
The ‘intervals’ argument allows the user to pass the limits as either intervals (the default) or
absolute values.
If ‘arrow.gap’ is greater than or equal to the upper or lower limit for a bar, ‘segments’ is used to
draw the upper and lower caps with no bars to avoid zero length arrows.
do.first 61

Value

nil

Author(s)

Jim Lemon

See Also

arrows, segments,lines

Examples
disptest<-matrix(rnorm(200),nrow=20)
disptest.means<-rowMeans(disptest)
row.order<-order(disptest.means)
se.disptest<-unlist(apply(disptest,1,std.error))
plot(disptest.means[row.order],main="Dispersion as error bars",
ylim=c(min(disptest.means-se.disptest),max(disptest.means+se.disptest)),
xlab="Occasion",ylab="Value")
dispersion(1:20,disptest.means[row.order],se.disptest[row.order])
plot(disptest.means[row.order],main="Dispersion as confidence band",
ylim=c(min(disptest.means-se.disptest),max(disptest.means+se.disptest)),
xlab="Occasion",ylab="Value")
dispersion(1:20,disptest.means[row.order],se.disptest[row.order],type="l",
fill="#eeccee",lty=2,pch=1)
disptest2<-matrix(sample(c(TRUE,FALSE),200,TRUE),nrow=10)
disptest.prop<-rowMeans(disptest2)
disptest.ulim<-disptest.llim<-rep(NA,10)
for(i in 1:10) {
disptest.ulim[i]<-binciWu(disptest2[i,],20)
disptest.llim[i]<-binciWl(disptest2[i,],20)
}
plot(disptest.prop,main="Dispersion as binomial confidence intervals",
ylim=c(min(disptest.llim),max(disptest.ulim)),
xlab="Sample",ylab="Proportion")
dispersion(1:10,disptest.prop,disptest.ulim,disptest.llim,
interval=FALSE,lty=2,pch=1)

do.first Execute a graphic function on a plot

Description

do.first allows the user to execute one or more commands before displaying values on a plot.
62 dotplot.mtb

Details
‘do.first’ is an argument in some plotrix functions that allows the user to do things like add a
background color or a grid to the plot before displaying the other plot elements.
The value of ‘do.first’ should be a character string that can be parsed to one or more valid R
commands. Remember to enclose the string in quotes, separate commands with semicolons and
escape quotes within the string with backslashes if necessary.

dotplot.mtb Minitab style dotplots.

Description
Create a dotplot of a data vector in the sense of "dotplot" as used in the Minitab© package.

Usage
dotplot.mtb(x, xlim = NULL, main = NULL, xlab = NULL, ylab = NULL,
pch = 19, hist = FALSE, yaxis = FALSE, mtbstyle=TRUE)

Arguments
x A numeric vector.
xlim The x limits of the plot.
main A title for the plot; defaults to blank.
xlab A label for the x axis; defaults to blank.
ylab A label for the y axis; defaults to blank.
pch The plotting symbol for the dots in the plot; defaults to a solid disc.
hist Logical scalar; should the plot be done "histogram" style, i.e. using vertical lines
rather than stacks of dots?
yaxis Logical scalar; should a y-axis be produced?
mtbstyle Logical scalar; should the dotplot be done in the "Minitab" style? I.e. should
the zero level be at the vertical midway point?

Details
The result of hist=TRUE looks less ugly than stacks of dots for very large data sets.

Value
Nothing. A plot is produced as a side effect.

Warnings
This function does something toadally different from the dotplot() (now dotchart()) function
in the graphics package.
The labelling of the y-axis is device dependent.
draw.arc 63

Author(s)
Barry Rowlingson <B.Rowlingson@lancaster.ac.uk> and Rolf Turner <r.turner@auckland.ac.nz>
http://www.stat.auckland.ac.nz/~rolf

Examples
## Not run:
set.seed(42)
x <- rpois(100,10)
dotplot.mtb(x,main="No y-axis.")
dotplot.mtb(x,yaxis=TRUE,main="With y-axis displayed.")
dotplot.mtb(x,hist=TRUE,main="An \"h\" style plot.")
dotplot.mtb(x,xlim=c(4,16),main="With the x-axis limited.")
dotplot.mtb(x,yaxis=TRUE,mtbstyle=FALSE,main="Non-Minitab style.")
dotplot.mtb(x,yaxis=TRUE,xlab="x",ylab="count",
main="With x and y axis labels.")

## End(Not run)

draw.arc Draw arc

Description
Draw one or more arcs using classic graphics.

Usage
draw.arc(x=1,y=NULL,radius=1,angle1=deg1*pi/180,angle2=deg2*pi/180,
deg1=0,deg2=45,n=0.05,col=NA,lwd=NA,...)

Arguments
x x coordinate of center. Scalar or vector.
y y coordinate of center. Scalar or vector.
radius radius. Scalar or vector.
angle1 Starting angle in radians. Scalar or vector.
angle2 Ending angle in radians. Scalar or vector.
deg1 Starting angle in degrees. Scalar or vector.
deg2 Ending angle in degrees. Scalar or vector.
n Number of polygons to use to approximate the arc.
col Arc colors.
lwd Line width for the arc.
... Other arguments passed to segments. Vectorization is not supported for these.
64 draw.circle

Details

Draws one or more arcs from angle1 to angle2. If angle1 is numerically greater than angle2,
then the angles are swapped.
Be sure to use an aspect ratio of 1 as shown in the example to avoid distortion. For argument ’n’
(which may be either a scalar or a vector, although most likely you will leave it at the default value),
an integer value means to use that number of segments to approximate the arc, while a non-integer
value means to use enough segments so that the angle that successive segments make with one
another is no more than n radians.

Value

Returns a matrix of expanded arguments invisibly.

Author(s)

Gabor Grothendieck. Improvements by Ted Toal.

Examples

plot(1:10, asp = 1,main="Test draw.arc")

draw.arc(5, 5, 1:10/10, deg2 = 1:10*10, col = "blue")
draw.arc(8, 8, 1:10/10, deg2 = 1:10*10, col = 1:10)
draw.arc(5, 5, 3, deg1=100, deg2=170, col="gold", lwd=50, lend=1)
# example taken from post by Hans Borcher:
# https://stat.ethz.ch/pipermail/r-help/2009-July/205728.html
# Note setting of aspect ratio to 1 first.
curve(sin(x), 0, pi, col="blue", asp=1)
draw.arc(pi/2, 0, 1, deg1=45, deg2=135, col="red")

draw.circle Draw a circle

Description

Draws a circle on an existing plot.

Usage

draw.circle(x,y,radius,nv=100,border=NULL,col=NA,lty=1,density=NULL,
angle=45,lwd=1)
draw.circle 65

Arguments

x,y Coordinates of the center of the circle.

radius Radius (or radii) of the circle(s) in user units.
nv Number of vertices to draw the circle.
border Color to use for drawing the circumference.
col Color to use for filling the circle.
lty Line type for the circumference.
density Density for patterned fill. See ‘polygon’.
angle Angle of patterned fill. See ‘polygon’.
lwd Line width for the circumference.

Details

‘draw.circle’ uses the dimensions of the plot and the ‘x’ and ‘y’ coordinates to draw a circle
rather than an ellipse.

Value

A list with the x and y coordinates of the points on the circumference of the last circle displayed.

Author(s)

Jim Lemon, thanks to David Winsemius for the density and angle args

See Also

polygon

Examples

plot(1:5,seq(1,10,length=5),type="n",xlab="",ylab="",main="Test draw.circle")
draw.circle(2,4,c(1,0.66,0.33),border="purple",
col=c("#ff00ff","#ff77ff","#ffccff"),lty=1,lwd=1)
draw.circle(2.5,8,0.6,border="red",lty=3,lwd=3)
draw.circle(4,3,0.7,border="green",col="yellow",lty=1,
density=5,angle=30,lwd=10)
draw.circle(3.5,8,0.8,border="blue",lty=2,lwd=2)
66 draw.ellipse

draw.ellipse Draw ellipse

Description
Draws ellipses on an existing plot.

Usage
draw.ellipse(x, y, a = 1, b = 1, angle = 0, segment = NULL,
arc.only = TRUE, deg = TRUE, nv = 100, border = NULL,
col = NA, lty = 1, lwd = 1, ...)

Arguments
x A vector or a matrix (if y is missing).
y A vector, can be missing.
a,b Vectors, radii of the ellypses along the two axes in user units.
angle Angle of rotation in degrees (if deg=TRUE) or in radians (if deg=FALSE).
segment Start and endpoints of arc in degrees (if deg=TRUE) or in radians (if deg=FALSE).
arc.only Logical, if segmen the full ellipse is not drawn, radii from the ends of the arc are
drawn to form a sector (see Examples).
deg Logical, if angles are given in degrees (TRUE) or radians.
nv Number of vertices to draw the ellipses.
border Color to use for drawing the circumference.
col Color to use for filling the circle.
lty Line type for the circumference.
lwd Line width for the circumference.
... Additional arguments passed to polygon.

Value
Draw ellipses as a side effect.

Author(s)
Peter Solymos <solymos@ualberta.ca>

See Also
polygon
draw.radial.line 67

Examples
plot(c(0,10), c(0,10), type="n", main="test draw.ellipse")
draw.ellipse(c(3,7), c(8,8), c(0.5,1), c(1,0.5), col=c(2,4),
angle=c(45,0), segment=rbind(c(0,45),c(45,360)))
draw.ellipse(c(3,7), c(6,6), c(0.5,1), c(1,0.5), col=c(2,4),
angle=c(45,0), segment=rbind(c(0,45),c(45,360)), arc.only=FALSE)
draw.ellipse(c(3,7), c(4,4), c(0.5,1), c(1,0.5), border=c(2,4),
angle=c(45,0), segment=rbind(c(0,45),c(45,360)), arc.only=FALSE)
draw.ellipse(c(3,7), c(2,2), c(0.5,1), c(1,0.5), border=1,
angle=c(45,0), lty=3)
draw.ellipse(c(3,7), c(2,2), c(0.5,1), c(1,0.5), border=c(5,3),
angle=c(45,0), nv=c(3,4), lty=2, lwd=2)

draw.radial.line Draw a radial line

Description
Draws a line radiating from a specified center, optionally expanding the line width as a function of
distance from center.

Usage
draw.radial.line(start, end, center=c(0, 0), angle=0, deg=NA,
expand=FALSE, col=NA, lwd=NA, ...)

Arguments
start Distance from center of circular area to start of line in x/y user units.
end Distance from center of circular area to end of line in x/y user units.
center The center of the circular area in x/y user units.
angle The angular position of the line in radians.
deg The angular position of the line in degrees (takes precedence if not NA).
expand TRUE to expand line width in proportion to distance from center.
col The color of the line, NA for par("col").
lwd The width of the line in device-specific units, NA for par("lwd").
... Arguments passed to ’lines’ (expand=FALSE) or ’polygon’ (expand=TRUE).

Details
If the user passes a value for ’deg’, this overrides any value passed to ’angle’.
If ’expand’ is FALSE, the line width is constant (as specified by par("lwd").
If ’expand’ is TRUE, the line width is equal to the lwd value at distance ’end’ and contracts as it
moves towards ’start’. When expand is ’TRUE’, lty is ignored.
68 draw.tilted.sector

Value
nil

Author(s)
Ted Toal

See Also
lines, linkdraw.arc

Examples
plot(0, xlim=c(1,5), ylim=c(1,5), main="Test of radial lines", xlab="", ylab="", type="n")
points(3, 3, pch=20)
draw.radial.line(1, 2, center=c(3,3))
draw.radial.line(1, 2, center=c(3,3), angle=pi/4)
draw.radial.line(1, 2, center=c(3,3), angle=pi/4+0.1, col="blue", lwd=4, lty=3)
draw.radial.line(0.2, 1.2, center=c(3,3), deg=120, col="red", lwd=10)
draw.radial.line(0.2, 1.2, center=c(3,3), deg=145, col="purple", lwd=10, lend=1)
draw.radial.line(0.5, 2, center=c(3,3), deg=225, expand=TRUE, col="gold")
draw.radial.line(0.7, 1.4, center=c(3,3), deg=180, expand=TRUE, col="orange", lwd=30)
draw.radial.line(0.5, 1.5, center=c(3,3), deg=235, expand=TRUE, lwd=5, col="brown")
draw.radial.line(0.1, 1.5, center=c(3,3), deg=325, expand=TRUE, lwd=5, col="green")

draw.tilted.sector Display a 3D pie sector

Description
Displays a 3D pie sector.

Usage
draw.tilted.sector(x=0,y=0,edges=NA,radius=1,height=0.1,theta=pi/6,
start=0,end=pi*2,border=par("fg"),col=par("bg"),explode=0,shade=0.8)

Arguments
x,y Position of the center of the pie sector in user units
edges Number of edges to draw a complete ellipse
radius the radius of the pie in user units
height the height of the pie in user units
theta The angle of viewing in radians
start Starting angle of the sector
end Ending angle of the sector
drawNestedBars 69

border The color of the sector border lines

col Color of the sector
explode How far to "explode" the sectors in user units
shade If > 0 and < 1, the proportion to reduce the brightness of the sector color to get
a better 3D effect.

Details

‘draw.tilted.sector’ displays a single 3D pie sector. It is probably only useful when called from
pie3D. The ‘shade’ argument proportionately reduces the brightness of the RGB color of the sector
to produce a top lighted effect.
If ‘explode’ is zero, only the top and outer side of each sector will be displayed. This will some-
times fix the problem of a pie with one huge sector greater than 3*pi/2 that cannot otherwise be
drawn.

Value

The bisector of the pie sector in radians.

Author(s)

Jim Lemon

See Also

pie3D

drawNestedBars Display nested bars

Description

Displays the nested bars for barNest.

Usage

drawNestedBars(x,start,end,shrink=0.1,errbars=FALSE,intervals=TRUE,col=NA,
labelcex=1,lineht=NA,showall=TRUE,Nwidths=FALSE,barlabels=NULL,
showlabels=TRUE,arrow.cap=NA)
70 drawNestedBars

Arguments

x One level of the breakdown produced by ‘brkdnNest’.

start,end The left and right x coordinates for the bar or group of bars to be displayed.
shrink The proportion to shrink the width of the bars at each level.
errbars Whether to display error bars on the bars.
intervals Whether to use offsets or absolute values when displaying measures of disper-
sion.
col The colors to use to fill the bars. See Details.
labelcex Character size for the group labels.
lineht The height of a margin line in user units.
showall Whether to display the bars at any levels above the last.
Nwidths Whether to scale the widths of the bars to the number of observations.
barlabels Optional labels to display below the bars.
showlabels Whether to display the labels below the bars.
arrow.cap The width of the "cap" on error bars in user units, defaulting to 0.01 of the width
of the plot.

Details

‘drawNestedBars’ displays the bars for the nested breakdown performed by ‘brkdnNest’. It starts
at the top of the list and calls itself for each level of the breakdown. It is unlikely to be useful for
anything else.
The combination of ‘showlabels=TRUE’ and ‘showall=FALSE’ allows the display of all of the
labels below the plot with only the last set of bars being displayed. To have a set of labels not
displayed, pass explicit ‘barlabels’ and have zero length labels for the level that is not to have
labels.

Value

nil

Author(s)

Jim Lemon and Ofir Levy

See Also

brkdnNest, drawNestedBars
drawSectorAnnulus 71

drawSectorAnnulus Display a radial pie sector

Description

Displays a radial pie sector with optional annuli.

Usage

drawSectorAnnulus(angle1,angle2,radius1,radius2,col,angleinc=0.03)

Arguments

angle1,angle2 Start and end angle for the sector.

radius1,radius2
Start and end of the radial extent of the annulus.
col Color of the sector.
angleinc The angular increment to use in drawing the arcs.

Details

‘drawSectorAnnulus’ displays a single radial pie sector. It is probably only useful when called
from radial.pie.

Value

nil

Author(s)

Jim Lemon

See Also

radial.pie
72 ehplot

ehplot Engelmann-Hecker-Plot - EH-Plot

Description

This R function provides a convenient way to visualize the distribution of grouped numerical data.

Usage

ehplot(data, groups, intervals=50, offset=0.1, log=FALSE,

median=TRUE, box=FALSE, boxborder="grey50",
xlab="groups", ylab="values", col="black",
add=FALSE, sort=TRUE, ...)

Arguments

data Vector of numerical data.

groups Vector of group names which should have the same length as data.
intervals The data is splitted into a certain number of intervals. If data points are in the
same interval they are drawn side-by-side.
offset x-distance between two data points at the same interval.
log Logarithmic display
median To show the median of each group. NAs in data are not considered for calculat-
ing the medians.
box To underlay a boxplot.
boxborder The color of the boxplot if a boxplot is drawn.
xlab x-axis label
ylab y-axis label
col vector of colors for the datapoints. (recycled as necessary).
add add this plot to an existing one (i.e. do not call plot.new).
sort normally, the groups are sorted by name. To keep the order as provided in the
groups-vector, set this to FALSE
... additional plot-parameters will be passed to the plot-function

Author(s)

Robby Engelmann <robby.engelmann@med.uni-rostock.de> and Michael Hecker <michael.hecker@rocketmail.com>

election 73

Examples
data(iris)
ehplot(iris$Sepal.Length, iris$Species, intervals=20, cex=1.8, pch=20)
ehplot(iris$Sepal.Width, iris$Species, intervals=20, box=TRUE, median=FALSE)
ehplot(iris$Petal.Length, iris$Species, pch=17, col="red", log=TRUE)
ehplot(iris$Petal.Length, iris$Species, offset=0.06, pch=as.numeric(iris$Species))

# Groups don't have to be presorted:

rnd <- sample(150)
plen <- iris$Petal.Length[rnd]
pwid <- abs(rnorm(150, 1.2))
spec <- iris$Species[rnd]
ehplot(plen, spec, pch=19, cex=pwid, col=rainbow(3, alpha=0.6)[as.numeric(spec)])

election Assign party members to seats

Description
Create a layout for an election result in an assembly

Usage
election(seats,result,formula,colours = sample(rainbow(length(counts))))

Arguments
seats A data frame of x and y positions, row numbers and angles (usually the output
from the seats function).
result A data frame with party names and seat counts.
formula A formula with the party name column on the left and the count column on the
right. Think of the twiddle symbol as "got".
colours A vector of colours. If missing a random rainbow is used. This may cause Green
parties to show as red.

Value
A data frame including:

x The x positions of the seats to be plotted on semi-circular arcs.

y The y positions of the seats to be plotted on semi-circular arcs.
r The row numbers for each seat.
theta The angle of each seat, going from pi to zero radians.
party The labels for the party holding each seat.
colour The colour that has been assigned to the party.
74 emptyspace

Author(s)
Barry Rowlingson

See Also
seats

Examples
# The EU parliament has 751 seats, and Wikipedia currently shows this
eu = structure(list(colour = c("#3399FF", "#F0001C", "#0054A5", "#FFD700",
"#990000", "#909090", "#32CD32", "#40E0D0"), party = c("EPP",
"S and D", "ECR", "ALDE", "GUE-NGL", "Non-Inscrits", "Greens-EFA",
"EFDD"), members = c(220L, 191L, 70L, 68L, 52L, 52L, 50L, 48L
)), .Names = c("colour", "party", "members"), row.names = c(NA,
-8L), class = "data.frame")
strasbourg = seats(751, 16)
eugov = election(strasbourg, eu, party~members, colours=eu$colour)
oldmar<-par(mar=c(2,4,4,2))
plot(eugov$x, eugov$y, col=eugov$colour, asp=1, pch=19, ylim=c(-2,2.5),
xlab="", ylab="", main="EU Parliament 2014", axes=FALSE)
legend(-0.7,-0.3,eu$party,fill=eu$colour)
par(oldmar)
# or using ggplot2
## Not run:
require(ggplot2)
blank = theme(axis.line=element_blank(),
axis.text.x=element_blank(),
axis.text.y=element_blank(),
axis.ticks=element_blank(),
axis.title.x=element_blank(),
axis.title.y=element_blank(),
panel.background=element_blank(),
panel.border=element_blank(),
panel.grid.major=element_blank(),
panel.grid.minor=element_blank(),
plot.background=element_blank())
ggplot(eugov, aes(x=x,y=y,col=party)) + geom_point() + coord_fixed() + blank

## End(Not run)

emptyspace Find an empty space on a plot

Description
Try to find the largest empty rectangle on a plot.
fan.plot 75

Usage
emptyspace(x,y=NULL)

Arguments
x,y x and y positions of the points on the plot.

Details
‘emptyspace’ searches the pairs of points on the plot to find the largest rectangular space within
which none of the points lie. It does not guarantee that the space will be large enough to fit a legend
or text.
Two alternatives are the ‘largest.empty’ function in the Hmisc package and the ‘maxEmptyRect’
function. While ‘maxEmptyRect’ will generally outperform ‘emptyspace’, ‘emptyspace’ will
sometimes find a slightly smaller, but "squarer" rectangle.

Value
The ‘x’ and ‘y’ coordinates of the center of the rectangle found.

Author(s)
Ray Brownrigg

Examples
x<-rnorm(100)
y<-rnorm(100)
plot(x,y,main="Find the empty space",xlab="X",ylab="Y")
es<-emptyspace(x,y)
# use a transparent background so that any overplotted points are shown
boxed.labels(es,labels="Here is the\nempty space",bg="transparent")

fan.plot Display a fan plot

Description
Displays numerical values as the arcs of overlapping sectors.

Usage
fan.plot(x,edges=200,radius=1,col=NULL,align.at=NULL,max.span=NULL,
labels=NULL,labelpos=NULL,label.radius=1.2,align="left",shrink=0.02,
main="",ticks=NULL,include.sumx=FALSE,...)
76 fan.plot

Arguments
x Vector of numbers.
edges The number of edges with which to draw a circle.
radius The radius of the sectors.
col The colors with which to fill the sectors.
align.at Where to align the sectors (see Details).
max.span The angle of the maximal sector in radians. The default is to scale ‘x’ so that it
sums to 2*pi.
labels Labels placed around the sector arcs.
labelpos Optional circumferential positions for the labels.
label.radius How far away from the sectors the labels will be placed. May be a vector with a
radius for each label.
align Position of the alignment of sectors (see Details).
shrink How much to shrink each successive sector in user units.
main Optional title for the plot.
ticks The number of ticks that would appear if the sectors were on a pie chart. Default
is no ticks, TRUE gives the number of ticks equal to the integer sum of ‘x’,
which is fairly sensible if ‘x’ is a vector of integers.
include.sumx Whether to include the sum of all ‘x’ values as the largest sector.
... Additional arguments passed to ‘polygon’.

Details
‘fan.plot’ displays sectors much like a pie chart except that the sectors are overlapped. this allows
the angular extents of the sectors to be visually compared much more accurately by the viewer.
Sectors are plotted from the largest to the smallest, shrinking the radius of each successive sector.
When sending output to the postscript device, the resulting image can be trimmed by changing the
values in BoundingBox in the header with a text editor.

Value
The circumferential positions of the labels in radians. These are returned in order of decreasing size
of the values plotted.

Author(s)
Jim Lemon, Anupam Tyagi

Examples
iucn.df<-data.frame(area=c("Africa","Asia","Europe","N&C America",
"S America","Oceania"),threatened=c(5994,7737,1987,4716,5097,2093))
fan.plot(iucn.df$threatened,max.span=pi,
labels=paste(iucn.df$area,iucn.df$threatened,sep="-"),
main="Threatened species by geographical area (fan.plot)",ticks=276)
feather.plot 77

feather.plot Display vectors along a horizontal reference line

Description
Displays vectors along a line usually representing time or position.

Usage
feather.plot(r,theta,xpos,yref=0,use.arrows=TRUE,
col.refline="lightgray",fp.type="s",main="",xlab="",ylab="",
xlabels=NULL,...)

Arguments
r radii of vectors
theta direction of vectors in radians
xpos where to start each vector along the reference line
yref vertical position to place the reference line
use.arrows whether to put arrow heads on the ends of the vectors
col.refline the color of the reference line
fp.type whether to use "standard" coordinates (begin at the right and move counterclock-
wise) or "meteorological" coordinates (begin at the top and move clockwise)
when interpreting the values of ‘theta’
main the title of the plot
xlab the label for the reference line
ylab the label for the vertical axis
xlabels optional labels for the reference line
... additional arguments passed to ‘arrows’ or ‘segments’

Details
This function places vectors of length ‘r’ and angle ‘theta’ along a reference line that may repre-
sent time or position or some other value. The user is responsible for spacing the vectors so that
they do not overlap if this is desired.
Feather plots are typically wider than high. The user will probably want to specify a graphics device
that doesn’t leave lots of blank space above and below the plot.

Value
nil

Author(s)
Jim Lemon, Eduardo Klein
78 fill.corner

See Also
spread.labels

Examples
dev.new(width=8,height=3)
r<-0.6+rnorm(24)/5
theta<-c(seq(15*pi/16,pi/16,length.out=12),
seq(17*pi/16,31*pi/16,length.out=12))
feather.plot(r,theta,xlabels=1:24,
main="Standard Coordinates",xlab="Time",ylab="Value")
# rearrange theta for meteorological coordinates
feather.plot(r,c(theta[19:24],rev(theta[7:18]),theta[1:6]),xlabels=1:24,fp.type="m",
main="Meteorological Coordinates",xlab="Time",ylab="Value")
dev.off()

fill.corner Fill a "corner" of a matrix with values

Description
Fills one corner of a matrix with the supplied values, leaving the rest filled with a default value.

Usage
fill.corner(x,nrow,ncol,na.value=NA)

Arguments
x A vector of values.
nrow,ncol The number of rows and columns in the matrix to be returned.
na.value The default value for unfilled cells.

Details
‘fill.corner’ creates an nrow by ncol matrix and fills the lower left corner with the values supplied
in ‘x’. If there are more values in ‘x’ than cells in the matrix, only the first nrow*ncol values will
be inserted.

Value
An nrow by ncol matrix containing the values in ‘x’.

Author(s)
Jim Lemon
floating.pie 79

floating.pie Display a floating pie chart

Description
Displays a pie chart at an arbitrary position on an existing plot

Usage
floating.pie(xpos=0,ypos=0,x,edges=200,radius=1,col=NULL,startpos=0,
shadow=FALSE,shadow.col=c("#ffffff","#cccccc"),explode=0,...)

Arguments
xpos,ypos x and y position of the center of the pie chart
x a numeric vector for which each value will be a sector
edges the number of lines forming a circle
radius the radius of the pie in user units
col the colors of the sectors - defaults to ‘rainbow’
startpos The starting position for drawing sectors in radians.
shadow Logical - whether to draw a shadow
shadow.col Colors to use for a shadow.
explode How much to "explode" one or more of the sectors.
... graphical parameters passed to ‘polygon’

Details
‘floating.pie’ displays a pie chart with an optional shadow on an existing plot (see ‘polygon.shadow’).
‘floating.pie’ now accepts NAs or zeros in ‘x’, but simply ignores them.
‘floating.pie’ can be useful when multiple pie charts are placed on a plot overlaying something
else, like a map.

Value
The bisecting angle of the sectors in radians. Useful for placing text labels for each sector. If any
values in ‘x’ were zero or NA, no angle is returned for that value. This means that the user must
adjust the labels accordingly if ‘pie.labels’ is called.
If ‘floating.pie’ is called with no graphics device, it will try to open one with the appropriate
dimensions.
If ‘pie.labels’ is called, ensure that the center of the pie chart and any ‘explode’ values are the
same.
80 fullaxis

Note
As with most pie charts, simplicity is essential. Trying to display a complicated breakdown of data
rarely succeeds.

Author(s)
Jim Lemon

See Also
pie.labels, boxed.labels, polygon.shadow

Examples
plot(1:5,type="n",main="Floating Pie test",xlab="",ylab="",axes=FALSE)
box()
polygon(c(0,0,5.5,5.5),c(0,3,3,0),border="#44aaff",col="#44aaff")
floating.pie(1.7,3,c(2,4,4,2,8),radius=0.5,
col=c("#ff0000","#80ff00","#00ffff","#44bbff","#8000ff"))
floating.pie(3.1,3,c(1,4,5,2,8),radius=0.5,
col=c("#ff0000","#80ff00","#00ffff","#44bbff","#8000ff"))
floating.pie(4,1.5,c(3,4,6,7),radius=0.5,
col=c("#ff0066","#00cc88","#44bbff","#8000ff"))
draw.circle(3.9,2.1,radius=0.04,col="white")
draw.circle(3.9,2.1,radius=0.04,col="white")
draw.circle(3.9,2.1,radius=0.04,col="white")
draw.circle(4,2.3,radius=0.04,col="white")
draw.circle(4.07,2.55,radius=0.04,col="white")
draw.circle(4.03,2.85,radius=0.04,col="white")
text(c(1.7,3.1,4),c(3.7,3.7,3.7),c("Pass","Pass","Fail"))
plot(0,xlim=c(-1.5,1.5),ylim=c(-1.5,1.5),type="n",axes=FALSE,
main="Floating pie with minor explosions",xlab="",ylab="")
floating.pie(x=1:5,explode=c(0,0.1,0,0.2,0))

fullaxis Add an axis with a line to the edge of the plot

Description
As ‘axis’, but draws a "box" line in the same color as the axis.

Usage
fullaxis(side=1,at=NULL,labels=TRUE,line=NA,pos=NA,outer=FALSE,
font=NA,lty="solid",lwd=1,lwd.ticks=lwd,col=NULL,col.ticks=NULL,
hadj=NA,padj=NA,...)
fullaxis 81

Arguments
side The side of the plot to draw the axis
at Optional positions in user units for the tick marks.
labels Optional labels for the tick marks.
line Optional line into the margin.
pos Optional position in user units for the axis. Defaults to the edge.
outer Whether to use the outer margin as for ‘axis’.
font Font for the labels.
lty Line type.
lwd Line width for the axis.
lwd.ticks Line width for the ticks.
col color for the axis and tick marks. See Details for label color.
col.ticks Color for the tick marks if different from the axis.
hadj,padj Justification for the labels. See ‘axis’.
... Further arguments passed to ‘axis’.

Details
‘fullaxis’ draws a line to the edges of the plot and then calls ‘axis’ to draw an axis. ‘fullaxis’
is mainly useful for drawing a colored axis on a boxed plot. In order to get the tick labels the same
color as the axis and ticks, pass the ‘col.axis’ argument (as part of ...) as well as ‘col’. See the
example for some useful tips.

Value
The positions of the tick marks in user units.

Author(s)
Jim Lemon

See Also
axis

Examples
plot(runif(20,-1,1),runif(20,-1,1),xlim=c(-1,1.5),main="Demo of fullaxis",
xlab="X",ylab="Y",axes=FALSE)
fullaxis(1,col="red",col.axis="red")
fullaxis(2,col="blue",col.axis="blue")
fullaxis(4,at=c(-0.5,0,0.5),labels=c("Negative","Zero","Positive"),pos=1.2,
col="green",las=1)
# add a top line to complete the "box"
xylim<-par("usr")
segments(xylim[1],xylim[4],xylim[2],xylim[4])
82 furc

furc Plot a dendrite

Description
Plot one level of a dendrogram displaying two or more mutually exclusive attributes.

Usage
furc(x,xpos,yrange,toplevel,maxx,cex=1,col)

Arguments
x A ‘dendrite’ object containing the counts of objects having combinations of
mutually exclusive attributes.
xpos The horizontal position on the plot to display the current level of the dendro-
gram.
yrange The range of values in which the current level of the dendrogram will be dis-
played.
toplevel A flag for the function to know whether it is at the top level of the dendrogram
or not. Do not change this argument.
maxx The maximum xpos value to suppress staggering of the category labels. This is
calculated in ‘plot.dendrite’.
cex The character expansion to use in the display.
col The color(s) to use for the backgrounds of the boxes containing the category
labels.

Details
‘furc’ displays one furcation of the dendrogram. A furcation is a single box displaying its label
and count that may split into finer divisions. If so, ‘furc’ calls itself for each furcation until there
are no more splits.
On the final level of categorization, the category labels are staggered to minimize overprinting.

Value
nil

Author(s)
Jim Lemon

See Also
plot.dendrite
gantt.chart 83

gantt.chart Display a Gantt chart

Description
Displays a Gantt chart with priority coloring

Usage
gantt.chart(x=NULL,format="%Y/%m/%d",xlim=NULL,taskcolors=NULL,
priority.legend=FALSE,vgridpos=NULL,vgridlab=NULL,
vgrid.format="%Y/%m/%d",
half.height=0.25,hgrid=FALSE,main="",xlab="",cylindrical=FALSE,
label.cex=1,border.col=NA,priority.label="Priorities",
priority.extremes=c("High","Low"),time.axis=3)

Arguments
x a list of task labels, start/end times and task priorities as returned by ‘get.gantt.info’.
If this is not present, get.gantt.info will be called.
format the format to be used in entering dates/times (see strptime).
xlim the horizontal limits of the plot (see Details).
taskcolors a vector of colors used to illustrate task priority.
priority.legend
Whether to display a priority color legend.
vgridpos optional positions of the vertical grid lines.
vgridlab optional labels for the vertical grid lines.
vgrid.format format for the vertical grid labels.
half.height the proportion of the spacing between task bars that will be filled by the bar on
each side - 0.5 will leave no space.
hgrid logical - whether to display grid lines between the bars.
main the title of the plot - note that this is actually displayed using ‘mtext’.
xlab horizontal axis label - usually suppressed.
cylindrical Whether to give the bars a cylindrical appearance.
label.cex Relative size for the task labels at the left side.
border.col The color for an optional border for the bars (NA=none).
priority.label Label for the priority color legend.
priority.extremes
Labels for each end of the priority color legend.
time.axis Where to place the time axis labels.
84 gantt.chart

Details
Because the "time" axis is calculated using POSIXct values, the values passed as ‘xlim’ must also
be POSIXct. See the second plot in the examples.
If task priority colors are not wanted, set ‘taskcolors’ to a single value to suppress the coloring.
If this is not done, ‘rainbow’ will be called to generate a different color for each task. If colors
other than ‘rainbow’ are wanted, remember to pass enough colors for one to the lowest (highest
numerically) priority.
There can now be more than one time interval for each task. If there is, more than one bar will be
displayed for each interval, which may not be a task at all, but rather intervals related to the labels.
Colors can be specified for labels or intervals and if there are not as many colors as intervals, the first
"number of unique labels" colors will be assigned to each unique label. This should make every bar
for each label the same color, but be aware that the colors will be distributed in alphabetical order
of the entity labels. If there are at least as many taskcolors as intervals, they will be assigned to
intervals in the order of the ‘taskcolors’ vector. The examples should make this clearer.
Since ‘gantt.chart’ can be used to display things other than prioritized tasks, the labels for the
priority legend can now be specified.

Value
The list used to create the chart - see get.gantt.info for details. This can be saved and reused rather
than manually entering the information each time the chart is displayed.

Author(s)
Jim Lemon (original by Scott Waichler - features by Ulrike Gromping - added label colors by
Nicolas Immelman)

See Also
get.gantt.info

Examples
Ymd.format<-"%Y/%m/%d"
gantt.info<-list(labels=
c("First task","Second task","Third task","Fourth task","Fifth task"),
starts=
as.POSIXct(strptime(
c("2004/01/01","2004/02/02","2004/03/03","2004/05/05","2004/09/09"),
format=Ymd.format)),
ends=
as.POSIXct(strptime(
c("2004/03/03","2004/05/05","2004/05/05","2004/08/08","2004/12/12"),
format=Ymd.format)),
priorities=c(1,2,3,4,5))
vgridpos<-as.POSIXct(strptime(c("2004/01/01","2004/02/01","2004/03/01",
"2004/04/01","2004/05/01","2004/06/01","2004/07/01","2004/08/01",
"2004/09/01","2004/10/01","2004/11/01","2004/12/01"),format=Ymd.format))
vgridlab<-
gap.barplot 85

c("Jan","Feb","Mar","Apr","May","Jun","Jul","Aug","Sep","Oct","Nov","Dec")
gantt.chart(gantt.info,main="Calendar date Gantt chart (2004)",
priority.legend=TRUE,vgridpos=vgridpos,vgridlab=vgridlab,hgrid=TRUE)
# add a little extra space on the right side
gantt.chart(gantt.info,main="Calendar date Gantt chart (2004)",
priority.legend=TRUE,vgridpos=vgridpos,vgridlab=vgridlab,hgrid=TRUE,
xlim=as.POSIXct(strptime(c("2004/01/01","2004/12/20"),
format=Ymd.format)))
# if both vgidpos and vgridlab are specified,
# starts and ends don't have to be dates
info2<-list(labels=c("Jim","Joe","Jim","John","John","Jake","Joe","Jed","Jake"),
starts=c(8.1,8.7,13.0,9.1,11.6,9.0,13.6,9.3,14.2),
ends=c(12.5,12.7,16.5,10.3,15.6,11.7,18.1,18.2,19.0))
gantt.chart(info2,vgridlab=8:19,vgridpos=8:19,
main="All bars the same color",taskcolors="lightgray")
gantt.chart(info2,vgridlab=8:19,vgridpos=8:19,
main="A color for each label",taskcolors=c(2,3,7,4,8))
gantt.chart(info2,vgridlab=8:19,vgridpos=8:19,
main="A color for each interval - with borders",
taskcolors=c(2,3,7,4,8,5,3,6,"purple"),border.col="black")

gap.barplot Display a barplot with a gap (missing range) on one axis

Description
Displays a barplot with a missing range.

Usage
gap.barplot(y,gap,xaxlab,xtics,yaxlab,ytics,xlim=NA,ylim=NA,xlab=NULL,
ylab=NULL,horiz=FALSE,col,...)

Arguments
y a vector of data values
gap the range of values to be left out
xaxlab labels for the x axis ticks
xtics position of the x axis ticks
yaxlab labels for the y axis ticks
ytics position of the y axis ticks
xlim Optional x limits for the plot
ylim optional y limits for the plot
xlab label for the x axis
ylab label for the y axis
horiz whether to have vertical or horizontal bars
col color(s) in which to plot the values
... arguments passed to ‘barplot’.
86 gap.boxplot

Details

Displays a barplot omitting a range of values on the X or Y axis. Typically used when there is
a relatively large gap in the range of values represented as bar heights. See axis.break for a brief
discussion of plotting on discontinuous coordinates.
If the user does not ask for specific y limits, the function will calculate limits based on the range of
the data values. If passing specific limits, remember to subtract the gap from the upper limit.

Value

The center positions of the bars.

Author(s)

Jim Lemon

See Also

gap.barplot

Examples
twogrp<-c(rnorm(10)+4,rnorm(10)+20)
gap.barplot(twogrp,gap=c(8,16),xlab="Index",ytics=c(3,6,17,20),
ylab="Group values",main="Barplot with gap")
gap.barplot(twogrp,gap=c(8,16),xlab="Index",ytics=c(3,6,17,20),
ylab="Group values",horiz=TRUE,main="Horizontal barplot with gap")

gap.boxplot Display a boxplot with a gap (missing range)

Description

Displays a boxplot with a missing range.

Usage

gap.boxplot(x,...,gap=list(top=c(NA,NA),bottom=c(NA,NA)),
range=1.5,width=NULL,varwidth=FALSE,notch=FALSE,outline=TRUE,
names,xlim=NA,ylim=NA,plot=TRUE,border=par("fg"),col=NULL,log="",
axis.labels=NULL,axes=TRUE,pars=list(boxwex=0.8,staplewex=0.5,outwex=0.5),
horizontal=FALSE,add=FALSE,at=NULL,main=NULL)
gap.boxplot 87

Arguments
x numeric vector or a list of vectors
... arguments passed to boxplot.
gap the range(s) to be omitted - a list with two components, ‘top’ and ‘bottom’ each
specifying a range to omit. The default range of ‘c(NA,NA)’ means no omitted
range
range how far to extend the whiskers, (see boxplot)
width the relative widths of the boxes
varwidth if TRUE, box widths are proportional to the square roots of the number of ob-
servations
notch whether to display the confidence intervals for the median as notches
outline whether to display outliers
names optional names to display beneath each boxplot
xlim,ylim Optional x and y axis limits for the plot.
boxwex scale factor for box widths
staplewex staple width proportional to box width
outwex outlier line width
plot dummy argument for consistency with ‘boxplot’ - always plots
border optional color(s) for the box lines
col optional color(s) to fill the boxes
log whether to use a log scale - currently does nothing
axis.labels Optional axis labels.
axes Whether to display axes.
pars optional parameters for consistency with ‘boxplot’
horizontal whether to plot horizontal boxplots - currently does nothing
add whether to add the boxplot(s) to a current plot - currently does nothing.
at optional horizontal locations for the boxplots.
main a title for the plot.

Details
Displays boxplot(s) omitting range(s) of values on the top and/or bottom of the plot. Typically
used when there are outliers far from the boxes. See boxplot for more detailed descriptions of
the arguments. If the gaps specified include any of the values in the ‘stats’ matrix returned from
‘boxplot’, the function will exit with an error message. This prevents generation of NAs in indexing
operations, which would fail anyway. A gap can include part of a box, but it is unlikely that this
would be intended by the user.
See axis.break for a brief discussion of plotting on discontinuous coordinates.
88 gap.plot

Value
A list with the same structure as returned by ‘boxplot’, except that the values of elements beyond
the gap(s) have their true positions on the plot rather than the original values. For example, in the
second example, the value returned for the upper staple of the right boxplot is 14 rather than 20, due
to the 6 unit gap.

Author(s)
Jim Lemon

See Also
gap.barplot,gap.plot

Examples
twovec<-list(vec1=c(rnorm(30),-6),vec2=c(sample(1:10,40,TRUE),20))
gap.boxplot(twovec,gap=list(top=c(12,18),bottom=c(-5,-3)),
main="Show outliers separately")
if(dev.interactive()) par(ask=TRUE)
gap.boxplot(twovec,gap=list(top=c(12,18),bottom=c(-5,-3)),range=0,
main="Include outliers in whiskers")
par(ask=FALSE)

gap.plot Display a plot with one or two gaps (missing ranges) on one axis

Description
Displays a plot with one or two missing ranges on one of the axes.

Usage
gap.plot(x,y,gap,gap.axis="y",bgcol="white",breakcol="black",brw=0.02,
xlim=range(x),ylim=range(y),xticlab,xtics=NA,yticlab,ytics=NA,
lty=rep(1,length(x)),col=rep(par("col"),length(x)),pch=rep(1,length(x)),
add=FALSE,stax=FALSE,...)

Arguments
x,y data values
gap the range(s) of values to be left out
gap.axis whether the gaps are to be on the x or y axis
bgcol the color of the plot background
breakcol the color of the "break" marker
brw break width relative to plot width
gap.plot 89

xlim,ylim the plot limits.

xticlab labels for the x axis ticks
xtics position of the x axis ticks
yticlab labels for the y axis ticks
ytics position of the y axis ticks
lty line type(s) to use if there are lines
col color(s) in which to plot the values
pch symbols to use in plotting.
add whether to add values to an existing plot.
stax whether to call staxlab for staggered axis labels.
... arguments passed to ‘plot’ and ‘points’.

Details
Displays a plot omitting one or two ranges of values on one axis. Typically used when there is a
relatively large gap or two in the overall range of one set of values, often because of outliers. The
function warns the user if any values may have been omitted by being in the "gap". See axis.break
for a brief discussion of plotting on discontinuous coordinates.
To add more data series to a gap plot, call ‘gap.plot’ with ‘add = TRUE’. The same ‘gap’ and
‘gap.axis’ arguments as in the initial call must be passed or the data will not be displayed correctly.
Remember to pass an explicit ‘xlim’ or ‘ylim’ to the initial call if the added data exceed the range of
the data initially displayed. Also remember to subtract the width(s) of the gap(s) if you are passing
an explicit ‘xlim’ or ‘ylim’.
Because the gaps take up some space, it is possible to have a data value that is just below a gap
plotted in the gap. The answer is to make the lower gap limit a little higher if this is a problem.
If at least four values are passed in ‘gap’, the first four will be used to calculate two "gaps" in the
plot instead of one. The function does not check whether these values are sensible, so it is quite
easy to ask for a very silly plot.
The default ticks are usually not ideal, and most users will want to pass their own tick positions and
perhaps labels. Note that ‘lines’ appears to use only the first ‘col’ and ‘lty’ argument value, so if
you must have lines with different colors and types, use ‘add=TRUE’ and add them separately (see
the third example for the problem and the solution).

Value
nil

Author(s)
Jim Lemon and Ben Bolker (thanks to Zheng Lu for the "add" idea, and Art Roberts for helping to
get the gaps right.)

See Also
gap.barplot, axis.break, do.first
90 get.breaks

Examples
twogrp<-c(rnorm(5)+4,rnorm(5)+20,rnorm(5)+5,rnorm(5)+22)
gpcol<-c(2,2,2,2,2,3,3,3,3,3,4,4,4,4,4,5,5,5,5,5)
gap.plot(twogrp,gap=c(8,16),xlab="Index",ylab="Group values",
main="Gap on Y axis",col=gpcol)
gap.plot(twogrp,rnorm(20),gap=c(8,16),gap.axis="x",xlab="X values",
xtics=c(4,7,17,20),ylab="Y values",main="Gap on X axis with added lines")
gap.plot(c(seq(3.5,7.5,by=0.5),seq(16.5,22.5,by=0.5)),
rnorm(22),gap=c(8,16),gap.axis="x",type="l",add=TRUE,col=2,)
gap.plot(twogrp,gap=c(8,16,25,35),
xlab="X values",ylab="Y values",xlim=c(1,30),ylim=c(0,42),
main="Test two gap plot with the lot",xtics=seq(0,30,by=5),
ytics=c(4,6,18,20,22,38,40,42),
lty=c(rep(1,10),rep(2,10)),
pch=c(rep(2,10),rep(3,10)),
col=c(rep(2,10),rep(3,10)),
type="b")
gap.plot(21:30,rnorm(10)+40,gap=c(8,16,25,35),add=TRUE,
lty=rep(3,10),col=rep(4,10),type="l")

get.breaks Get the breakpoints for a weighted histogram

Description
Gets the breakpoints for a weighted histogram.

Usage
get.breaks(x,breaks)

Arguments
x A numeric vector.
breaks Either the name of the function to calculate breakpoints, the number of cate-
gories or a vector of breakpoints.

Details
‘get.breaks’ either calls the same functions as ‘hist’ to get breakpoints or calculates a given
number or just returns ‘breaks’ if they are already specified.

Value
A vector of breakpoints.

Author(s)
Jim Lemon
get.gantt.info 91

See Also
hist

get.gantt.info Gather the information to create a Gantt chart

Description
Allows the user to enter the information for a Gantt chart.

Usage
get.gantt.info(format="%Y/%m/%d")

Arguments
format the format to be used in entering dates/times. Defaults to YYYY/mm/dd. See
strptime for various date/time formats.

Value
The list used to create the chart. Elements are:

labels The task labels to be displayed at the left of the chart.

starts,ends The task starts/ends as POSIXct dates/times.
priorities Task priorities as integers in the range 1 to 10. There can be less than 10 levels of
priority, but if priorities do not start at 1 (assumed to be the highest), the default
priority colors will be calculated from 1.

Author(s)
Jim Lemon

See Also
gantt.chart

Examples
cat("Enter task times using HH:MM (hour:minute) format\n")
get.gantt.info("%H:%M")
92 get.segs

get.segs Calculate the midpoints and limits for a centipede plot

Description

Calculates midpoints and limits for a list or data frame for use with centipede.plot.

Usage

get.segs(x,mct="mean",lower.limit="std.error",upper.limit=lower.limit)

Arguments

x a list or data frame.

mct The name of the function to calculate midpoints.
lower.limit,upper.limit
The names of the function(s) to calculate lower and upper limits.

Details

‘get.segs’ calls the functions whose names are passed to calculate midpoints and limits for each
list element or data frame column. The user can define special functions for the central and disper-
sion measures if desired.

Value

A matrix with four rows and as many columns as were in the object ‘x’. The first row contains the
midpoint values, the second and third the lower and upper limit values respectively and the fourth
row the number of valid observations in the columns.

Author(s)

Jim Lemon

See Also

centipede.plot
get.soil.texture 93

get.soil.texture Enter soil texture data

Description

‘get.soil.texture’ calls ‘get.triprop’ to allow the user to enter soil textures as the proportions
or percentages of three components, sand, silt and clay.

Usage

get.soil.texture(use.percentages=FALSE,cnames=c("sand","silt","clay"))

Arguments
use.percentages
Logical - whether to treat the entries as percentages and scale to proportions.
cnames column names for the resulting three column matrix.

Value

A matrix of the components of one or more soil samples.

Author(s)

Sander Oom and Jim Lemon

See Also

soil.texture,get.triprop

Examples

if(dev.interactive()) {
newsp<-get.soil.texture()
# show the soil triangle
soil.texture()
# now plot the observations
show.soil.texture(newsp)
}
94 get.tablepos

get.tablepos Get the position for a legend or table

Description

Gets the x and y positions and justification for a legend or table in user units from the string de-
scriptors like "top".

Usage

get.tablepos(x)

Arguments

x A valid position descriptor like "top".

Details

‘get.tablepos’ checks for one of the nine valid position descriptors:

topleft, top, topright, left, center, right, bottomleft, bottom and bottomright.
If none of these descriptors are found, it will return the center position and justification.

Value

A list containing:

x x position
y y position
xjust x (horizontal) justification
yjust y (vertical) justification

Author(s)

Jim Lemon

See Also

addtable2plot, legendg
get.triprop 95

get.triprop Enter three proportion data - usually soil textures

Description
‘get.triprop’ allows the user to enter triplets of proportions or percentages of three components
such as sand, silt and clay in soils.

Usage
get.triprop(use.percentages=FALSE,cnames=c("1st","2nd","3rd"))

Arguments
use.percentages
Logical - whether to treat the entries as percentages and scale to proportions.
cnames column names for the resulting three column matrix.

Details
The three proportions of each row must sum to 100 or 1 within 1% or the function will warn the
operator.

Value
A matrix of the components of one or more observations.

Author(s)
Jim Lemon

See Also
triax.plot, soil.texture

Examples
if(dev.interactive()) {
# get some proportions
newsp<-get.triprop()
# show the triangle
triax.frame(main="Test triax.plot")
# now plot the observations
triax.points(newsp)
}
96 getIntersectList

getFigCtr Get coordinates in the figure region in user units.

Description
Calculates the coordinates of a proportional point of the figure region in user units.

Usage
getFigCtr(pos=c(0.5,0.5))

Arguments
pos The proportion of the figure region to find (see Details).

Details
‘getFigCtr’ reads parameters about the current plot and calculates the vertical and horizontal cen-
ters of the figure region by default. This is typically useful for placing a centered title on plots where
the left and right margins are very different.
By changing ‘pos’, any proportional points of the figure region can be returned. For example,
‘pos=c(0,0)’ will return the left and bottom coordinates of the figure region.

Value
A two element vector containing the coordinates of the center of the figure region in user units.

Author(s)
Jim Lemon (thanks to Karl Brand for the adjustable coordinates)

getIntersectList Enter a set intersection list

Description
Enter the information for a set intersection display.

Usage
getIntersectList(nelem,xnames=NULL,sep="+")
getIntersectList 97

Arguments
nelem The number of sets for which the intersections will be displayed.
xnames The labels for the set intersections. The function creates names from combina-
tions of the first ‘nelem’ capital letters if none are given.
sep The separator to use when calling ‘paste’.

Details
‘getIntersectList’ allows the user to manually enter the counts of set intersections rather than
build this information from a matrix of data. It is probably most useful for producing an intersection
diagram when the counts of the intersections are already known, or when the values are proportions
rather than counts as in the example.
It is very helpful when there are large numbers of elements, as the ‘makeIntersectList’ function
runs very slowly.

Value
A list of the counts of elements in the set intersections.

Author(s)
Jim Lemon

See Also
makeIntersectList, intersectDiagram

Examples
# this example is from a haplotype mapping problem submitted by Mao Jianfeng
## Not run:
hapIntList<-
getIntersectList(3,xnames=c("hap.Pd","hap.Pt","hap.Py"))
# enter the data as follows:
# Number of elements in hap.Pd - 1: 27.586
# Number of elements in hap.Pt - 1: 20.689
# Number of elements in hap.Py - 1: 31.035
# Number of elements in hap.Pd-hap.Pt - 1: 10.345
# Number of elements in hap.Pd-hap.Py - 1: 10.345
# Number of elements in hap.Pt-hap.Py - 1: 0
# Number of elements in hap.Pd-hap.Pt-hap.Py - 1: 0
# Total number of elements - 1: 100

## End(Not run)
hapIntList<-structure(list(structure(c(27.586, 20.689, 31.035),
.Names = c("hap.Pd","hap.Pt","hap.Py")),
structure(c(10.345, 10.345, 0),
.Names = c("hap.Pd-hap.Pt","hap.Pd-hap.Py","hap.Pt-hap.Py")),
structure(0, .Names = "hap.Pd-hap.Pt-hap.Py"),100),
class = "intersectList")
98 getMarginWidth

intersectDiagram(hapIntList)

getMarginWidth Find the margin width necessary to fit text or a legend next to a plot

Description
Calculates the margin width necessary to fit text or a legend next to a plot.

Usage
getMarginWidth(side=4,labels,is.legend=FALSE)

Arguments
side Which side of the plot (as in axis).
labels The text to place next to the plot.
is.legend Whether the text is in a legend or not.

Details
‘getMarginWidth’ reads parameters about the current plot and calculates the left or right (default)
margin necessary to fit the strings passed as ‘labels’ or a legend containing those strings.

Value
A two element list containing the number of margin lines necessary to fit the text or legend and the
horizontal center of the margin in user units.

Author(s)
Jim Lemon

Examples
plot(rnorm(10))
newmarinfo<-getMarginWidth(labels=c("Long label","Even longer label"))
oldmar<-par("mar")
par(mar=c(oldmar[1:3],newmarinfo$newmar))
plot(rnorm(10))
par(xpd=TRUE)
text(rep(newmarinfo$marcenter,2),c(0.5,-0.5),
c("Long label","Even longer label"))
par(mar=oldmar,xpd=FALSE)
getYmult 99

getYmult Correct for aspect and coordinate ratio

Description
Calculate a multiplication factor for the Y dimension to correct for unequal plot aspect and coordi-
nate ratios on the current graphics device.

Usage
getYmult()

Details
‘getYmult’ retrieves the plot aspect ratio and the coordinate ratio for the current graphics device,
calculates a multiplicative factor to equalize the X and Y dimensions of a plotted graphic object.

Value
The correction factor for the Y dimension.

Author(s)
Jim Lemon

See Also
draw.circle

get_axispos3d Get axis positions on a 3D plot

Description
Calculate the axis positions on a 3D plot.

Usage
get_axispos3d(edge,pmat,at,pos=NULL, dist=0)

Arguments
edge which axis to calculate.
pmat matrix to transform coordinates.
at position on the axis.
pos position of the axis relative to the other axes.
dist Offset of the axis.
100 gradient.rect

Value

A position in 2D coordinates

Author(s)

Ben Bolker

gradient.rect Display a rectangle filled with an arbitrary color gradient

Description

‘gradient.rect’ draws a rectangle consisting of ‘nslices’ subrectangles of the colors in ‘col’

or those returned by ‘color.gradient’ if ‘col’ is NULL. The rectangle is ’sliced’ in the direction
specified by ‘gradient’.

Usage

gradient.rect(xleft,ybottom,xright,ytop,reds,greens,blues,col=NULL,
nslices=50,gradient="x",border=par("fg"))

Arguments
xleft,ybottom,xright,ytop
Positions of the relevant corners of the desired rectangle, as in ‘rect’.
reds,greens,blues
vectors of the values of the color components either as 0 to 1 or ,if any value is
greater than 1, 0 to 255.
col Vector of colors. If supplied, this takes precedence over ‘reds, greens, blues’
and ‘nslices’ will be set to its length.
nslices The number of sub-rectangles that will be drawn.
gradient whether the gradient should be horizontal (x) or vertical.
border The color of the border around the rectangle (NA for none).

Value

the vector of hexadecimal color values from ‘color.gradient’ or ‘col’.

Author(s)

Jim Lemon
hexagon 101

Examples
# get an empty box
plot(0:10,type="n",axes=FALSE)
# run across the three primaries
gradient.rect(1,0,3,6,reds=c(1,0),
greens=c(seq(0,1,length=10),seq(1,0,length=10)),
blues=c(0,1),gradient="y")
# now a "danger gradient"
gradient.rect(4,0,6,6,c(seq(0,1,length=10),rep(1,10)),
c(rep(1,10),seq(1,0,length=10)),c(0,0),gradient="y")
# now just a smooth gradient across the bar
gradient.rect(7,0,9,6,col=smoothColors("red",38,"blue"),border=NA)

hexagon Draw a hexagon

Description
Draws a hexagon on the current graphic device

Usage
hexagon(x,y,unitcell=1,col=NA,border="black")

Arguments
x,y x and y position of the bottom left corner of the square that would pack into the
same space as the hexagon.
unitcell The dimension of the side of the abovementioned square.
col The color to fill the hexagon - default is no fill.
border The color of the perimeter of the hexagon.

Value
nil

Note
Draws a hexagon with the same center as a square that would pack into the same dimensions as
the hexagon. That is, given a grid of squares with alternate rows shifted one half the length of the
sides, the hexagons drawn would be close packed. Its use in the plotrix package is to provide an
alternative unit cell for the ‘color2D.matplot’ function.

Author(s)
Jim Lemon
102 histStack

See Also
color2D.matplot

histStack Histogram "stacked" by categories

Description
Histogram of a quantitative variable with bars that are "stacked" by the values of a factor variable.

Usage
histStack(x,...)

## S3 method for class 'formula'

histStack(x,data,breaks="Sturges",col="rainbow",
right=TRUE,main="",xlab=NULL,legend.pos=NULL,cex.legend=0.75,...)

## Default S3 method:
histStack(x,z,breaks="Sturges",col="rainbow",
right=TRUE,main="",xlab=NULL,legend.pos=NULL,cex.legend=0.75,...)

Arguments
x A vector of quantitative data or a formula of the form x~z (see z below).
z A vector of categorical data (a factor) that will define the “stacks”.
data A data frame that contains both x and z.
breaks Breaks to use in categorizing values of x.
col Either a vector of colors in any legitimate form or a character string that specifies
a function that requires only the length of the vector as an argument and will
return a vector of colors with that length. (see Details)
right A logical that indicates whether the bins are right-open (left-closed; =TRUE) or
right-closed (left-open; =FALSE; default).
main A character string that forms the main title for the plot.
xlab A character string for labeling the x-axis.
legend.pos A character string or two numeric values indicating the position for the stacking
legend.
cex.legend A numeric character expansion value for the legend. Values less than 1 will
make the legend smaller.
... Additional arguments sent to the hist function.
intersectDiagram 103

Details
‘histStack’ displays a “stacked histogram” while using many of the same arguments as hist(). The
argument ‘z’ will be converted to a factor with a warning if it is not already a factor.
The color functions in grDevices (e.g. "gray.colors") should always be valid when passed as
the ‘col’ argument. Any function that will return a vector of ‘n’ colors when called with a sin-
gle argument ‘n’ and that exists in the current environment should work. An error will occur if
length(col)==1 and the value is not a function as described for ‘col’ (e.g., ‘col="blue"’ will result
in an error).If fewer colors than levels of ‘z’ are passed, they will be recycled.

Value
nil. A plot is displayed.

Note
This function is currently experimental.

Author(s)
Derek Ogle with modifications by Jim Lemon

See Also
hist, legend

Examples
set.seed(409)
df<-data.frame(len=rnorm(100)+5,
grp=sample(c("A","B","C","D"),100,replace=TRUE))
histStack(len~grp,data=df,main="Default (rainbow) colors",
xlab="Length category")
histStack(len~grp,data=df,col="heat.colors",main="Heat colors",
xlab="Length category",legend.pos="topright")
histStack(len~grp,data=df,col=2:5,main="Colors by number",
xlab="Length category",legend.pos=c(2.8,18))

intersectDiagram Display set intersections

Description
Display set intersections as rows of rectangles.

Usage
intersectDiagram(x,pct=FALSE,show.nulls=FALSE,xnames=NULL,sep="+",
mar=c(0,0,3,0),main="Intersection Diagram",cex=1,col=NULL,
minspacing=NA,all.intersections=FALSE,include=NULL,null.label="Non-set")
104 intersectDiagram

Arguments
x A list containing as many numeric vectors as there are sets. The first vector
contains the counts or percentages of the elements that are only in one set, the
next vector contains the counts or percentages of elements that are in two sets
and so on. A matrix of set membership indicators or a two column matrix of
object identifiers and attribute identifiers can be passed - see Details.
pct Whether to display counts (FALSE) or percentages (TRUE) of the number of
entities.
show.nulls Whether to display the number of original objects that are not members of any
set. Any value that is not NA will become the label for this category.
xnames Optional user supplied names for the set categories (see Details).
sep The separator to use between category names (see Details).
mar The margins for the diagram. The margins that were in effect when the function
is called are restored.
main The title for the diagram.
col Colors for the sets (see Details).
cex Character expansion for the intersection labels.
minspacing The minimum spacing between the rectangles (see Details).
all.intersections
Whether to display all intersections, even if empty (Dangerous - see Detail).
include Which set identifiers to include in the diagram (see Details).
null.label The label for the non-set entities if displayed.

Details
‘intersectDiagram’ displays rows of optionally colored rectangles that represent the intersections
of set memberships (attributes) of a set of objects. The topmost row represents the intersections of
the fewest sets, and succeeding rows represent the intersections of more sets. If there were objects
in the original data set that were not members of any set, any percentages calculated will reflect
this. By setting ‘show.nulls’ to TRUE, the counts or percentages of such objects will be displayed
below the intersections over an empty rectangle scaled to the count or percentage.
Important - If the ‘all.intersections’ argument is TRUE, all intersections will be displayed,
whether empty or not (see the example). This is mostly for demonstration purposes, and if the num-
ber of sets is large, is likely to produce a very messy diagram. Similarly, sets with large numbers of
intersections that are populated will require very large displays to be readable, even if there are small
numbers in the intersections. If you would like to see this in action, pass the data frame ‘setdf’ in
the categoryReshape example to ‘intersectDiagram’ with ‘all.intersections’ TRUE.
‘intersectDiagram’ does not attempt to display the set intersections as a pattern of overlapping
geometric figures, but rather the relative numbers of objects sharing each intersection. More than
three intersecting sets generally produce a complex and difficult to interpret Venn diagram, and this
provides an alternative way to display the size of intersections between larger numbers of sets.
‘intersectDiagram’ now allows the user to display only part of the set intersections, which is
useful for analyzing very complex intersections. This is controlled by the ‘include’ argument.
This defaults to all sets or attributes when ‘include=NULL’. If one or more of the labels of the
intersectDiagram 105

sets or attributes is passed, only the intersections containing those labels will be displayed. See
examples 2 and 3 below.
Each set (attribute) is assigned a color if ‘col’ is not NA. ‘rainbow’ is called if ‘col’ is NULL, oth-
erwise the colors passed are used. For each intersection, the colors representing the sets intersecting
are included in the rectangle.
The strings displayed on each rectangle are taken from the argument ‘xnames’ unless that is NULL,
then the ‘names’ of the intersectList object passed as ‘x’ or returned from the call to ‘makeIntersectList’.
If a matrix or data frame of set membership indicators is passed as ‘x’, it will be passed to makeIn-
tersectList for conversion. Each column must represent a set, and the values in the columns must be
0 or 1, or FALSE or TRUE. Similarly, if a matrix or data frame in which the first column is object
identifiers and the second column is attributes, this will be passed to ‘makeIntersectList’.
The spacing between the largest rectangles is controlled by ‘minspacing’. ‘minspacing’ is in units
of object counts and defaults to 0.1 times the largest number of objects in an intersection. When the
number of objects in different intersections at a given level varies widely, the labels of intersections
with few objects may overlap if they are wide relative to the rectangle representing the number of
objects. This can be corrected by passing a ‘minspacing’ argument that will increase the space
between rectangles and/or decreasing the character size of the labels. If the labels for each set are
relatively long, setting ‘namesep="\n"’ may help. Note that if a different separator is passed, that
separator must be explicitly passed in any subsequent calls using the same ‘intersectList’ object
- see examples 1 to 3 below.

Value
Returns the intersectionList object invisibly.

Author(s)
Jim Lemon

See Also
makeIntersectList, getIntersectList, categoryReshape

Examples
# create a matrix where each row represents an element and
# a 1 (or TRUE) in each column indicates that the element is a member
# of that set.
druguse<-matrix(c(sample(c(0,1),200,TRUE,prob=c(0.15,0.85)),
sample(c(0,1),200,TRUE,prob=c(0.35,0.65)),
sample(c(0,1),200,TRUE,prob=c(0.5,0.5)),
sample(c(0,1),200,TRUE,prob=c(0.9,0.1))),ncol=4)
colnames(druguse)<-c("Alc","Tob","THC","Amp")
druglist<-makeIntersectList(druguse,sep="\n")
# first display it as counts
intersectDiagram(druglist,main="Patterns of drug use",sep="\n")
# then display only the intersections containing "Alc"
intersectDiagram(druglist,main="Patterns of drug use (Alcohol users only)",
sep="\n",include="alc")
106 jiggle

# now display only the intersections containing "Amp"

intersectDiagram(druglist,main="Patterns of drug use (Speed users only)",
sep="\n",include="amp")
# then as percent with non.members, passing the initial matrix
intersectDiagram(druguse,pct=TRUE,show.nulls=TRUE)
# alter the data to have more multiple intersections
druguse[which(as.logical(druguse[,1]))[1:40],2]<-1
druguse[which(as.logical(druguse[,1]))[31:70],3]<-1
druguse[,4]<-sample(c(0,1),200,TRUE,prob=c(0.9,0.1))
intersectDiagram(druguse,main="Smaller font in labels",
col=c("gray20","gray40","gray60","gray80"),cex=0.8)
# transform the spacing - usually makes it too close, first try minspacing
intersectDiagram(druguse,col="gray",main="Minimum spacing = 30 cases",
minspacing=30)
# then try cex - may need both for large differences
intersectDiagram(druguse,main="Very boring single color",col="gray",cex=0.8)
# create a matrix with empty intersections
druguse<-matrix(c(sample(c(0,1),20,TRUE),
sample(c(0,1),20,TRUE),
sample(c(0,1),20,TRUE),
sample(c(0,1),20,TRUE)),ncol=4)
# show only the populated intersections
intersectDiagram(druguse,main="Display only populated intersections")
# show all intersections
intersectDiagram(druguse,main="Display empty intersections",all.intersections=TRUE)

jiggle Calculate equally spaced values within a range.

Description
Calculates a specified number of equally spaced values in a range

Usage
jiggle(n,range=c(-1,1))

Arguments
n The number of values to calculate.
range The range within which to fit the values.

Details
‘jiggle’ is an alternative to the ‘jitter’ function. Instead of using ‘runif’ to provide the values,
it calls ‘sample’ and then scales the resulting values to the range specified. This guarantees that the
values will be evenly spaced.
joyPlot 107

Value
A vector of n values within the range specified.

Author(s)
Jim Lemon

Examples
ahw.df<-data.frame(Age=rnorm(100,35,10),
Height=rnorm(100,160,15),Weight=rnorm(100,75,20))
par(mfrow=c(1,3))
boxplot(ahw.df$Age,main="Age")
points(jiggle(100,c(0.5,1.5)),ahw.df$Age,col="red")
boxplot(ahw.df$Height,main="Height")
points(jiggle(100,c(0.5,1.5)),ahw.df$Height,col="green")
boxplot(ahw.df$Weight,main="Weight")
points(jiggle(100,c(0.5,1.5)),ahw.df$Weight,col="blue")

joyPlot Display a series of density curves.

Description
‘joyPlot’ displays a matrix of density curves or other two component lists whose names are ‘x’
and ‘y’. The labels for each line/polygon are displayed on the left axis of the plot. The labels default
to the names of the components of ‘x’ if these are present.

Usage
joyPlot(x,mar=c(5,4,4,2),newrange=c(0,1),border=NA,fill=NULL,
main="",xlab="",ylab="",xlim=NA,line_labels=names(x),xat=NULL,
xaxlab=NULL)

Arguments
x A list of density curves or other objects with x and y values.
mar Margins for the plot.
newrange Passed to ‘rescale’ to scale the values to fit the bands on the plot. See Details.
border The border colors for the polygons.
fill Optional fill colors for the polygons.
main Text for the title for the plot.
xlab,ylab The x and y axis labels.
xlim Optional limit for the x axis as ‘density’ returns values outside the range of the
values in ‘x’.
108 kiteChart

line_labels Labels for the lines/polygons dieplayed.

xat Optional custom x tick positions.
xaxlab Optional custom x tick labels.

Details
The density curves or other x/y lists will be scaled so that the largest will fit into the one user unit
band allocated for each curve by default. If the second value of ‘newrange’ is changed, the heights
of the curves will change proportionately. See the third exampls.

Value
nil

Author(s)
Jim Lemon

See Also
plot, stackpoly

Examples
x1<-c(sample(20:50,20),sample(40:80,30))
x2<-c(sample(10:40,30),sample(50:90,30))
x3<-sample(20:90,50)
xdens1<-density(x1)
xdens2<-density(x2)
xdens3<-density(x3)
joyPlot(list(xdens1,xdens2,xdens3),main="joyPlot with lines",
xlab="Position",xlim=c(0,100))
xlist<-list(first=xdens1,second=xdens2,third=xdens3)
joyPlot(xlist,main="joyPlot with polygons",xlab="Position",
fill=c("#ffcccc","#ccffcc","#ccccff"),xlim=c(0,100))
joyPlot(xlist,main="joyPlot with overlapping polygons",
fill=c("#ffcccc","#ccffcc","#ccccff"),xlim=c(0,100),
newrange=c(0,1.5),xlab="Position")

kiteChart Magnitude by position chart.

Description
Display numeric values as the widths of a polygon along a dimension such as time.
kiteChart 109

Usage
kiteChart(x,xlim=NA,ylim=NA,timex=TRUE,main="Kite chart",
xlab=ifelse(timex,"Time","Groups"),ylab=ifelse(timex,"Groups","Time"),
border=par("fg"),col=NULL,varpos=NA,varlabels=NA,varscale=FALSE,
timepos=NA,timelabels=NA,mar=c(5,4,4,4),axlab=c(1,2,3,4),
normalize=FALSE,shownorm=TRUE,...)

Arguments
x Numeric matrix or data frame
xlim Horizontal extent of the chart. Defaults to 1:dim(x)[2].
ylim Vertical extent of the chart. Defaults to 0.5:dim(x)[1]+0.5.
timex Whether the "time" axis is x (horizontal) or not.
main,xlab,ylab As in ‘plot’.
border The border color(s) for the polygons.
col The fill colors for the polygons.
varpos Optional positions for the "kite lines". Defaults to 1:dimx[1]. (see Details)
varlabels Labels for the rows of values - defaults to the rownames, or if these are missing,
varpos[1:dim(x)[1]].
varscale Whether to show the maximum extent of each "kite line".
timepos The positions of the values along the x axis, usually times, defaulting to 1:dim(x)[2].
timelabels Labels for the positions, defaulting to ‘timepos’.
mar Plot margins. These leave space for the normalization multipliers on the right or
top side (see Details).
axlab Where to put axis tick labels and multipliers. See Details.
normalize Whether to scale each row of values to a maximum width of 1.
shownorm Whether to display the normalization multipliers.
... additional arguments passed to ‘plot’.

Details
‘kiteChart’ displays each row of ‘x’ as a sequence of widths, allowing the relationships between
those values and the dimension along which they occur (usually time) to be illustrated.
The values in x are scaled to a maximum polygon width of 1 if ‘normalize’ is TRUE. This is to
avoid overlapping of the polygons. There may be some cases where the values can be displayed
directly. If normalized, the multipliers will be displayed for each row on the right or top side of the
chart unless ‘shownorm’ is FALSE. Remember to specify the ‘mar’ argument if more space at the
top is needed.
The ‘axlab’ argument allows the user to place the axis tick labels and normalization multipliers on
different axes. The default places the tick labels on the bottom and left sides of the plot and the
multipliers on the right or top. Using ‘axlab=c(3,4,1,2)’ places the tick labels on the top and
right and the multipliers on the left or bottom. The ‘mar’ argument may have to be adjusted.
110 kiteChart

The user can display raw values by default, or by setting ‘varpos’ to TRUE. Setting ‘varpos’ to
a vector of positions will place the "kite lines" on those values. If there are no row names and the
‘varlabels’ argument is NA, the values of ‘varpos’ will be used as labels for each "kite line". The
maximum extent of each "kite line" can be displayed by setting ‘varscale’ to TRUE. If ‘varscale’
is TRUE, one extra line will be added to the top margin. If ‘varpos[1]’ is not NA, ‘normalize’ is
FALSE by default.

Value

The values of ‘mar’ that were current when ‘kiteChart’ was called.

Author(s)

Jim Lemon (Thanks to Michael Bedward for suggestions on the arguments and Nikolaus Lampadar-
iou for the suggestions on displaying raw values)

See Also

polygon

Examples

testmat<-matrix(c(runif(50),sample(1:50,50),rnorm(50)+5,
sin(1:50)),ncol=50,byrow=TRUE)
kiteChart(testmat,varlabels=c("Uniform","Sample","Normal","Sine"),
timepos=seq(1,50,by=5),timex=FALSE)
# not enough space for the last label, add it
mtext("Sine",at=65,side=1,line=2)
# now show it with kite line maxima
kiteChart(testmat,varlabels=c("Uniform","Sample","Normal","Sine"),
timepos=seq(1,50,by=5),timex=FALSE,varscale=TRUE)
mtext("Sine",at=65,side=1,line=2)
musicmat<-matrix(c(c(0.5,0.4,0.3,0.25,0.2,0.15,0.1,rep(0.05,44))+runif(51,0,0.05),
c(0.1,0.2,0.3,0.35,0.4,0.5,0.4,rep(0.5,14),rep(0.4,15),rep(0.3,15))+runif(51,0,0.1),
rep(0.15,51)+runif(51,0,0.1),
c(rep(0,29),c(0.1,0.2,0.4,0.5,0.3,0.2,rep(0.05,16))+runif(22,0,0.05)),
c(rep(0,38),c(rep(0.05,6),0.08,0.15,0.20,0.25,0.2,0.25,0.3)+runif(13,0,0.05))),
ncol=51,byrow=TRUE)
kiteChart(musicmat,varlabels=c("Swing","Rock","Jazz","Disco","Rap"),
main="An utterly imaginary chart of music popularity",
timepos=seq(1,51,by=10),timelabels=seq(1950,2000,by=10),mar=c(5,4,4,2))
# now flip it to vertical, normalize and show the normalization factors
kiteChart(musicmat,varlabels=c("Swing","Rock","Jazz","Disco","Rap"),
main="An utterly imaginary chart of music popularity",xlab="Style",
timepos=seq(1,51,by=10),timelabels=seq(1950,2000,by=10),mar=c(5,4,4,2),
timex=FALSE,normalize=TRUE,shownorm=TRUE)
labbePlot 111

labbePlot Display a L’Abbe plot

Description
Display the percentages of successes for two conditions to be compared as circles, the area of which
is proportional to the number of observations.

Usage
labbePlot(x,main="L'Abbe plot",xlab="Percent positive response with placebo",
ylab="Percent positive response with treatment",labels=NULL,col=NA,
circle.mag=0.5,add=FALSE,...)

Arguments
x A list of either 2x2 tables or three element vectors (see Details).
main The title of the plot.
xlab,ylab The x and y axis labels as in ‘plot’.
labels Text strings that will be displayed in the center of the circles.
col A list of colors for the circles.
circle.mag A fudge factor for very small or very large numbers of observations.
add Whether to add the information in ‘x’ to an existing L’Abbe plot.
... additional arguments passed to ‘plot’.

Details
The elements of ‘x’ may be tables in which rows represent the conditions being compared, with
the comparison condition first (often "placebo") and the condition of interest (often "intervention")
second. The columns represent the counts of successes and failures. The elements of ‘x’ can
also be vectors with three numeric values, first the percentage of successes for the comparison
condition, second the percentage of successes for the condition of interest and finally the number of
observations. Tables and vectors can be mixed.
The radius of each circle is the square root of the number of observations multiplied by ‘circle.mag’.
This allows very small numbers of observations to be expanded and very large numbers to be re-
duced in size. As the area of each circle is proportional to the number of observations, ‘circle.mag’
must be the same for all circles. The user may wish to expand or contract all the circles on a plot so
that they will fit within the box.
The labels, if not NULL, are displayed on the circles. The function tries to work out whether
white or black text will be more easily read based on the background color and displays the text
accordingly.

Value
nil
112 ladderplot

Author(s)
Jim Lemon - thanks to Whitney Melroy for asking for it.

See Also
draw.circle

Examples
# first fake something like the data from a clinical trial
didf<-data.frame(subject=1:50,interv=rep(c("therapist","ex-drinker"),each=25),
outcome=sample(c("more","less"),50,TRUE))
# make it into a table
didf.tab<-table(didf$interv,didf$outcome)
# now mix in some raw percentages just for the example
didf2<-c(74,46,200)
didf3<-c(33,87,500)
x<-list(didf.tab,didf2,didf3)
labbecol<-list("red","green","blue")
labbePlot(x,main="Ex-drinkers vs therapists",
xlab="Percent reduced drinking (ex-drinkers)",
ylab="Percent reduced drinking (therapists)",
labels=list("A","B52","X117"),col=labbecol)
labbePlot(list(c(20,40,20)),col=list("purple"),labels=list("Z"),add=TRUE)

ladderplot Ladder Plot

Description
Makes a ladder plot, similar to parcoord but with more flexibility and graphical options.

Usage
ladderplot(x, ...)
## Default S3 method:
ladderplot(x, scale=FALSE, col=1, pch=19, lty=1,
xlim=c(0.5, ncol(x) + 0.5), ylim=range(x), vertical = TRUE, ordered=FALSE,...)

Arguments
x A matrix or data frame with at least 2 columns.
scale Logical, if the original data columns should be scaled to the unit (0-1) interval.
col Color values to use for rows of ‘x’. If longer than 1, its value is recycled.
pch Point type to use. If longer than 1, its value is recycled.
lty Line type to use. If longer than 1, its value is recycled.
xlim, ylim Limits for axes.
ladderplot 113

vertical Logical, if the orientation of the ladderplot should be vertical or horizontal.

ordered Logical, if the columns in ‘x’ should be ordered.
... Other arguments passed to the function stripchart.

Details
The function uses stripchart to plot 1-D scatter plots for each column in ‘x’. Then points are joined
by lines for each rows of ‘x’.

Value
Makes a plot as a side effect. Returns ‘NULL’ invisibly.

Author(s)
Peter Solymos <solymos@ualberta.ca>

See Also
lines, points, stripchart
Almost identical function: parcoord

Examples
x<-data.frame(A=c(1:10), B=c(2:11)+rnorm(10))
y<-data.frame(x, C=c(1:10)+rnorm(10))
opar <- par(mfrow=c(1,3))
ladderplot(x)
ladderplot(x, col=1:10, vertical=FALSE)
ladderplot(y, col=1:10)
par(opar)

## examples from parcoord

## Not run:
if (require(MASS)) {
opar <- par(mfrow=c(2,3))
z1 <- state.x77[, c(7, 4, 6, 2, 5, 3)]
parcoord(z1, main="parcoord state.x77")
ladderplot(z1, pch=NA, scale=TRUE, main="ladderplot state.x77 original")
ladderplot(z1, main="ladderplot state.x77 original")
ir <- rbind(iris3[,,1], iris3[,,2], iris3[,,3])
z2 <- log(ir)[, c(3, 4, 2, 1)]
parcoord(z2, col = 1 + (0:149))
ladderplot(z2, scale=TRUE, col = 1 + (0:149),
main="ladderplot iris original")
ladderplot(z2, col = 1 + (0:149))
par(opar)
}

## End(Not run)
114 legendg

legendg Legend with grouped bars, lines or symbols

Description
Displays a legend with more than one rectangle, symbol or line.

Usage
legendg(x,y=NULL,legend,fill=NULL,col=par("col"),
border=list("black"),lty,lwd,pch=NULL,angle=45,density=NULL,
bty="o",bg=par("bg"),box.lwd=par("lwd"),box.lty=par("lty"),
box.col=par("fg"),pt.bg=NA,cex=1,pt.cex=cex,pt.lwd=lwd,
pt.space=1,xjust=0,yjust=1,x.intersp=1,y.intersp=1,
adj=c(0,0.5),text.width=NULL,text.col=par("col"),merge=FALSE,
trace=FALSE,plot=TRUE,ncol=1,horiz=FALSE,title=NULL,
inset=0,xpd,title.col=text.col)

Arguments
x,y Position of the legend as in ‘legend’.
legend Labels for the legend as in ‘legend’.
fill List of fill colors for the rectangles.
col Color(s), perhaps as a list, for the symbols.
border Border color(s) for the rectangles.
lty Line type, currently ignored and set to 1.
lwd Line width, currently ignored.
pch List of symbols for the legend.
angle,density Currently ignored.
bty Legend box type to be displayed.
bg Background color for the legend.
box.lwd,box.lty,box.col
Line width, type and color for the surrounding box.
cex Character expansion for text.
pt.bg,pt.cex,pt.lwd
Background color, character expansion and line width for the symbols.
pt.space Spacing for the symbols as a multiplier for ‘strwidth("O")’.
xjust,yjust Justification for the legend.
x.intersp,y.intersp
x and y character spacing for the legend text.
adj Text adjustment.
legendg 115

text.width,text.col
Width and color of the legend text.
merge Whether to merge points and lines.
trace Show how the legend is calculated.
plot Whether to plot the legend.
ncol Number of columns in the legend.
horiz Whether to display a horizontal legend.
title Title for the legend.
inset Inset distances for use with keywords.
xpd An optional value for ‘par(xpd=)’.
title.col Color for the legend title.

Details
‘legendg’ calls ‘legend’ to display a legend with a blank space to the left of the labels. It then at-
tempts to display groups of colored rectangles or symbols in that space depending upon the contents
of either ‘fill’ or ‘pch’. These should be in the form of a list with the number of elements equal
to the number of labels, and one or more fills or symbols for each label. ‘legendg’ will display up
to four fills or symbols next to each label, allowing the user to label a group of these rather than just
one per label.

Value
The value returned by ‘legend’ returned invisibly.

Author(s)
Jim Lemon

See Also
legend

Examples
plot(0.5,0.5,xlim=c(0,1),ylim=c(0,1),type="n",
main="Test of grouped legend function")
legendg(0.5,0.8,c("one","two","three"),pch=list(1,2:3,4:6),
col=list(1,2:3,4:6),pt.space=1.5)
legendg(0.5,0.5,c("one","two","three"),fill=list(1,2:3,4:6))
# fake a line/point with text points
legendg(0.2,0.25,c("letter","number"),
pch=list(c("-","A","-"),c("-","1","-")),
col=list(rep(2,3),rep(3,3)))
116 lengthKey

lengthKey Key for interpreting lengths in a plot

Description
Key for interpreting lengths in a plot

Usage
lengthKey(x,y,tickpos,scale)

Arguments
x,y The position of the left end of the key in user units.
tickpos The labels that will appear above the key.
scale A value that will scale the length of the key.

Details
‘lengthKey’ displays a line with tick marks and the values in ‘tickpos’ above those tickmarks. It
is useful when line segments on a plot represent numeric values. Note that if the plot does not have
a 1:1 aspect ratio, a length key is usually misleading.

Value
nil

Author(s)
Jim Lemon

See Also
segments, arrows

Examples
# manufacture a matrix of orientations in radians
o<-matrix(rep(pi*seq(0.1,0.8,by=0.1),7),ncol=8,byrow=TRUE)
m<-matrix(rnorm(56)+4,ncol=8,byrow=TRUE)
# get an empty plot of approximately 1:1 aspect ratio
plot(0,xlim=c(0.7,8.3),ylim=c(0.7,7.3),type="n")
vectorField(o,m,vecspec="rad")
# the scaling usually has to be worked out by trial and error
lengthKey(0.3,-0.5,c(0,5,10),0.24)
listDepth 117

listDepth Find the maximum depth of a list

Description
Descend a list and find the maximum number of levels.

Usage
listDepth(x)

Arguments
x A list.

Details
A possibly nested list of lists is descended to determine the maximum number of levels. Currently
used to set up the dimensions of a dendrite plot.

Value
The maximum number of levels in the list.

Author(s)
Jim Lemon

See Also
plot.dendrite

makeDendrite Build a list of the mutually exclusive attributes of objects

Description
Build a list of mutually exclusive attributes from a matrix of category indicators.

Usage
makeDendrite(x)

Arguments
x A data frame or matrix where rows represent objects and columns mutually
exclusive attributes of a given class.
118 makeIntersectList

Details
The values in ‘x’ indicate which attribute of a particular class is possessed by the object. For
instance, the attributes dead and alive are mutually exclusive. ‘makeDendrite’ creates a nested list
that contains the counts of successive combinations of the attributes. The top level attributes are
taken from the first column, then those are combined with the attributes in the second column and
so on.

Value
A list of the counts of objects for each combination of the attribute classes.

Author(s)
Jim Lemon

See Also
plot.dendrite

Examples
sex<-sample(c("M","F"),100,TRUE)
hair<-sample(c("Blond","Black","Brown","Red"),100,TRUE)
eye<-sample(c("Blue","Black","Brown","Green"),100,TRUE)
charac<-data.frame(sex=sex,hair=hair,eye=eye)
characlist<-makeDendrite(charac)
characlist

makeIntersectList Count set intersections

Description
Create a list of set intersections from a matrix of indicators

Usage
makeIntersectList(x,xnames=NULL,sep="+")

Arguments
x A data frame or matrix where rows represent objects and columns attributes. A
‘1’ or ‘TRUE’ indicates that the object (row) has that attribute or is a member
of that set (column). ‘x’ can also be a matrix or data frame in which the first
column contains object identifiers and the second contains attribute codes.
xnames Optional user-supplied names for the attributes of x.
sep A character to use as a separator for attribute labels.
makeIntersectList 119

Details

‘makeIntersectList’ reads a matrix (or data frame where all values are the same type) containing
dichotomous values (either 0/1 or FALSE/TRUE) or labels (see next paragraph). In the first type
of input, each row represents an object and each column represents a set. A value of 1 or TRUE
indicates that that object is a member of that set. The function creates a list of vectors that corre-
spond to all combinations of the sets (set intersections) and inserts the counts of elements in each
combination. If a row of ‘x’ is all zeros, it will not be counted, but the second last element of the
list returned contains the count of rows in ‘x’ and thus non-members can be calculated.
If a matrix (or data frame where all values are the same type) containing values other than 0/1 or
TRUE/FALSE, it will be passed to ‘categoryReshape’ for conversion to a data frame as described
above. See ‘categoryReshape’ for details of this.
makeIntersectList combines the set or attribute names to form intersection names. For the inter-
section of sets A and B, the name will be A+B (unless ‘sep’ is changed) and so on. These are the
names that will be displayed by ‘intersectDiagram’. To change these, use the ‘xnames’ argument.

Value

A list of the intersection counts or percentages, the total number of objects and the attribute codes.

Author(s)

Jim Lemon

See Also

intersectDiagram, pasteCols, linkcategoryReshape

Examples
# create a matrix where each row represents an element and
# a 1 (or TRUE) in each column indicates that the element is a member
# of that set.
setdf<-data.frame(A=sample(c(0,1),100,TRUE,prob=c(0.7,0.3)),
B=sample(c(0,1),100,TRUE,prob=c(0.7,0.3)),
C=sample(c(0,1),100,TRUE,prob=c(0.7,0.3)),
D=sample(c(0,1),100,TRUE,prob=c(0.7,0.3)))
makeIntersectList(setdf)
ns<-sample(1:8,20,TRUE)
objects<-0
for(i in 1:length(ns)) objects<-c(objects,rep(i,ns[i]))
attributes<-"Z"
for(i in 1:length(ns)) attributes<-c(attributes,sample(LETTERS[1:8],ns[i]))
setdf2<-data.frame(objects[-1],attributes[-1])
makeIntersectList(setdf2)
120 maxEmptyRect

maxEmptyRect Find an empty space on a plot

Description
Try to find the largest empty rectangle on a plot.

Usage
maxEmptyRect(ax,ay,x,y)

Arguments
ax,ay The rectangle within which all of the points are contained. Usually the limits of
a plot.
x,y x and y positions of the points.

Details
‘maxEmptyRect’ searches the pairs of points on the plot to find the largest rectangular space within
which none of the points lie. It does not guarantee that the space will be large enough to fit a legend
or text.
Two alternatives are the ‘largest.empty’ function in the Hmisc package and the ‘emptyspace’
function. ‘maxEmptyRect’ appears to outperform ‘emptyspace’, particularly in running time. How-
ever, ‘emptyspace’ will sometimes find a "squarer" rectangle when ‘maxEmptyRect’ finds a slightly
larger narrow rectangle.

Value
A list containing the area of the rectangle and the coordinates of the lower left and upper right
corners (as used in ‘rect’) of the rectangle found.

Author(s)
Hans Borchers

References
A. Naamad, D. T. Lee, and W.-L. Hsu (1984). On the Maximum Empty Rectangle Problem. Dis-
crete Applied Mathematics, 8: 267-277.

Examples
x<-runif(100)
y<-runif(100)
plot(x,y,main="Find the maximum empty rectangle",xlab="X",ylab="Y")
mer<-maxEmptyRect(c(0,1),c(0,1),x,y)
rect(mer$rect[1],mer$rect[2],mer$rect[3],mer$rect[4],border="red")
mtext3d 121

mtext3d Display text in the margins of a 3D plot

Description
Display text in the margins of a 3D plot.

Usage
mtext3d(edge,pmat,labels=TRUE,at=NULL,dist=0.3,xpd=NA,...)

Arguments
edge which axis to calculate.
pmat matrix to transform coordinates.
labels labels to display in the margin.
at position on the axis.
dist Offset of the axis.
xpd set clipping for display.
... additional arguments passed to ptext3d.

Value
nil

Author(s)
Ben Bolker

multhist Plot a multiple histogram, as a barplot

Description
Given a list, plots a side-by-side barplot containing the histograms of the elements

Usage
multhist(x,beside=TRUE,freq=NULL,probability=!freq,plot.it=TRUE,...)
122 multivari

Arguments
x a list of numeric vectors
beside plot histogram bars for groups side-by-side?
freq logical; if ’TRUE’, the histogram graphic is a representation of frequencies, the
’counts’ component of the result; if ’FALSE’, probability densities, component
’density’, are plotted (so that the histogram has a total area of one). Defaults to
’TRUE’ if ’probability’ is not specified (does not consider equidistant breaks as
in hist)
probability an alias for ’!freq’, for S compatibility
plot.it Whether or not to display the histogram.
... additional arguments to hist or barplot

Value
A list including the return value for the first call to ‘hist’ (itself a list) and the values for the bar
heights.

Note
The ’inside’ argument to barplot (which is not currently implemented in barplot anyway) is deleted
from the argument list. The default value of NULL for ‘freq’ is for consistency with ‘hist’ but is
equivalent to TRUE.

Author(s)
Ben Bolker

See Also
hist,barplot

Examples
l <- list(runif(10)*10,1:10,c(1,1,1,1,4,8))
multhist(l)

multivari Function to draw a multivari chart

Description
A multivari chart of one quantitative response variable depending on two to four categorical vari-
ables can be drawn.
multivari 123

Usage
multivari(var, fac1, fac2, fac3 = NULL, fac4 = NULL, data, sort = FALSE,
fun = mean, pch = list(15, 16, 17), col = list("black", "blue", "red"),
col0 = "black", cex = 1, fac.cex = 2, xlab.depth = 3, legend = FALSE,
main = paste("multivari chart of", var), add = FALSE, ...)

Arguments
var variable name (character string) or column index of response variable, required
fac1 variable name (character string) or column index of first level factor, required;
precedes fac2 and fac3 (if present) in the hierarchy (see Details)
fac2 variable name (character string) or column index of second level factor, required;
follows fac1 and precedes fac3 (if present) in the hierarchy (see Details)
fac3 variable name (character string) or column index of third level factor, optional;
if present, fac3 is the last factor in the hierarchy (see Details)
fac4 variable name (character string) or column index of fourth level factor, optional;
can only be specified if there is also a third level factor; if present, this factor is
the first in the hierarchy (see Details), and separate multivari charts for the first
three factors are drawn for each level of this factor
data a data frame, required
sort logical, specifying whether or not levels are sorted, when converting character
vectors to factors (a single choice for all factors is needed); default: FALSE
fun a function to be used in aggregation; default: mean
pch a list of length 2 or 3, depending on whether or not fac3 is specified; the ith
list element can be an individual plotting symbol (like the usual pch entry) or a
vector of plot symbols for each level of fac_i
col a list of length 2 or 3, depending on whether or not fac3 is specified; the ith list
element can be an individual color or a vector of colors for each level of fac_i;
this color specification is used for the plot symbols of fac_i levels and for the
lines connecting the symbols for the next level in the hierarchy
col0 the color for the first line to be drawn
cex the size of axis annotation text (annotation of the fourth level header is 1.5 times
this size)
fac.cex a multiplier for cex; plot symbol sizes are fac.cex*cex; default: 2
xlab.depth labels for the horizontal axis are printed down to this level of the hierarchy
(default: 3); if the depth is reduced, different plot symbols should be used, and
a legend should be drawn
legend logical determining whether or not a legend should be drawn (default: FALSE);
the function determines wether top right or bottom right yields a better position
(it is not guaranteed that there is no overlab); if this does not work well, one can
manually draw a legend in the outer margin
main title, as usual; a default is provided
124 multivari

add logical; add to an existing plot (which of course has to have suitable axis limits)?;
default: FALSE; note that horizontal axis labeling will always be printed by
function multivari, while vertical axis labeling will be omitted for add=TRUE
... further arguments to functions plot, lines, points, mtext

Details
The function is inspired by Minitabs behavior for multivari charts (see also Bruno Scibilia’s blog
which is linked in the references). It does not attempt to visualize individual observations.
A multivari chart mainly serves exploratory purposes. It works particularly well with balanced data,
but can also be used for messy data. multivari can visualize the dependence of a single quantitative
variable on up to four factors (i.e., interactions of order up to four can be visualized). The display is
hierarchical: for factors later in the hierarchy, conditional means given level combinations of factors
earlier in the hierarchy are displayed. Therefore, the order of the factors can make a big difference
in the display. If there is no natural order, it may be worthwhile to inspect several orders.
For interactions with two factors only, it is often preferrable to use function interaction.plot or
raw.means.plot.

Value
a list of (lists of) data frames with summary statistics to be plotted

Author(s)
Ulrike Groemping

References
Scibilia, Bruno (2013). Using Multi-Vari Charts to Analyze Families of Variations. http://blog.
minitab.com/blog/applying-statistics-in-quality-projects/using-multi-vari-charts-to-analyze-familie

See Also
See also interaction.plot, raw.means.plot

Examples
##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##--or do help(data=index) for the standard data sets.
## Not run:
require(car)
multivari("cycles", "len", "load", "amp", data=Wool,
col=list("black","red",c("grey70","grey45","grey20")),
pch=list(15,17,8), legend=TRUE, xlab.depth = 2, lwd=2)
multivari("cycles", "load", "len", "amp", data=Wool,
col=list("black",c("red","blue","darkgreen"),
c("grey70","grey45","grey20")),
pch=list(15,17,8), legend=TRUE, xlab.depth = 2, lwd=2)
multsymbolbox 125

## create a fake fourth factor

fakedat <- rbind(cbind(newfac="blabla",Wool),cbind(newfac="albalb",Wool))
## make it character for demonstrating the effect of sort option
fakedat$newfac <- as.character(fakedat$newfac)

## default: sort order in the data is respected (order of unique is used)

multivari("cycles", "load", "len", "amp", "newfac", data=fakedat,
col=list("black",c("red","blue","darkgreen"),
c("grey70","grey45","grey20")),
pch=list(15,17,8), legend=TRUE, xlab.depth = 2, lwd=2, cex=0.8)

## sort=TRUE: levels are sorted (order of sort(unique))

multivari("cycles", "load", "len", "amp", "newfac", data=fakedat,
col=list("black",c("red","blue","darkgreen"),
c("grey70","grey45","grey20")),
pch=list(15,17,8), legend=TRUE, xlab.depth = 2, lwd=2, cex=0.8,
sort=TRUE)

## End(Not run)

multsymbolbox Draw boxes filled with symbols

Description
Draw boxes on the current figure filled with symbols representing individual counts.

Usage
multsymbolbox(x1,y1,x2,y2,tot,relw=0.8,fg=par("fg"),bg=par("bg"),
box=TRUE,debug=FALSE,...)

Arguments
x1 numeric vector: left sides of boxes
y1 numeric vector: bottom sides of boxes
x2 numeric vector: right sides of boxes
y2 numeric vector: top sides of boxes
tot numeric vector: total numbers of symbols to put in each box
relw relative width (relative to height) of symbolsn
fg foreground color(s)
bg background color(s)
box (logical) draw box borders?
debug debug output?
... additional arguments to polygon() for drawing boxes
126 oz.windrose

Value
none

Author(s)
Ben Bolker

Examples
plot(1:10,1:10,type="n")
multsymbolbox(c(2,4),5,c(4,5),8,tot=c(10,8))

oz.windrose Display an Australian wind rose

Description
Displays a wind rose in the style used by the Australian Bureau of Meteorology.

Usage
oz.windrose(windagg,maxpct=20,wrmar=c(4,5,6,5),scale.factor=30,
speed.col=c("#dab286","#fe9a66","#ce6733","#986434"),
speed.width=NA,show.legend=TRUE,legend.pos=NA,...)

Arguments
windagg A matrix of percentages with the rows representing speed ranges and the columns
indicating wind directions.
maxpct The maximum percentage displayed on the radial grid.
wrmar Plot margins for the diagram.
scale.factor The scale factor for the diagram.
speed.col Colors representing speed ranges.
speed.width Half widths of the bars representing speed ranges.
show.legend Logical indicating whether to display a legend.
legend.pos The vertical position of the wind rose legend. The Australian Bureau of Meteo-
rology displays the legend at the top of the plot
... additional arguments passed to ‘plot’.

Details
‘oz.windrose’ displays a wind rose in the style used by the Australian Bureau of Meteorology.
Each limb represents a bin of wind directions, and there are conventionally eight bins. If ‘windagg’
has more than eight columns, more limbs will be displayed. The rows of ‘windagg’ represent the
speed ranges used by the Australian Bureau of Meteorology (0, 0-10, 10-20, 20-30 and over 30 in
km/hour). The diameter of the central circle is calculated as (percent calm observations)/(number of
direction bins). The remaining grid circles are spaced from the circumference of the "Calm" circle.
oz.windrose.legend 127

Value
nil

Note
If a title is desired, remember to move the legend to the bottom of the plot. If the function is passed
values that do not sum to 100, the resulting plot will at best be misleading.

Author(s)
Jim Lemon (thanks to Anna in the Sydney BoM office and Alejo for finding the problem with
heavily prevailing winds.)

See Also
oz.windrose.legend, draw.circle, bin.wind.records

Examples
windagg<-matrix(c(8,0,0,0,0,0,0,0,4,6,2,1,6,3,0,4,2,8,5,3,5,2,1,1,
5,5,2,4,1,4,1,2,1,2,4,0,3,1,3,1),nrow=5,byrow=TRUE)
oz.windrose(windagg)

oz.windrose.legend Display an Australian wind rose legend

Description
Displays a wind rose legend in the style used by the Australian Bureau of Meteorology.

Usage
oz.windrose.legend(maxpct=20,scale.factor=30,
speed.col=c("#dab286","#fe9a66","#ce6733","#986434"),
speed.width=NA,legend.pos=NA)

Arguments
maxpct The maximum percentage to display on the radial grid.
scale.factor The scale factor for the plot.
speed.col Colors representing speed ranges.
speed.width Half widths of the bars representing speed ranges.
legend.pos The vertical position of the wind rose legend. The Australian Bureau of Meteo-
rology displays the legend at the top of the plot
128 p2p_arrows

Value
nil

Author(s)
Jim Lemon (thanks to Anna in the Sydney BoM office)

See Also
oz.windrose

Examples
plot(0,xlim=c(-20,20),ylim=c(-20,20),type="n",axes=FALSE,xlab="",ylab="")
par(xpd=TRUE)
oz.windrose.legend()
par(xpd=FALSE)

p2p_arrows Draw arrows between points

Description
Displays arrows on an existing plot between specified points.

Usage
p2p_arrows(x1,y1,x2,y2,space=0.05,col=par("fg"),...)

Arguments
x1 Starting x positions for the labels.
y1 Starting y positions for the labels.
x2 Ending x positions for the labels.
y2 Ending y positions for the labels.
space The proportion of the distance between the points to leave as space before and
after the arrow.
col Color(s) for the arrows.
... Extra arguments passed to ‘arrows’.

Details
‘p2p_arrows’ displays arrows on a plot between one or more pairs of specified points.

Value
nil
panes 129

Author(s)
Jim Lemon

See Also
arrows

panes Prepare a "panel" type layout

Description
Split the graphics device into a "panel" type layout for a group of plots

Usage
panes(mat=NULL,widths=rep(1,ncol(mat)),heights=rep(1,nrow(mat)),
nrow=2,ncol=2,mar=c(0,0,1.6,0),oma=c(2.5,1,1,1))

Arguments
mat A matrix representing the number of panes to be created and their order of plot-
ting.
widths,heights The widths and heights of the panes. See ‘layout’.
nrow,ncol The numbers of rows and columns in the layout. See ‘par(mfrow)’.
mar The margins for each plot in the panes.
oma The outer margins for the entire group of panes.

Details
‘panes’ combines the information for displaying a set of plots in a "panel" layout. The default
values will usually produce the desired result by calling ‘par(mfrow)’. If ‘mat’ is not NULL, the
‘layout’ function will be called instead of ‘par(mfrow)’. The two methods are included for the
convenience of the user.
Note that ‘panes’ does not produce any plots and that the user must call ‘tab.title’ to get the
"look" of the panel plot. The overall title is usually centered at the left edge (as in the example) or
in the center of one of the plots in the bottom row.

Value
The values of ‘par’ options that existed when ‘panes’ was called. This list is usually used to restore
those values.

Author(s)
Jim Lemon
130 panes

See Also
par,layout

Examples
y<-runif(8)
oldpar<-panes(matrix(1:4,nrow=2,byrow=TRUE))
par(mar=c(0,2,1.6,0))
boxplot(y,axes=FALSE)
axis(2)
box()
par(mar=c(0,0,1.6,2))
tab.title("Boxplot of y",tab.col="#88dd88")
barplot(y,axes=FALSE,col=2:9)
axis(4)
box()
tab.title("Barplot of y",tab.col="#88dd88")
par(mar=c(2,2,1.6,0))
pie(y,col=2:9)
tab.title("Pie chart of y",tab.col="#88dd88")
box()
par(mar=c(2,0,1.6,2))
plot(y,xaxs="i",xlim=c(0,9),axes=FALSE,col=2:9)
axis(4)
box()
tab.title("Scatterplot of y",tab.col="#88dd88")
# center the title at the left edge of the last plot
mtext("Test of panes function",at=0,side=1,line=0.8,cex=1.5)
panes(matrix(1:3,ncol=1),heights=c(0.7,0.8,1))
par(mar=c(0,2,2,2))
plot(sort(runif(7)),type="l",axes=FALSE)
axis(2,at=seq(0.1,0.9,by=0.2))
box()
tab.title("Rising expectations",tab.col="#ee6666")
barplot(rev(sort(runif(7))),col="blue",axes=FALSE)
axis(2,at=seq(0.1,0.9,by=0.2))
box()
tab.title("Diminishing returns",tab.col="#6666ee")
par(mar=c(4,2,2,2))
tso<-c(0.2,0.3,0.5,0.4,0.6,0.8,0.1)
plot(tso,type="n",axes=FALSE,xlab="")
# the following needs a Unicode locale to work
points(1:7,tso,pch=c(rep(-0x263a,6),-0x2639),cex=2)
axis(1,at=1:7,
labels=c("Tuesday","Wednesday","Thursday","Friday","Saturday","Sunday","Monday"))
axis(2,at=seq(0.1,0.9,by=0.2))
box()
tab.title("The sad outcome",tab.col="#66ee66")
mtext("A lot of malarkey",side=1,line=2.5)
par(oldpar)
pasteCols 131

pasteCols Paste the columns of a matrix together

Description

Paste the columns of a matrix together to form as many "words" as there are columns.

Usage

pasteCols(x,sep="")

Arguments

x A matrix.
sep The separator to use in the ‘paste’ command.

Details

‘pasteCols’ pastes the columns of a matrix together to form a vector in which each element is the
concatenation of the elements in each of the columns of the matrix. It is intended for producing
identifiers from a matrix returned by the ‘combn’ function.

Value

A vector of character strings.

Author(s)

Jim Lemon

See Also

makeIntersectList

Examples
# create a matrix of the combinations of the first five letters of the
# alphabet taken two at a time.
alpha5<-combn(LETTERS[1:5],2,simplify=TRUE)
pasteCols(alpha5,sep="+")
132 paxis3d

paxis3d Display text in the margins of a 3D plot

Description
Display text in the margins of a 3D plot.

Usage
paxis3d(edge,pmat,at=NULL,labels=TRUE,tick=TRUE,
pos=NULL,nticks=5,ticklen=0.05,labdist=0.15,xpd=NA,...)

Arguments
edge which axis to calculate.
pmat matrix to transform coordinates.
at position on the axis.
labels labels to display in the margin.
tick whether to draw axis tick marks.
pos axis position relative to other axes.
nticks number of tick marks.
ticklen length of tick marks as a proportion of plot dimensions.
labdist distance of labels from axis.
xpd parameter to set plot clipping.
... additional arguments passed to ptext3d.

Value
nil

Author(s)
Ben Bolker

Examples
x <- 1:10
y <- 1:10
z <- outer(x,y,function(x,y) { 3*sin(2*pi*x)/(2*pi*x)+exp(y/10)+(x*y)/1000 })
par(mar=c(5,10,2,2))
pp <- perspx(x,y,z,ticktype="detailed",phi=30,theta=80,nticks=3,r=10,
axes=FALSE)
## axis labels not drawn when axes=FALSE
paxis3d("X-",pp,at=c(1,2,9))
paxis3d("Y+",pp)
perspx 133

paxis3d("Z-",pp)
mtext3d("X-",pp,expression(alpha^sqrt(beta)))
## if you want labels parallel to axis, still have to figure out 'srt'
## by trial and error
mtext3d("Y+",pp,expression("velocity ("*gamma*", furlongs/fortnight)"),
xpd=NA,srt=6)
mtext3d("Z-",pp,"Range\n(r*)",dist=0.5)

perspx Display perspective plot

Description
Display an enhanced perspective plot with additional return values

Usage
perspx(x,y,z,...)

Arguments
x,y,z x, y and z coordinates to plot.
... Other arguments passed to ‘persp’.

Details
Displays ‘z’ values plotted on an x,y grid.

Value
A list with three elements, the ranges of ‘x’, ‘y’ and ‘z’.

Author(s)
Ben Bolker

Examples
x <- 1:10
y <- 1:10
z <- outer(x,y,function(x,y) { 3*sin(2*pi*x)/(2*pi*x)+exp(y/10)+(x*y)/1000 })
par(mar=c(5,10,2,2))
pp <- perspx(x,y,z,ticktype="detailed",phi=30,theta=80,nticks=3,r=10,
axes=FALSE)
134 pie.labels

pie.labels Place labels on a pie chart

Description
Places labels on a pie chart

Usage
pie.labels(x=0,y=0,angles,labels,radius=1.05,bg="white",border=TRUE,
minangle=NA,boxed=FALSE,explode=0,...)

Arguments
x,y x and y position of the center of the pie chart
angles A numeric vector representing angles in radians. This is the return value of
‘floating.pie’.
labels Text strings to label each sector.
radius The radius at which to place the labels in user units. The default is 1.05.
bg The color of the rectangles on which the labels are displayed.
border Whether to draw borders around the rectangles.
minangle Minimum angle between labels.
boxed Whether to use ‘text’ or ‘boxed.labels’ to display the labels.
explode How much the pie chart has been "exploded".
... Arguments passed to ‘text’ or ‘boxed.labels’.

Details
Labels may be placed within the pie (radius less than the pie radius), on the edge or outside as in
the examples below. If within the pie, it is probably best to use ‘boxed=TRUE’.
If some labels overlap, passing a value in radians for ‘minangle’ may be used to spread them out.

Value
nil

Note
Remember that ‘x’ and ‘y’ specify the center of the pie chart and that the label positions are specified
by angles and radii from that center.

Author(s)
Jim Lemon
pie3D 135

See Also
floating.pie, boxed.labels, spreadout

Examples
pieval<-c(2,1,3,94)
plot(0,xlim=c(1.5,5),ylim=c(1,5),type="n",axes=FALSE,xlab="",ylab="")
box()
bisect.angles<-floating.pie(3,3,pieval,explode=c(0.1,0.2,0.3,0))
pie.labels(3,3,bisect.angles,c("two","one","three","ninety\nfour"),
minangle=0.2,,explode=c(0.1,0.2,0.3,0))

pie3D Display a 3D pie chart

Description
Displays a 3D pie chart with optional labels.

Usage
pie3D(x,edges=NA,radius=1,height=0.1,theta=pi/6,start=0,border=par("fg"),
col=NULL,labels=NULL,labelpos=NULL,labelcol=par("fg"),labelcex=1.5,
sector.order=NULL,explode=0,shade=0.8,mar=c(4,4,4,4),pty="s",...)

Arguments
x a numeric vector for which each value will be a sector
edges the number of lines forming an ellipse
radius the radius of the pie in user units
height the height of the pie in user units
theta The angle of viewing in radians
start The angle at which to start drawing sectors.
border The color of the sector border lines
col The colors of the sectors
labels Optional labels for each sector
labelpos Optional positions for the labels (see examples)
labelcol The color of the labels
labelcex The character expansion factor for the labels
sector.order Allows the operator to specify the order in which the sectors are drawn.
explode The amount to "explode" the pie in user units
shade If > 0 and < 1, the proportion to reduce the brightness of the sector color to get
a better 3D effect.
mar Margins around the pie.
pty Whether to force a square plot region or not. (see Details)
... graphical parameters passed to ‘plot’
136 pie3D

Details
‘pie3D’ scales the values in ‘x’ so that they total 2*pi, dropping zeros and NAs. It then displays
an empty plot, calculates the sequence for drawing the sectors and calls ‘draw.tilted.sector’
to draw each sector. If labels are supplied, it will call ‘pie3D.label’ to place these outside each
sector. If supplied, the number of labels, label positions and sector colors must be at least equal to
the number of values in ‘x’. If the labels are long, it may help to reduce the radius of the pie or
change the position as in the example below.
In order to make the dimensions of the pie reasonably accurate, a square plot region (‘pty="s"’) is
the default. If ‘pty’ is set to "m", the user can change the margins, usually resulting in a non-square
plot area. This will probably distort the pie somewhat.

Value
The bisecting angle of the sectors in radians.

Note
Due to the somewhat primitive method used to draw sectors, a sector that extends beyond both
pi/2 and 3*pi/2 radians in either direction may not display properly. Setting ‘start’ to pi/2 will
often fix this, but the user may have to adjust ‘start’ and the order of sectors in extreme cases.
The argument ‘sector.order’ allows the user to specify a vector of integers that will override the
calculation of the order in which the sectors are drawn. This is usually necessary when a very large
sector that extends past 3*pi/2 is overlapped by a smaller sector next to it. As a last resort, the user
can try setting ‘explode’ to zero. This only draws the top and outer sides of each sector.
Also due to the sector drawing method, setting ‘theta’ to values smaller than about pi/8 or larger
than about pi/4 will produce obviously misaligned sectors.
Contributed fixes and improvements: thanks to Jesse Brown for the "shade" fix and Qinghua Zhao
for alerting me to the problem with labels and margins

Author(s)
Jim Lemon

See Also
pie3D.labels, draw.tilted.sector

Examples
pieval<-c(2,4,6,8)
pielabels<-
c("We hate\n pies","We oppose\n pies","We don't\n care","We just love pies")
# grab the radial positions of the labels
lp<-pie3D(pieval,radius=0.9,labels=pielabels,explode=0.1,main="3D PIE OPINIONS")
# lengthen the last label and move it to the left
pielabels[4]<-"We cannot survive without our pies"
lp[4]<-4.8
# specify some new colors
pie3D(pieval,radius=0.9,labels=pielabels,explode=0.1,main="3D PIE OPINIONS",
pie3D.labels 137

col=c("brown","#ddaa00","pink","#dd00dd"),labelpos=lp)

pie3D.labels Display labels on a 3D pie chart

Description
Displays labels on a 3D pie chart.

Usage
pie3D.labels(radialpos,radius=1,height=0.1,theta=pi/6,
labels,labelcol=par("fg"),labelcex=1.5,labelrad=1.25,minsep=0.3)

Arguments
radialpos Position of the label in radians
radius the radius of the pie in user units
height the height of the pie in user units
theta The angle of viewing in radians
labels The label to display
labelcol The color of the labels
labelcex The character expansion factor for the labels
labelrad The expansion for the labels around the pie.
minsep The minimum angular separation between label positions.

Details
‘pie3D.label’ displays labels on a 3D pie chart. The positions of the labels are given as angles in
radians (usually the bisector of the pie sectors). As the labels can be passed directly to pie3D, this
function would probably not be called by the user.
‘pie3D.labels’ tries to separate labels that are placed closer than ‘minsep’ radians. This simple
system will handle minor crowding of labels. If labels are very crowded, capturing the return value
of ‘pie3D’ and editing the label positions may allow the user to avoid manually placing labels.

Value
nil

Author(s)
Jim Lemon

See Also
pie3D, draw.tilted.sector
138 placeLabels

Examples
pieval<-c(2,4,6,8)
bisectors<-pie3D(pieval,explode=0.1,main="3D PIE OPINIONS")
pielabels<-
c("We hate\n pies","We oppose\n pies","We don't\n care","We just love pies")
pie3D.labels(bisectors,labels=pielabels)

placeLabels Place labels in boxes

Description
Places labels in boxes on an existing plot

Usage
placeLabels(x,y=NA,labels,pointer=TRUE,cex=1,labelcol=par("fg"),
labelbg="white",border=par("fg"),pointercol=par("fg"),
pch=1,col=1,bg="white",flagcol="red")

Arguments
x,y x and y position of the centers of the labels. ‘x’ can be an xy.coords list.
labels Text strings
pointer Whether to draw a line segment from the label to the points labeled.
cex Character expansion. See ‘text’.
labelcol The color(s) of the text in the labels.
labelbg The background color(s) for the labels.
border The color(s) for the borders around the rectangles.
pointercol The color(s) of the pointer lines.
pch The symbol(s) to use when redisplaying the original points (see Details).
col The color(s) of the original points.
bg The background color(s) of the original points.
flagcol The color to use for "flagging" each point.

Details
‘placeLabels’ steps through the points indexed by ‘x’ and ‘y’, allowing the operator to manually
place the labels for each point. Each point is "flagged" by displaying a small colored circle (red by
default). When the label for that point has been placed, the original symbol is displayed and the
next point is flagged.
Each point and label can have different colors and backgrounds.
plot.dendrite 139

Value
nil - adds labels to an existing plot.

Note
This function is handy for one-off plots with a moderate number of points. It can be very useful for
plots with clumps of points.

Author(s)
Jim Lemon - thanks to Marna Wagley for the idea.

See Also
spread.labels, thigmophobe.labels

Examples
# won't check because of the call to locator
## Not run:
x<-rnorm(10)
y<-rnorm(10)
plot(x,y)
placeLabels(x,y,LETTERS[1:10],flagcol="purple")

## End(Not run)

plot.dendrite Plot a dendrogram of a dendrite object

Description
Plot a dendrogram for two or more mutually exclusive attributes.

Usage
## S3 method for class 'dendrite'
plot(x,xlabels=NULL,main="",mar=c(1,0,3,0),cex=1,
col="white",...)

Arguments
x A ‘dendrite’ object containing the counts of objects having combinations of
mutually exclusive attributes.
xlabels The category labels that will be displayed beneath the dendrogram.
main The title of the plot.
mar Margins for the plot.
140 plotCI

cex Character expansion for the leaves of the dendrogram.

col Background colors for the boxes (see Details).
... Additional arguments passed to ‘plot’.

Details
‘plot.dendrite’ sets up a plot for a dendrogram. The actual plotting of the dendrogram is done
by ‘furc’.
If sampcol is a vector of colors as long as the number of category labels, each category label will be
displayed in a different colored box. This may may cause problems when different category labels
are used at each level with common names, as the color for a name will be the same at all levels.

Value
nil

Author(s)
Jim Lemon

See Also
furc

Examples
sex<-sample(c("M","F"),100,TRUE)
hair<-c(sample(c("Blond","Black","Brown","Red"),90,TRUE),rep(NA,10))
eye<-sample(c("Blue","Black","Brown","Green"),100,TRUE)
charac<-data.frame(sex=sex,hair=hair,eye=eye)
characlist<-makeDendrite(charac)
shecol<-c(Black="black",Blond="yellow",Blue="blue",Brown="brown",
F="pink",Green="green",M="lightblue","NA"="gray",Red="orange")
plot.dendrite(characlist,names(charac),main="Test dendrogram",
col=shecol)

plotCI Plot confidence intervals/error bars

Description
Given a set of x and y values and upper and lower bounds, this function plots the points with error
bars.

Usage
plotCI(x,y=NULL,uiw,liw=uiw,ui=NULL,li=NULL,err="y",
sfrac=0.01,gap=0,slty=par("lty"),add=FALSE,scol=NULL,pt.bg=par("bg"),...)
plotCI 141

Arguments
x The x coordinates of points in the plot
y The y coordinates of points in the plot
uiw The width of the upper portion of the confidence region, or (if ‘liw’ is missing)
the width of both halves of the confidence region
liw The width of the lower portion of the confidence region (if missing, the function
assumes symmetric confidence bounds)
ui The absolute upper limit of the confidence region
li The absolute lower limit of the confidence region
err The direction of error bars: "x" for horizontal, "y" for vertical ("xy" would be
nice but is not implemented yet; don’t know quite how everything would be
specified. See examples for composing a plot with simultaneous horizontal and
vertical error bars)
gap Size of gap in error bars around points (default 0;gap=TRUE gives gap size of
0.01)
sfrac Scaling factor for the size of the "serifs" (end bars) on the confidence bars, in
x-axis units
add If FALSE (default), create a new plot; if TRUE, add error bars to an existing
plot.
slty Line type of error bars
scol Color of error bars: if ‘col’ is specified in the optional arguments, ‘scol’ is set
the same; otherwise it’s set to ‘par(col)’
pt.bg Background color of points (use pch=21, pt.bg=par("bg") to get open points
superimposed on error bars)
... Any other parameters to be passed through to plot.default, points, arrows, etc.
(e.g. ‘lwd’, ‘col’, ‘pch’, ‘axes’, ‘xlim’, ‘ylim’). ‘xlim’ and ‘ylim’ are set by
default to include all of the data points and error bars. ‘xlab’ and ‘ylab’ are
set to the names of ‘x’ and ‘y’. If ‘pch==NA’, no points are drawn (e.g. leaving
room for text labels instead)

Value
invisible(x,y); creates a plot on the current device.

Author(s)
Ben Bolker (documentation and tweaking of a function provided by Bill Venables, additional feature
ideas from Gregory Warnes)

See Also
boxplot
142 plotH

Examples
y<-runif(10)
err<-runif(10)
plotCI(1:10,y,err,main="Basic plotCI")
plotCI(1:10,y,err,2*err,lwd=2,col="red",scol="blue",
main="Add colors to the points and error bars")
err.x<-runif(10)
err.y<-runif(10)
plotCI(1:10,y,err.y,pt.bg=par("bg"),pch=21,xlim=c(0,11),
main="plotCI with extra space on the x axis")
plotCI(1:10,y,err.x,pt.bg=par("bg"),pch=21,err="x",add=TRUE)
mtext("for adding horizontal error bars",3,0.5)
data(warpbreaks)
attach(warpbreaks)
wmeans<-by(breaks,tension,mean)
wsd<-by(breaks,tension,sd)
## note that barplot() returns the midpoints of the bars, which plotCI
## uses as x-coordinates
plotCI(barplot(wmeans,col="gray",ylim=c(0,max(wmeans+wsd))),wmeans,wsd,add=TRUE)
## using labels instead of points
labs<-sample(LETTERS,replace=TRUE,size=10)
plotCI(1:10,y,err,pch=NA,gap=0.02,main="plotCI with labels at points")
text(1:10,y,labs)

plotH Scatterplot with histogram-like bars.

Description
Scatterplot with histogram-like bars; a modification of ‘plot(...,type="h")’.

Usage
plotH(x,...)

## S3 method for class 'formula'

plotH(x,data=NULL,xlab=names(mf)[2],ylab=names(mf)[1],...)

## Default S3 method:
plotH(x,y,xlab=paste(deparse(substitute(x))),
ylab=paste(deparse(substitute(y))),width=0.6,ylim=NULL,col="gray",...)

Arguments
x Vector of x-coordinates or a formula of the form y~x (see below for y).
y Vector of y-coordinates.
xlab A string for labeling the x-axis.
ylab A string for labeling the y-axis.
plotH 143

data The data frame from which the formula should be evaluated.
width A numeric that indicates the width of the bars.
ylim A vector of length two that indicates the limits over which to plot the y-axis. See
details.
col A string that indicates the fill color for the bars.
... Additional arguments sent to the ‘plot’ or ‘barplot’ functions.

Details
‘plotH’ is meant to be a modification of the type="h" version of ‘plot’ such that the "bars" appears
as actual rectangles rather than vertical lines. It defaults so that the lower bound of the y-axis is 0;
change to ‘ylim=NULL’ to over-ride this default (and return to the default used in ‘plot’.
A pass-through to ‘barplot’ is used if the ‘x’ (or "RHS") variable is categorical.

Value
None, but a plot is produced.

Note
This function is currently experimental.

Author(s)
Derek Ogle

See Also
plot, barplot

Examples
d<-data.frame(x=c(1,5,10:20),y=runif(13)+1,
yn1=runif(13)-0.5,yn2=runif(13)-2,
g=factor(sample(c("A","B","C"),13,replace=TRUE)))
# new plotH function with formula notation
plotH(y~x,data=d)
# old plot() function with formula notation -- for comparison's purpose
plot(y~x,data=d,type="h")
# new function over-riding default ylim, increasing bar width,
# and changing bar color
plotH(y~x,data=d,ylim=range(d$y),width=0.9,col="red")
# handling some negative values
plotH(yn1~x,data=d) # not so good, because of default ylim
plotH(yn1~x,data=d,ylim=c(0,max(d$yn1))) # old look
# handling all negative values
plotH(yn2~x,data=d)
plotH(yn2~x,data=d,ylim=range(d$yn2)) # old look
# example of pass-through to barplot
smry<-by(d$y,d$g,mean)
144 plot_bg

plotH(levels(d$g),smry,ylab="Mean of Random Variable",xlab="Group")

# example of non-formula usage
x1 <- d$x
y1 <- d$y
plotH(x1,y1,col="blue")

plot_bg Add a background color to a plot

Description

Displays a colored rectangle over the entire area of a plot

Usage

plot_bg(col="lightgray")

Arguments

col The color of the background

Details

‘plot_bg’ is probably only useful when part of the ‘do.first’ argument in another plot function
to add a background color to the plot.

Value

nil

Author(s)

Jim Lemon

Examples

barp(1:5,do.first="plot_bg()",col=1:5)
polar.plot 145

polar.plot Plot values on a circular grid of 0 to 360 degrees

Description
‘polar.plot’ displays a plot of radial lines, symbols or a polygon centered at the midpoint of
the plot frame on a 0:360 circle. Positions are interpreted as beginning at the right and moving
counterclockwise unless ‘start’ specifies another starting point or ‘clockwise’ is TRUE.
If ‘add=TRUE’ is passed as one of the additional arguments, the values will be added to the current
plot. If a ‘radial.lim’ argument was passed on the initial plot, it must be passed again to add
values or the values will be displayed incorrectly.

Usage
polar.plot(lengths,polar.pos=NULL,labels,label.pos=NULL,
start=0,clockwise=FALSE,rp.type="r",...)

Arguments
lengths numeric data vector. Magnitudes will be represented as the radial positions of
symbols, line ends or polygon vertices.
polar.pos numeric vector of positions on a 0:360 degree circle. These will be converted to
radians when passed to ‘radial.plot’.
labels text labels to place on the periphery of the circle. This defaults to labels every
20 degrees. For no labels, pass an empty string.
label.pos positions of the peripheral labels in degrees
start The position for zero degrees on the plot in degrees.
clockwise Whether to increase angles clockwise rather than the default counterclockwise.
rp.type Whether to plot radial lines, symbols or a polygon.
... additional arguments passed to ‘radial.plot’ and then to ‘plot’.

Value
A list of the parameters altered by radial.plot.

Author(s)
Jim Lemon

See Also
radial.plot
146 polygon.shadow

Examples
testlen<-c(rnorm(36)*2+5)
testpos<-seq(0,350,by=10)
polar.plot(testlen,testpos,main="Test Polar Plot",lwd=3,line.col=4)
oldpar<-polar.plot(testlen,testpos,main="Test Clockwise Polar Plot",
radial.lim=c(0,15),start=90,clockwise=TRUE,lwd=3,line.col=4)
# reset everything
par(oldpar)

polygon.shadow Display a shadow effect for an arbitrary polygon

Description
Displays a shadow effect on an existing plot

Usage
polygon.shadow(x,y=NULL,offset=NA,inflate=NA,col=c("#ffffff","#cccccc"))

Arguments
x,y x and y coordinate of the vertices of the polygon. ‘y’ can be missing if ‘x’ is a
list with ‘x’ and ‘y’ components.
offset a vector containing the values of the x and y offsets for the shadow. Defaults to
1/20 of the maximum x and y dimensions of the polygon.
col the colors of the shadow from the outer edge to the central part.
inflate the amount to "inflate" the shadow relative to the polygon (i.e. the penumbra).
Defaults to the values in ‘offset’.

Details
‘polygon.shadow’ is typically called just before drawing a polygon. It displays a shadow effect by
drawing the polygon ten times, beginning with the first color in ‘col’ and stepping through to the
second color to create a "shadow" (or a "halo" if you prefer). Each successive polygon is shrunk by
10% of ‘inflate’. The default shadow effect has the light at the upper left. This effect may also be
used as a text background.

Value
nil

Note
The background must be a constant color or the shadow effect will not look right. A good starting
point for the two colors is the color of the background and the RGB components of that color
multiplied by 0.8. Use a smaller multiplier for a darker shadow.
print.brklist 147

Author(s)
Jim Lemon

See Also
polygon

Examples
par(pty="s")
plot(1:5,type="n",main="Polygon Shadow test",xlab="",ylab="",axes=FALSE)
box()
# do a shadow on a yellow square
polygon(c(1,2.2,2.2,1),c(5,5,3.8,3.8),col="#ffff00")
polygon.shadow(c(1.2,2,2,1.2),c(4.8,4.8,4,4),col=c("#ffff00","#cccc00"))
polygon(c(1.2,2,2,1.2),c(4.8,4.8,4,4),col=c("#ff0000"))
# a green triangle on a light blue square with a big offset
polygon(c(4,5,5,4),c(2,2,1,1),col="#aaaaff")
polygon.shadow(c(4.5,4.8,4.2),c(1.7,1.2,1.2),col=c("#aaaaff","#8888cc"),
offset=c(0.1,-0.1),inflate=c(0.2,0.2))
polygon(c(4.5,4.8,4.2),c(1.7,1.2,1.2),col=c("#00ff00"))
# now a circle as a background
polygon.shadow(cos(seq(0,2*pi,by=pi/20))+3,sin(seq(0,2*pi,by=pi/20))+3,
offset=c(0,0),inflate=c(0.1,0.1))
text(3,3,"Polygon shadow\nas a circular\ntext background",cex=1.5)

print.brklist Display the output of brkdnNest

Description
Displays the list of values produced by ‘brkdnNest’.

Usage
## S3 method for class 'brklist'
print(x,...)

Arguments
x a list of summary values produced by ‘\link{brkdnNest}’
... additional arguments passed to ‘print’.

Details
‘print.brklist’ displays frequency tables produced by ‘brkdnNest’. It is mainly for convenience,
but does make a nicer display than when passed directly to ‘print’
148 propbrk

Value
nil

Author(s)
Jim Lemon

See Also
brkdnNest

Examples
printbrktest<-data.frame(A=c(sample(1:10,99,TRUE),NA),
B=sample(c("Yes","No"),100,TRUE),
C=sample(LETTERS[1:3],100,TRUE))
pbt<-brkdnNest(A~B+C,printbrktest)
print(pbt)

propbrk Calculate the proportion of specified values in a vector

Description
Calculates the proportion of values in a vector that are equal to a specified value.

Usage
propbrk(x,trueval=TRUE,na.rm=TRUE)

Arguments
x a character, factor or numeric vector.
trueval the value to be matched in ‘x’.
na.rm whether to remove NA values.

Details
‘propbrk’ calculates the proportion of values matching a specified value. It is mainly to allow
proportions to be calculated in the ‘brkdnNest’ function. It always discards NAs in ‘x’ when
summing the number equal to ‘trueval’, but respects the ‘na.rm’ argument when calculating the
total number of values in ‘x’.

Value
nil
psegments3d 149

Author(s)

Jim Lemon

See Also

brkdnNest

Examples
propbrk(sample(LETTERS,100,TRUE),trueval="M")

psegments3d Draw segments on a 3D plot

Description

Draw segments on a 3D plot defined by a list of coordinates

Usage

psegments3d(x,y=NULL,z=NULL,pmat,...)

Arguments

x,y,z x, y and z coordinates to plot. ‘x’ may be a list with three components.
pmat matrix to transform coordinates.
... Other arguments passed to ‘segments’.

Details

Draws segments on a perspective plot.

Value

nil

Author(s)

Ben Bolker
150 pyramid.plot

ptext3d Display text on a 3D plot

Description
Display text on a 3D plot defined by a list of coordinates

Usage
ptext3d(x,y=NULL,z=NULL,texts,pmat,...)

Arguments
x,y,z x, y and z coordinates to plot. ‘x’ may be a list with three components.
pmat matrix to transform coordinates.
texts text to display.
... Other arguments passed to ‘segments’.

Details
Draws text on a perspective plot.

Value
nil

Author(s)
Ben Bolker

pyramid.plot Pyramid plot

Description
Displays a pyramid (opposed horizontal bar) plot on the current graphics device.

Usage
pyramid.plot(lx,rx,labels=NA,top.labels=c("Male","Age","Female"),
main="",laxlab=NULL,raxlab=NULL,unit="%",lxcol,rxcol,gap=1,space=0.2,
ppmar=c(4,2,4,2),labelcex=1,add=FALSE,xlim,show.values=FALSE,ndig=1,
do.first=NULL)
pyramid.plot 151

Arguments
lx,rx Vectors or a matrix or data frame (see Details) which should be of equal length.
labels Labels for the categories represented by each pair of bars. There should be a
label for each lx or rx value, even if empty. If ‘labels’ is a matrix or data
frame, the first two columns will be used for the left and right category labels
respectively.
top.labels The two categories represented on the left and right sides of the plot and a head-
ing for the labels in the center.
main Optional title for the plot.
laxlab Optional labels for the left x axis ticks.
raxlab Optional labels for the right x axis ticks.
unit The label for the units of the plot.
lxcol,rxcol Color(s) for the left and right sets of bars. Both of these default to ‘rainbow(length(labels))’.
gap One half of the space between the two sets of bars for the ‘labels’ in user units.
space Space between the bars. Should be 0 <= space < 1.
ppmar Margins for the plot (see Details).
labelcex Expansion for the category labels.
add Whether to add bars to an existing plot. Usually this involves overplotting a
second set of bars, perhaps transparent.
xlim Optional x limit for the plot (see Details).
show.values Whether to display ‘lx’ and ‘rx’ at the ends of the bars.
ndig The number of digits to round the values if displayed.
do.first Optional expression to evaluate before displaying anything.

Details
‘pyramid.plot’ is principally intended for population pyramids, although it can display other types
of opposed bar charts with suitable modification of the arguments. If the user wants a different unit
for the display, just change ‘unit’ accordingly. The default gap of two units is usually satisfactory
for the four to six percent range of most bars on population pyramids. If ‘labels’ is a matrix or
data frame of at least two columns, the first column will be displayed on the on the left side of
the gap in the center, and the second on the right. This will almost always require increasing the
gap width and perhaps also specifying a wider plotting device. Displaying the values will usually
require increasing the left and/or right margins of the plot, or setting ‘xlim’ larger than the largest
value.
If a gap width of zero is passed, the category labels will be displayed at the left and right extents of
the plot. This usually requires setting ‘xlim’ to values larger than the maximum extent of ‘lx’ and
‘rx’. The user can pass two different values to ‘xlim’, but this is almost always a bad idea, as the
lengths of the bars will not be in the same proportion to the values on the left and right sides. Both
the bars and category labels are vertically centered on integer values, allowing the user to easily add
components to the plot.
‘lx’ and ‘rx’ are the values specifying the left and right extents of the left and right bars respectively.
If both are matrices or data frames, ‘pyramid.plot’ will produce opposed stacked bars with the
152 pyramid.plot

first columns innermost. In this mode, colors are limited to one per column. The stacked bar mode
will in general not work with the ‘add’ method or with a gap of zero. Note that the stacked bar
mode can get very messy very quickly.
The ‘add’ argument allows one or more sets of bars to be plotted on an existing plot. If these are not
transparent, any bar that is shorter than the bar that overplots it will disappear. Only some graphic
devices (e.g. ‘pdf’) will handle transparency.
In order to add bars, the function cannot restore the initial margin values or the new bars will not
plot properly. To automatically restore the plot margins, call the function as in the example.

Value
The return value of ‘par("mar")’ when the function was called.

Author(s)
Jim Lemon (thanks to Susumu Tanimura for the patch that omits ticks for NA values in vector input
and Igor Rebeiro for the space argument)

See Also
rect

Examples
xy.pop<-c(3.2,3.5,3.6,3.6,3.5,3.5,3.9,3.7,3.9,3.5,3.2,2.8,2.2,1.8,
1.5,1.3,0.7,0.4)
xx.pop<-c(3.2,3.4,3.5,3.5,3.5,3.7,4,3.8,3.9,3.6,3.2,2.5,2,1.7,1.5,
1.3,1,0.8)
agelabels<-c("0-4","5-9","10-14","15-19","20-24","25-29","30-34",
"35-39","40-44","45-49","50-54","55-59","60-64","65-69","70-74",
"75-79","80-44","85+")
mcol<-color.gradient(c(0,0,0.5,1),c(0,0,0.5,1),c(1,1,0.5,1),18)
fcol<-color.gradient(c(1,1,0.5,1),c(0.5,0.5,0.5,1),c(0.5,0.5,0.5,1),18)
par(mar=pyramid.plot(xy.pop,xx.pop,labels=agelabels,
main="Australian population pyramid 2002",lxcol=mcol,rxcol=fcol,
gap=0.5,show.values=TRUE))
# three column matrices
avtemp<-c(seq(11,2,by=-1),rep(2:6,each=2),seq(11,2,by=-1))
malecook<-matrix(avtemp+sample(-2:2,30,TRUE),ncol=3)
femalecook<-matrix(avtemp+sample(-2:2,30,TRUE),ncol=3)
# group by age
agegrps<-c("0-10","11-20","21-30","31-40","41-50","51-60",
"61-70","71-80","81-90","91+")
oldmar<-pyramid.plot(malecook,femalecook,labels=agegrps,
unit="Bowls per month",lxcol=c("#ff0000","#eeee88","#0000ff"),
rxcol=c("#ff0000","#eeee88","#0000ff"),laxlab=c(0,10,20,30),
raxlab=c(0,10,20,30),top.labels=c("Males","Age","Females"),gap=4,
do.first="plot_bg(\"#eedd55\")")
# put a box around it
box()
# give it a title
radial.grid 153

mtext("Porridge temperature by age and sex of bear",3,2,cex=1.5)

# stick in a legend
legend(par("usr")[1],11,c("Too hot","Just right","Too cold"),
fill=c("#ff0000","#eeee88","#0000ff"))
# don't forget to restore the margins and background
par(mar=oldmar,bg="transparent")

radial.grid Display a radial grid

Description
‘radial.grid’ displays a radial grid for the ‘radial.plot’ and ‘radial.pie’ functions.

Usage
radial.grid(labels=NA,label.pos=NULL,radlab=FALSE,radial.lim=NULL,
start=0,clockwise=FALSE,label.prop=1.1,grid.pos,rad.col="gray",
grid.col="gray",grid.bg="transparent",show.radial.grid=TRUE,
start.plot=FALSE)

Arguments
labels The labels to display around the circumference of the grid.
label.pos Radial positions for the labels.
radlab Whether to rotate the labels to a radial orientation.
radial.lim Optional radial limits for the circular plot. If specified, these must be the same
as the radial limits of the original plot.
start The zero position on the plot in the units of ‘label.pos’.
clockwise Whether to increase angles clockwise rather than the default counterclockwise.
label.prop Proportion of ‘radial.lim’ to place the labels.
grid.pos Radial positions for the circular grid lines.
rad.col Color for the radial grid lines.
grid.col Color for the circumferential grid lines.
grid.bg Background color for the radial grid.
show.radial.grid
Whether to display the radial lines on the grid.
start.plot If TRUE, sets up a blank radial grid.

Value
nil

Author(s)
Jim Lemon
154 radial.pie

radial.pie Plot sectors/annuli on a circular grid of 0 to 2*pi radians

Description
Plot numeric values as sectors with optional annuli on a circular field in the directions defined by
angles in radians.

Usage
radial.pie(radial.extents,sector.edges=NULL,
sector.colors=NULL,cs1=c(0,1),cs2=c(0,1),cs3=c(0,1),
alpha=1,labels=NA,label.pos=NULL,radlab=FALSE,start=0,
clockwise=FALSE,label.prop=1.1,radial.lim=NULL,main="",xlab="",ylab="",
mar=c(2,2,3,2),show.grid=TRUE,show.grid.labels=4,show.radial.grid=TRUE,
grid.col="gray",grid.bg="transparent",grid.unit=NULL,
radial.labels=NULL,boxed.radial=TRUE,add=FALSE,...)

Arguments
radial.extents A numeric data vector or list. If ‘radial.extents’ is a list, the elements of the
list will be considered separate data vectors.
sector.edges A numeric vector of positions in radians. These are interpreted as beginning at
the right (0 radians) and moving counterclockwise unless ‘clockwise’ is TRUE.
sector.colors Optional colors for the sectors and annuli. Defaults to ‘rainbow(nsectors)’
with fading outward if annuli are specified.
cs1, cs2, cs3, alpha
Color scaling arguments - see color.scale.
labels Character strings to be placed at the outer ends of the lines. If set to NA, will
suppress printing of labels, but if missing, the radial positions will be used.
label.pos The positions of the labels around the plot in radians.
radlab Whether to rotate the outer labels to a radial orientation.
start Where to place the starting (zero) point. Defaults to the 3 o’clock position.
clockwise Whether to interpret positive positions as clockwise from the starting point. The
default is counterclockwise.
label.prop The label position radius as a proportion of the maximum line length.
radial.lim The inner and outer radial limits for the plot. Defaults to the range of ra-
dial.extents, although zero to ‘max(radial.extents)’ is often what is wanted.
main The title for the plot.
xlab,ylab Normally x and y axis labels are suppressed.
mar Margins for the plot. Allows the user to leave space for legends, long labels, etc.
show.grid Logical - whether to draw a circular grid.
radial.pie 155

show.grid.labels
Whether and where to display labels for the grid - see Details.
show.radial.grid
Whether to draw radial lines to the plot labels.
grid.col Color of the circular grid.
grid.bg Fill color of above.
grid.unit Optional unit description for the grid.
radial.labels Optional labels for the radial grid. The default is the values of radial.lim.
boxed.radial Whether to use boxed.labels or text for radial labels.
add Whether to add one or more series to an existing plot.
... Additional arguments are passed to ‘plot’.

Details

‘radial.pie’ displays a plot of radial sectors with optional annular sections centered at the mid-
point of the plot frame, the lengths corresponding to the numeric magnitudes of ‘radial.extents’.
If more series are added to an existing plot, ‘radial.pie’ will try to maintain the current plot
parameters. However, it seems unlikely that adding series would be sensible in ‘radial.pie’. This
argument may be dropped if it proves useless.
The size of the labels on the outside of the plot can be adjusted by setting ‘par(cex.axis=)’ and
that of the labels inside by setting ‘par(cex.lab=)’. If ‘radlab’ is TRUE, the labels will be rotated
to a radial alignment. This may help when there are many values and labels. If some labels are still
crowded, try running ‘label.pos’ through the ‘spreadout’ function. If the ‘show.grid.labels’
argument is a number from 1 to 4, the labels will be placed along a horizontal or vertical radius. The
numbers represent the same positions as in ‘axis’, with the default (4) on the right. To suppress
these labels, pass zero or FALSE.
‘radial.pie’ works somewhat differently from the ‘radial.plot’ family and is still under devel-
opment. I have released it in order to get feedback to improve both the design and the programming.
If successful, I hope to merge the code with the ‘radial.plot’ function.

Value

The ‘par’ values that are changed in the function as they were at the time ‘radial.pie’ was called.

Author(s)

Jim Lemon - thanks to Patrick Jemison for asking for it.

See Also

radial.plot
156 radial.plot

Examples
pie1<-c(3,6,5,4,7,8,9,1,4)
pie2<-list(0:3,1:6,2:5,1:4,0:7,4:8,2:9,0:1,0:4)
pie3<-sample(10:60,36)
pie4<-list(sort(sample(1:60,8)))
for(sector in 2:36) pie4[[sector]]<-sort(sample(1:60,8))
oldpar<-radial.pie(pie1,labels=LETTERS[1:9])
radial.pie(pie2,labels=letters[2:10])
radial.pie(pie3,labels=1:36)
radial.pie(pie4,labels=1:36)
# restore the par values
par(oldpar)

radial.plot Plot values on a circular grid of 0 to 2*pi radians

Description
Plot numeric values as distances from the center of a circular field in the directions defined by angles
in radians.

Usage
radial.plot(lengths,radial.pos=NULL,labels=NA,label.pos=NULL,radlab=FALSE,
start=0,clockwise=FALSE,rp.type="r",label.prop=1.1,main="",xlab="",ylab="",
line.col=par("fg"),lty=par("lty"),lwd=par("lwd"),mar=c(2,2,3,2),
show.grid=TRUE,show.grid.labels=4,show.radial.grid=TRUE,rad.col="gray",
grid.col="gray",grid.bg="transparent",grid.left=FALSE,grid.unit=NULL,
point.symbols=1,point.col=par("fg"),show.centroid=FALSE,radial.lim=NULL,
radial.labels=NULL,boxed.radial=TRUE,poly.col=NA,add=FALSE,...)

Arguments
lengths A numeric data vector or matrix. If ‘lengths’ is a matrix, the rows will be
considered separate data vectors.
radial.pos A numeric vector or matrix of positions in radians. These are interpreted as be-
ginning at the right (0 radians) and moving counterclockwise. If ‘radial.pos’
is a matrix, the rows must correspond to rows of ‘lengths’.
labels Character strings to be placed at the outer ends of the lines. If set to NA, will
suppress printing of labels, but if missing, the radial positions will be used.
label.pos The positions of the labels around the plot in radians.
radlab Whether to rotate the outer labels to a radial orientation.
start Where to place the starting (zero) point. Defaults to the 3 o’clock position.
clockwise Whether to interpret positive positions as clockwise from the starting point. The
default is counterclockwise.
radial.plot 157

rp.type Whether to draw (r)adial lines, a (p)olygon, (s)ymbols or some combination of

these. If ‘lengths’ is a matrix and rp.type is a vector, each row of ‘lengths’
can be displayed differently.
label.prop The label position radius as a proportion of the maximum line length.
main The title for the plot.
xlab,ylab Normally x and y axis labels are suppressed.
line.col The color of the radial lines or polygons drawn.
lty The line type(s) to be used for polygons or radial lines.
lwd The line width(s) to be used for polygons or radial lines.
mar Margins for the plot. Allows the user to leave space for legends, long labels, etc.
show.grid Logical - whether to draw a circular grid.
show.grid.labels
Whether and where to display labels for the grid - see Details.
show.radial.grid
Whether to draw radial lines to the plot labels.
rad.col Color of the radial lines on the grid.
grid.col Color of the circumferential lines on the grid.
grid.bg Fill color of above.
grid.left Whether to place the radial grid labels on the left side.
grid.unit Optional unit description for the grid.
point.symbols The symbols for plotting (as in pch).
point.col Colors for the symbols.
show.centroid Whether to display a centroid.
radial.lim The range of the grid circle. Defaults to ‘pretty(range(lengths))’, but if
more than two values are passed, the exact values will be displayed.
radial.labels Optional labels for the radial grid. The default is the values of radial.lim.
boxed.radial Whether to use boxed.labels or text for radial labels.
poly.col Fill color if polygons are drawn. Use NA for no fill.
add Whether to add one or more series to an existing plot.
... Additional arguments are passed to ‘plot’.

Details
‘radial.plot’ displays a plot of radial lines, polygon(s), symbols or a combination of these cen-
tered at the midpoint of the plot frame, the lengths, vertices or positions corresponding to the
numeric magnitudes of the data values. If ‘show.centroid’ is TRUE, an enlarged point at the
centroid of values is displayed. The centroid is calculated as the average of x and y values unless
‘rp.type="p"’. In this case, the barycenter of the polygon is calculated. Make sure that these suit
your purpose, otherwise calculate the centroid that you really want and add it with the ‘points’
function. Note that if the observations are not taken at equal intervals around the circle, the centroid
may not mean much.
158 radial.plot

If the user wants to plot several sets of lines, points or symbols by passing matrices or data frames
of ‘lengths’ and ‘radial.pos’, remember that these will be grouped by row, so transpose if the
data are grouped by columns.
If more series are added to an existing plot, ‘radial.plot’ will try to maintain the current plot
parameters. Resetting the parameters after doing the initial plot will almost certainly mess up any
series that are added. Series that are added will be plotted "on top" of the existing plot, possi-
bly overplotting other things. If the added series have a larger range than the initial series, set
‘radial.lim’ to account for this in the initial plot, and if ‘radial.lim’ is specified in the initial
plot, remember to repeat it for added series as in the example.
The size of the labels on the outside of the plot can be adjusted by setting ‘par(cex.axis=)’ and
that of the labels inside by setting ‘par(cex.lab=)’. If ‘radlab’ is TRUE, the labels will be rotated
to a radial alignment. This may help when there are many values and labels. If some labels are still
crowded, try running ‘label.pos’ through the ‘spreadout’ function. If the ‘show.grid.labels’
argument is a number from 1 to 4, the labels will be placed along a horizontal or vertical radius.
The numbers represent the same positions as in ‘axis’, with the default (4) on the right.
The radial.plot family of plots is useful for illustrating cyclic data such as wind direction or speed
(but see ‘oz.windrose’ for both), activity at different times of the day, and so on. While ‘radial.plot’
actually does the plotting, another function is usually called for specific types of cyclic data.

Value
The ‘par’ values that are changed in the function as they were at the time ‘radial.plot’ was
called.

Author(s)
Jim Lemon - thanks to Jeremy Claisse and Antonio Hernandez Matias for the ‘lty’ and ‘rp.type’
suggestions respectively, Patrick Baker for the request that led to ‘radlab’, Thomas Steiner for the
request for the ‘radial.lim’ and ‘radial.labels’ modifications, Evan Daugharty for requesting
the ‘add’ argument, James MacCarthy for requesting better radial labels, Steve Ellison for noticing
that the return values of the functions had changed, Don Dennerline for requesting the rank clock,
Mehdi Nellen for the different colors for the radial and circumferential lines for the grid and Mayeul
Kauffmann for noticing the radial label bug when a separate radial.grid was included.

See Also
polar.plot,clock24.plot

Examples
testlen<-runif(10,0,10)
testpos<-seq(0,18*pi/10,length=10)
testlab<-letters[1:10]
oldpar<-radial.plot(testlen,testpos,main="Test Radial Lines",line.col="red",
lwd=3,rad.col="lightblue")
testlen<-c(sin(seq(0,1.98*pi,length=100))+2+rnorm(100)/10)
testpos<-seq(0,1.98*pi,length=100)
radial.plot(testlen,testpos,rp.type="p",main="Test Polygon",line.col="blue",
labels=LETTERS[1:8])
radial.plot.labels 159

# now do a 12 o'clock start with clockwise positive

radial.plot(testlen,testpos,start=pi/2,clockwise=TRUE,show.grid.labels=2,
rp.type="s",main="Test Symbols (clockwise)",radial.lim=c(0,3.5),
point.symbols=16,point.col="green",show.centroid=TRUE,labels=LETTERS[1:6])
# one without the circular grid and multiple polygons
# see the "diamondplot" function for variation on this
posmat<-matrix(sample(2:9,30,TRUE),nrow=3)
radial.plot(posmat,labels=paste("X",1:10,sep=""),rp.type="p",
main="Spiderweb plot",line.col=2:4,show.grid=FALSE,lwd=1:3,
radial.lim=c(0,10))
# dissolved ions in water
ions<-c(3.2,5,1,3.1,2.1,4.5)
ion.names<-c("Na","Ca","Mg","Cl","HCO3","SO4")
radial.plot(ions,labels=ion.names,rp.type="p",main="Dissolved ions in water",
grid.unit="meq/l",radial.lim=c(0,5),poly.col="yellow",show.grid.labels=1)
# add points inside the polygon - radial.lim is supplied by plotrix_env
radial.plot(ions-0.4,rp.type="s",point.symbols=4,point.col="red",add=TRUE)
radmat<-matrix(c(sample(1:4,4),sample(1:4,4),sample(1:4,4),sample(1:4,4),
sample(1:4,4),sample(1:4,4),sample(1:4,4),sample(1:4,4),
sample(1:4,4),sample(1:4,4)),nrow=4)
# finally a rank clock
radial.plot(radmat,rp.type="l",radial.pos=seq(0,20*pi/11.1,length.out=10),
label.pos=seq(0,20*pi/11.1,length.out=10),start=pi/2,clockwise=TRUE,
labels=2001:2010,radial.lim=c(0.2,4),main="Rank clock")
legend(-1.7,4,c("Black","Red","Green","Blue"),col=1:4,lty=1)
par(xpd=oldpar$xpd,mar=oldpar$mar,pty=oldpar$pty)
# reset the margins
par(mar=c(5,4,4,2))

radial.plot.labels Display labels on a circular grid

Description
‘radial.plot.labels’ displays a labels on a circular plot produced by one of the radial.plot family
of functions.

Usage
radial.plot.labels(lengths,radial.pos=NULL,units="radians",radial.lim=NULL,
start=0,clockwise=FALSE,labels,adj=NULL,pos=NULL,...)

Arguments
lengths numeric data vector. Magnitudes will be represented as the radial positions of
symbols, line ends or polygon vertices.
radial.pos numeric vector of radial positions. These will be converted to radians if the
‘units’ argument is not "radians".
160 radial.plot.labels

units The units of ‘radial.pos’ may be degrees or 24 hour clock positions. If ‘units’
is "polar" or "clock24" respectively, the values of radial.pos will be converted
into radians.
radial.lim Optional radial limits for the circular plot. These must be the same as the radial
limits of the original plot.
start The zero position on the plot in the units of ‘radial.pos’.
clockwise Whether to increase angles clockwise rather than the default counterclockwise.
labels text labels to display on the plot.
adj Text justification as in the ‘text’ function.
pos Text position as in the ‘text’ function.
... additional arguments passed to ‘text’.

Details
Don’t confuse this function with the ‘radial.labels’ argument in the radial.plot function. This
labels the values rather than the grid.

Value
nil

Author(s)
Jim Lemon

See Also
text

Examples
testlen<-c(rnorm(10)*2+5)
# do the labels in clock24 units
testpos<-c(6.74,8.3,10.55,12.33,13.75,15.9,17.15,19.36,21.02,23.27)
oldpar<-clock24.plot(testlen,testpos,main="Test radial.plot.labels",
rp.type="s",point.symbols=3,point.col="blue")
radial.plot.labels(testlen,testpos,units="clock24",labels=LETTERS[1:10],
pos=3,col="blue")
testangle<-c(25,42,67,94,128,173,191,234,268,307)
# now a polar plot
polar.plot(testlen,testangle,main="Test radial.plot.labels",rp.type="p",
poly.col="green")
radial.plot.labels(testlen,testangle,units="polar",labels=LETTERS[1:10])
# reset par
par(oldpar)
radialtext 161

radialtext Display text in a radial line

Description
Displays a string in a radial line, rotating it to flow in the radial direction and optionally scaling
each letter’s size according to its distance from the center.

Usage
radialtext(x, center=c(0,0), start=NA, middle=1, end=NA, angle=0,
deg=NA, expand=0, stretch=1, nice=TRUE, cex=NA, ...)

Arguments
x A character string.
center The center of the circular area in x/y user units.
start The starting distance of the string from the center in x/y user units.
middle The middle distance of the string from the center in x/y user units.
end The ending distance of the string from the center in x/y user units.
angle The angular position of the string in radians.
deg The angular position of the string in degrees (takes precedence if not NA).
expand Size expansion factor for characters, used only if ‘start’ specified.
stretch How much to stretch the string for appearance, 1 for none.
nice TRUE to auto-flip text to keep it upright, FALSE to let it be upside down.
cex The overall character expansion factor, NA for par("cex").
... Additional arguments passed to ‘text’.

Details
This may not work on all devices, as not all graphic devices can rotate text to arbitrary angles. The
output looks best on a Postscript or similar device that can rotate text without distortion. Rotated text
often looks very ragged on small bitmaps. If the user passes a value for ‘start’, this will override
a value for ‘middle’ or ‘end’. Likewise, a value for ‘end’ will override a value for ‘middle’. Also,
a value for ‘deg’ overrides any value passed to ‘angle’. If ‘expand’ is 0, all characters will be the
same size, while a value of 1 will scale characters so that one that is twice as far from the center
will be twice as large. Negative values are permitted too, but ‘expand’ is only used if ‘start’ was
specified.

Value
nil
162 raw.means.plot

Author(s)
Ted Toal

See Also
text, arctext

Examples
plot(0, xlim=c(1,5), ylim=c(1,5), main="Test of radialtext",
xlab="", ylab="", type="n")
points(3, 3, pch=20)
radialtext("uncooked spaghetti", center=c(3,3),
col="blue")
radialtext("uncooked spaghetti", center=c(3,3),
start=1.2, angle=pi/4, cex=0.8)
radialtext("uncooked spaghetti", center=c(3,3),
middle=1.2, angle=pi/4+0.1, cex=0.8)
radialtext("uncooked spaghetti", center=c(3,3),
end=1.2, angle=pi/4+0.2, cex=0.8)
radialtext("uncooked spaghetti", center=c(3,3),
start=0.5, deg=135, cex=0.8, col="green")
radialtext("uncooked spaghetti", center=c(3,3),
start=0.5, deg=145, cex=0.8, stretch=2)
radialtext("uncooked spaghetti", center=c(3,3),
start=0.5, deg=20, expand=0, col="red")
radialtext("uncooked spaghetti", center=c(3,3),
start=0.5, deg=250, expand=0.35)
radialtext("uncooked spaghetti", center=c(3,3),
start=0.75, deg=225, expand=1, col="gold")
radialtext("uncooked spaghetti", center=c(3,3),
start=0.5, deg=325, expand=-0.25, cex=2)

raw.means.plot raw.means.plot: Raw-Means Plots for Experimental Designs

Description
raw.means.plot is a function for visualizing results of experimental designs with up to two factors.
It plots both raw data (background) and factor/cell means (foreground) to provide a more accurate
visualization of the underlying distribution.

Usage
raw.means.plot(data, col.offset = 2, col.x = 3, col.value = 4, na.rm = FALSE,
avoid.overlap = c("y", "x", "both"), y.factor = 1, y.amount = NULL,
x.amount = 0.05, pch = 21:25, lty = 1:5, bg.b.col = "darkgrey",
bg.f.col = NULL, fg.b.col = "black",fg.f.col = "black", type = "o",
pt.cex = 1, lwd = 1, xlab = "", ylab = "", ylim, max.offset = 0.2,
raw.means.plot 163

xaxis = TRUE, x.labels, xaxt = "n", plot = TRUE, legend = TRUE, mar = NULL,
reset.mar = TRUE, l.pos, yjust = 0.5, l.bty = "n", l.adj = c(0, 0.5), ...)

raw.means.plot2(data, col.id, col.offset, col.x, col.value,

fun.aggregate = "mean", ...)

Arguments
data a ‘data.frame’ in long format (i.e., each datapoint one row, see ‘\link{reshape}’
or the reshape package) that contains at least three columns: one column coding
the first factor (‘col.offset’), one column coding the second factor (‘col.x’),
and one column containing the values (‘col.value’).
col.id a ‘character’ scalar, specifiying the name of the column specifying the id col-
umn. (only for ‘raw.means.plot2’)
col.offset a ‘character’ or ‘numeric’ (only ‘raw.means.plot’) scalar, specifiying either
name or number of the column coding the different lines (the offset or first fac-
tor).
col.x a ‘character’ or ‘numeric’ (only ‘raw.means.plot’) scalar, specifiying either
name or number of the column coding the x-axis factor. Default is 3.
col.value a ‘character’ or ‘numeric’ (only ‘raw.means.plot’) scalar, specifiying either
name or number of the data column. Default is 4.
na.rm ‘logical’ indicating whether ‘NA’ values should be stripped before the com-
putation proceeds. Default is ‘FALSE’. Throws an error message if FALSE and
NAs are encountered.
avoid.overlap character. What should happen to datapoints within one cell of the two factors
that have the same value.
• ‘"y"’ (the default) jitter is added so that overlapping points are distinguish-
able on the y-axis
• ‘"x"’ jitter is added so that overlapping points are distinguishable on the
x-axis
• ‘"both"’ jitter is added so that overlapping points are distinguishable on
both the y- and the x-axis.
• anything else. No jitter is added.
y.factor ‘factor’ for controlling the amount of jitter on the y-axis (will be passed to
jitter).
y.amount ‘amount’ for controlling the amount of jitter on the y-axis (will be passed to
jitter).
x.amount ‘amount’ for controlling the amount of jitter on the x-axis (will be passed to
jitter).
pch ‘pch’ values (plot symbols) taken for plotting the data. Note that the same values
are taken for raw data and means. see points for more details. Recycled if too
short (with warning). Default is 21:25, because those are the only values that
can be displayed filled and non-filled. All other values should not be used.
164 raw.means.plot

lty ‘lty’ values (line types) for connecting the means. See par for more details.
Recycled if too short (with warning). Default is 1:5.
bg.b.col background border color: border color of raw data points. Silently recycled.
Default: ‘"darkgrey"’
bg.f.col background filling color: fill color of raw data points. Silently recycled. Default:
‘NULL’
fg.b.col foreground border color: border color of mean data points. Silently recycled.
Default: ‘black’
fg.f.col foreground fill color: fill color for mean data points. Silently recycled. Default:
‘black’
type same as type in plot. Default: ‘o’ ("overplotted")
pt.cex ‘numeric’ specifying the ‘cex’ value used for plotting the points. Default is 1.
lwd ‘numeric’ specifying the ‘lwd’ value used for plotting the lines. Default is 1.
xlab x-axis label. Default: ‘""’
ylab y-axis label. Default: ‘""’
ylim the y-axis limits of the plot. If not specified (the default) will be taken from
data so that all raw data points are visible and a warning message is displayed
specifying the ylim.
max.offset ‘numeric’. maximal offset of factor levels from the offset factor (‘col.offset’)
specifying the different lines. The centre of each factor on the x-axis is at full
numbers (starting from 1 to ...). The maximum will only be reached if the num-
ber of factor levels (from ‘col.offset’) is even. Default: 0.2.
xaxis ‘logical’ value indicating whether or not the x-axis should be generated by
‘raw.means.plot’. If ‘TRUE’, labels for the x-axis will be taken either from the
unique values of ‘col.x’ or can be specified with ‘x.labels’.
x.labels ‘character’ vector specifiying ‘col.x’ levels. Only relevant if ‘xaxis=TRUE’.
Then, the values given here will be displayed at the x-axis for each factor level
of ‘col.x’.
xaxt A character which specifies whether ot not the x-axis should be plotted by the
call to plot function. Interfers with the aforementioned ‘xaxis’ argument and
the automatic ‘xaxis’ function by ‘raw.means.plot’. Just there for complete-
ness. Default ‘"n"’ (and should not be changed).
plot ‘logical’. Should the ‘raw.means.plot’ be drawn or not. If ‘TRUE’ (the de-
fault) plot will be drawn. If ‘FALSE’ only the legend will be drawn (if ‘legend = TRUE’)
See details.
legend ‘logical’ indicating whether or not ‘raw.means.plot’ should automatically
add a legend on the right outside the plot area indicating which line and points
refer to which ‘col.offset’ factor levels. Default is ‘TRUE’.
mar ‘NULL’ or ‘numerical’ vector of length 4 indicating the margins of the plot (see
par). If ‘NULL’ (the default) the right margin (i.e., ‘par("mar")[4]’) will be
(imperfectly) guessed from the ‘col.offset’ factors for placing the legend right
to the plot. If length is four this value will be taken. Ignored for ‘plot = FALSE’.
raw.means.plot 165

reset.mar ‘logical’ indicating if the margins (‘mar’) shall be resetted after setting inter-
nally. Will be ignored if ‘legend = FALSE’. Default is ‘TRUE’ and should not
be changed (especially with ‘plot = FLASE’).
l.pos ‘numeric’ vector of length 2 indicating the position of the legend. If not speci-
fied automatically determined. See details.
yjust how the legend is to be justified relative to the legend y location. A value of 0
means top, 0.5 means centered and 1 means bottom justified. Default is 0.5.
l.bty the type of box to be drawn around the legend. The allowed values are ‘"o"’
and ‘"n"’ (the default).
l.adj ‘numeric’ of length 1 or 2; the string adjustment for legend text. Useful for
y-adjustment when labels are plotmath expression. see legend and plotmath for
more info.
... further arguments which are either passed to plot or legend (or ‘raw.means.plot’
for ‘raw.means.plot2’). The following arguments are passed to legend, all oth-
ers are passed to plot: ‘"fill", "border", "angle", "density", "box.lwd", "box.lty", "box.co
fun.aggregate Function or function name used for aggregating the data across the two factors.
Default is ‘"mean"’. (only for ‘raw.means.plot2’)

Details

‘raw.means.plot2’ is probably the more useful function, as it allows for using a data.frame with
more than two-factors and aggregates across the other factors, but needs a column specifying the
experimental unit (e.g., participant).
‘raw.means.plot’ is basically an advanced wrapper for two other functions: plot and (if ‘legend=TRUE’)
legend. Furthermore, raw data is plotted with a call to points and the means with a call to lines.
You can use ‘raw.means.plot’ to plot only a legend by setting ‘plot = FALSE’ and ‘legend = TRUE’.
Then, ‘raw.means.plot’ will draw an invisible plot with ‘xlim = c(0,10)’ and ‘ylim = c(0, 10)’
and place the legend on this invisible plot. You can specify ‘l.pos’ to position the legend, other-
wise it will be plotted at ‘c(5,5)’ (i.e., in the middle of the plot). Note that ‘xpd = TRUE’ in the
call to ‘legend’ (see par).

Value

Nothing. This function is invoked for its side effects.

Author(s)

Henrik Singmann (<henrik.singmann@psychologie.uni-freiburg.de>) with ideas from Jim

Lemon

See Also

add.ps can be used in addition to‘raw.means.plot’ to compare the factors at each x-axis position,
by adding p-values from t-tests to the x-axis.
166 raw.means.plot

Examples

x <- data.frame(id = 1:150, offset = rep(c("Group A", "Group B", "Group C"),
each = 50), xaxis = sample(c("A", "B", "C", "D"),150, replace = TRUE),
data = c(rnorm(50, 10, 5), rnorm(50, 15,6), rnorm(50, 20, 5)))

raw.means.plot(x)

raw.means.plot(x, main = "Example", ylab = "Values", xlab = "Factor",

title = "Groups")

raw.means.plot(x, "offset", "xaxis", "data")

raw.means.plot(x, "xaxis", "offset", "data")

raw.means.plot(x, 3, 2, 4)

# different colors:
raw.means.plot(x, main = "Example", ylab = "Values", xlab = "Factor",
title = "Groups", fg.f.col = c("red","blue", "green"))

x2 <- data.frame(id = 1:150, offset = rep(c("Group A", "Group B", "Group C"),
each = 50), xaxis = sample(c("A", "B", "C", "D"),150, replace = TRUE),
data = c(rnorm(50, 10, 5), rnorm(50, 15,6), rnorm(50, 20, 5)))

layout(matrix(c(1,2,3,3), 2,2,byrow = TRUE), heights = c(7,1))

raw.means.plot(x, main = "Data x1", ylab = "Values", xlab = "Factor",
legend = FALSE, mar = c(4,4,4,1)+0.1)
raw.means.plot(x2, main = "Data x2", ylab = "Values", xlab = "Factor",
legend = FALSE, mar = c(4,4,4,1)+0.1)
raw.means.plot(x2, plot = FALSE, title = "Groups")

y <- data.frame(id = 1:300, offset = rep(1, 300),

axis = sample(LETTERS[1:6],300, replace = TRUE), data = c(rnorm(100, 1),
rnorm(100), rnorm(100,1)))

par(mfrow = c(2,2))

raw.means.plot(y, legend = FALSE)

raw.means.plot(y, type = "p", legend = FALSE)

raw.means.plot(y, type = "l", legend = FALSE)

raw.means.plot(y, 3, 2, x.labels = "one group only")

# Example with overlapping points

z <- data.frame (id = 1:200, offset = rep(c("C 1", "C 2"), 200),
axis = sample(LETTERS[1:4], 200, replace = TRUE),
data = sample(1:20, 200, replace = TRUE))
raw.means.plot 167

# x versus y jitter
par(mfrow = c(2,2))
raw.means.plot(z, avoid.overlap = "none", main = "no-jitter")
raw.means.plot(z, main = "y-axis jitter (default)")
raw.means.plot(z, avoid.overlap = "x", main = "x-axis jitter")
raw.means.plot(z, avoid.overlap = "both", main = "both-axis jitter")

# y-axis jitter (default)

par(mfrow = c(2,2))
raw.means.plot(z, avoid.overlap = "none", main = "no jitter")
raw.means.plot(z, y.factor = 0.5, main = "smaller y-jitter")
raw.means.plot(z, main = "standard y-jitter")
raw.means.plot(z, y.factor = 2, main = "bigger y-jitter")

# x-axis jitter (default)

par(mfrow = c(2,2))
raw.means.plot(z, avoid.overlap = "none", main = "no jitter")
raw.means.plot(z, avoid.overlap = "x", x.amount = 0.025,
main = "smaller x -jitter")
raw.means.plot(z, avoid.overlap = "x", main = "standard x-jitter")
raw.means.plot(z, avoid.overlap = "x", x.amount= 0.1,
main = "bigger x-jitter")

## Not run:

#The examples uses the OBrienKaiser dataset from car and needs reshape.
require(reshape)
require(car)
data(OBrienKaiser)
OBKnew <- cbind(factor(1:nrow(OBrienKaiser)), OBrienKaiser)
colnames(OBKnew)[1] <- "id"
OBK.long <- melt(OBKnew)
OBK.long[, c("measurement", "time")] <-
t(vapply(strsplit(as.character(OBK.long$variable), "\\."), "[", c("", "")))

raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")

raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")

# also use add.ps:

# For this example the position at each x-axis are within-subject comparisons!
raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")
add.ps(OBK.long, "id", "measurement", "gender", "value", paired = TRUE)
#reference is "fup"

raw.means.plot2(OBK.long, "id", "measurement", "gender", "value")

add.ps(OBK.long, "id", "measurement", "gender", "value", ref.offset = 2,
paired = TRUE) #reference is "post"
168 rectFill

# Use R's standard (i.e., Welch test)

raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")
add.ps(OBK.long, "id", "treatment", "gender", "value",
prefixes = c("p(control vs. A)", "p(control vs. B)"))

# Use standard t-test

raw.means.plot2(OBK.long, "id", "treatment", "gender", "value")
add.ps(OBK.long, "id", "treatment", "gender", "value", var.equal = TRUE,
prefixes = c("p(control vs. A)", "p(control vs. B)"))

## End(Not run)

rectFill Draw a rectangle filled with symbols

Description
Draws a rectangle on the current figure filled with arbitrary symbols.

Usage
rectFill(x1,y1,x2,y2,fg=par("fg"),bg=par("bg"),xinc=NA,yinc=NA,
pch=1,pch.cex=1,pch.col=par("fg"),...)

Arguments
x1,y1,x2,y2 Rectangle limits as in ‘rect’.
fg Foreground color
bg Background color
xinc,yinc The x and y increments of spacing for the symbols.
pch Which symbol to use
pch.cex Character expansion for the symbols.
pch.col Color(s) for the symbols.
... Additional arguments to ‘points’ for the symbols.

Details
‘rectFill’ draws a rectangle and fills the rectangle with the symbols requested. It is probably most
useful as a substitute for fill colors in a black and white environment.

Value
nil
rescale 169

Author(s)
Jim Lemon

See Also
rect, points

Examples
plot(1:7,type="n",xlab="",ylab="",main="Test of rectFill")
rectFill(1:6,1:6,2:7,2:7,bg=2:7,pch=c("+","*","o",".","#","^"),
xinc=c(0.2,0.1,0.2,0.1,0.2,0.2),yinc=c(0.2,0.1,0.2,0.1,0.2,0.2),
pch.col=1:6)
barp(matrix(runif(9),nrow=3),main="Black and white bar plot",pch=1:3)

rescale Scale numbers into a new range

Description
Scale a vector or matrix of numbers into a new range.

Usage
rescale(x,newrange)

Arguments
x A numeric vector, matrix or data frame.
newrange The minimum and maximum value of the range into which ‘x’ will be scaled.

Details
‘rescale’ performs a simple linear conversion of ‘x’ into the range specified by ‘newrange’. Only
numeric vectors, matrices or data frames with some variation will be accepted. NAs are now pre-
served - formerly the function would fail.

Value
On success, the rescaled object, otherwise the original object.

Author(s)
Jim Lemon
170 revaxis

Examples
# scale one vector into the range of another
normal.counts<-rnorm(100)
normal.tab<-tabulate(cut(normal.counts,breaks=seq(-3,3,by=1)))
normal.density<-rescale(dnorm(seq(-3,3,length=100)),range(normal.tab))
# now plot them
plot(c(-2.5,-1.5,-0.5,0.5,1.5,2.5),normal.tab,xlab="X values",
type="h",col="green")
lines(seq(-3,3,length=100),normal.density,col="blue")

revaxis Plot with axis direction(s) reversed

Description
Reverses the sense of either or both the ‘x’ and ‘y’ axes.

Usage
revaxis(x, y, xrev=FALSE, yrev=TRUE, xside=if (yrev) 3 else 1,
yside=if (xrev) 4 else 2, xlab=NULL, ylab=NULL, bty=NULL, ...)

Arguments
x Vector of ‘x’-coordinates of the data to be plotted.
y Vector of ‘y’-coordinates of the data to be plotted.
xrev Logical scalar; should the sense of the ‘x’-axis be reversed?
yrev Logical scalar; should the sense of the ‘y’-axis be reversed?
xside The side of the plot on which the ‘x’-axis labels should go.
yside The side of the plot on which the ‘y’-axis labels should go.
xlab Character string for labelling the ‘x’-axis.
ylab Character string for labelling the ‘y’-axis.
bty Single letter indicating the type of box to be drawn around the plot. See par for
the possible letters and their meaning.
... Other arguments to be passed to plot.

Value
nil

Author(s)
Rolf Turner
ruginv 171

See Also
plot, box, par

Examples
x <- runif(20)
y <- runif(20)
revaxis(x,y,yside=4)

ruginv Add an Inverse Rug to a Plot

Description
Adds a rug representation (1D plot) of the data to the plot, but with the coloring inverted.

Usage
ruginv(x,ticksize=0.03,side=1,lwd=0.5,col=par("fg"),col.ticks="white",
quiet=getOption("warn") < 0,...)

Arguments
x A numeric vector.
ticksize The length of the ticks making up the ’rug’. Positive lengths produce inward
ticks.
side On which side of the plot box the rug will appear. Usually 1 (bottom) or 3 (top).
lwd The line width of the ticks.
col Color of the background of the ticks.
col.ticks The color of the ticks.
quiet Logical indicating if there should be a warning about clipped values.
... Further arguments passed to polygon when plotting the background for the ticks.

Author(s)
Peter Solymos

See Also
rug

Examples
require(stats)
plot(density(faithful$eruptions,bw=0.15))
ruginv(faithful$eruptions,ticksize=-0.05)
ruginv(jitter(faithful$eruptions,amount=0.01),side=3,col="lightblue")
172 seats

seats Arrange N seats in M semicircular rows

Description

Compute seat positions in a semicircular parliament

Usage

seats(N, M, r0 = 2.5)

Arguments

N Total number of seats.

M Number of semicircular arcs on which to distribute the seats.
r0 Radius of the inner arc in user units.

Value

A data frame including:

x The x positions of the seats to be plotted on semi-circular arcs.

y The y positions of the seats to be plotted on semi-circular arcs.
r The row numbers for each seat.
theta The angle of each seat, going from pi to zero radians.

Author(s)

Duncan Murdoch and Barry Rowlingson

See Also

election
sizeplot 173

sizeplot Plot with repeated symbols by size

Description
Plots a set of (x,y) data with repeated points denoted by larger symbol sizes

Usage
sizeplot(x, y, scale=1, pow=0.5, powscale=TRUE, size=c(1,4), add=FALSE, ...)

Arguments
x x coordinates of data
y y coordinates of data
scale scaling factor for size of symbols
pow power exponent for size of symbols
powscale (logical) use power scaling for symbol size?
size (numeric vector) min and max size for scaling, if powscale=FALSE
add (logical) add to an existing plot?
... other arguments to ‘plot()’ or ‘points()’

Details
Most useful for plotting (e.g.) discrete data, where repeats are likely. If all points are repeated
equally, gives a warning. The size of a point is given by scale ∗ np ow, where n is the number of
repeats, if powscale is TRUE, or it is scaled between size[1] and size[2], if powscale is FALSE.

Value
A plot is produced on the current device, or points are added to the current plot if ‘add=TRUE’.

Author(s)
Ben Bolker

See Also
symbols

Examples
x <- c(0.1,0.1,0.1,0.1,0.1,0.2,0.2,0.2,0.2,0.3,0.3)
y <- c( 1, 1, 1, 1, 2, 2, 2, 3, 3, 4, 5 )
plot(x,y)
sizeplot(x,y)
sizeplot(x,y,pch=2)
174 sizetree

sizetree Display a hierarchical breakdown of disjunct categories

Description
Display a data frame in which the values in each successive column represent subcategories of the
previous column as stacked rectangles.

Usage
sizetree(x,left=0,top,right=1,lastcenter=NA,showval=TRUE,showcount=TRUE,
stacklabels=TRUE,firstcall=TRUE,col=NULL,border=NA,toplab=NULL,base.cex=1,
...)

Arguments
x A data frame in which each successive column represents subcategories of the
previous column.
left The left edge of the current stack of rectangles in user units.
top The top of the current stack of rectangles in user units.
right The right edge of the current stack of rectangles in user units.
lastcenter The center of the previous rectangle from which the next breakdown of cate-
gories arises. There is almost no reason to change it.
showval Whether to display the values representing the categories.
showcount Whether to display the count for the categories.
stacklabels Whether to display the names of the dataframe beneath the stacked rectangles.
firstcall A flag for the function - do not alter this.
col Optional fill colors for the rectangles. See Details
border Color for border around the rectangles. See details
toplab Optional labels to display a the top of each stack.
base.cex The base character expansion for the labels.
... additional arguments passed to ‘plot’.

Details
‘sizetree’ displays disjunct hierarchical categories as stacked rectangles. It accepts a data frame
in which the values in the first column represent categories, the values in the second column repre-
sent subcategories of the first column, and so on. The first column will be displayed as a stack of
rectangles, the height of each proportional to the count for each category. Each substack of rectan-
gles in the second stack will represent the breakdown of counts for its superordinate category and
so on through the columns. Empty categories are ignored and NAs will produce gaps, which will
propagate across subsequent stacks.
sizetree 175

The user can simply pass the data frame, which should only contain columns that are hierarchical
categories (example 1). The colors will probably not be ideal. The user can pass the same colors for
the all levels (example 2). If this is done, ‘sizetree’ will try to match colors to categories when
the number of categories is diminishing (e.g. some levels are missing in the sub-categories) and the
columns of ‘x’ are factors with the same levels in the same order. This will work if the category
labels are the same in each level, but remember to add the names to the colors before passing them
to the function. This will not work if there are more categories in the lower levels. If ‘col’ is a
list, this is not done, and the user will have to work out the correct colors for each level. This is
particularly important when the category labels and the number of categories is different in different
levels (example 3).
In some sizetrees, the subcategory counts are very low compared to the overall number of data
objects. This results in rectangles that are very thin vertically. One way to get better legibility of
the labels is to use dark colors for the rectangles, so that the labels are white, and no borders (set
‘border’ to NA). The user can also select only part of the data frame ‘x’ to expand sections of the
sizetree as in the last example.
The labels are sized to fit the vertical extent of the bars. However, it is possible that the labels may
extend horizontally beyond the bar(s). The ‘base.cex’ argument can be used to shrink the labels
if this happens. Remember that ‘base.cex’ will shrink all the labels, not just the ones that are too
wide.
The ‘firstcall’ argument is necessary for the function to initialize the plot, as each breakdown
involves a recursive call. If it is changed, the best that can be expected is an uninformative plot.

Value
nil

Author(s)
Jim Lemon

See Also
plot

Examples
cat1<-factor(sample(c("None","Low","Medium","High","Extreme"),40,TRUE),
levels=c("None","Low","Medium","High","Extreme"))
cat2<-factor(sample(c("None","Low","Medium","High"),40,TRUE),
levels=c("None","Low","Medium","High"))
cat3<-factor(sample(c("None","Low","High"),40,TRUE),
levels=c("None","Low","High"))
hcats<-data.frame(cat1,cat2,cat3)
# throw in a few NAs
hcats$cat1[10]<-NA
hcats$cat2[c(15,20)]<-NA
hcats$cat3[c(11,14,25)]<-NA
# first let sizetree work out the colors
sizetree(hcats,main="Sizetree with automatic colors")
# now see what happens with a list of the same colors for each level
176 size_n_color

bhcol<-c("#ff8080","#dddd80","#80ff80","#0000ff","#80dddd")
sizetree(hcats,col=list(bhcol,bhcol,bhcol),
main="Sizetree with the same colors each level")
# finally, specify different colors for categories with different labels
sexhaireye<-data.frame(sex=factor(sample(c("Male","Female"),50,TRUE)),
hair=factor(sample(c("Blond","Red","Brown","Black"),50,TRUE)),
eye=factor(sample(c("Gold","Green","Blue"),50,TRUE)))
shecol<-list(c("pink","lightblue"),c("#000000","#dddd00","#886600","#ee8800"),
c("blue","gold","green"))
sizetree(sexhaireye,main="Sex, hair and eye color",
col=shecol,toplab=c("Sex","Hair color","Eye color"))
# now expand the female part of the sizetree
sizetree(sexhaireye[sexhaireye[,1]=="Female",],
main="Sex, hair and eye color (Females only)",
col=shecol,toplab=c("Sex","Hair color","Eye color"))

size_n_color Display circles with specified size and color

Description
Display a plot of circles at specified locations, each with a specified size and color.

Usage
size_n_color(x=NULL,y,size,sizefun="sqrt",col,main="",
xlim=NA,xlab="",xat=NULL,xaxlab=NULL,xcex=1,xlas=0,xgrid=FALSE,
ylim=NA,ylab="",yat=NULL,yaxlab=NULL,ycex=1,ylas=1,ygrid=TRUE,
mar=c(5,4,4,2),boxit=TRUE,add=FALSE,...)

Arguments
x,y Vectors or matrices of x and y positions for the symbols.
size Sizes for the symbols expressed as numbers.
sizefun The function to use for transforming the values to radii of circles. Square root
gives areas proportional to the values.
col Colors for the symbols (see Details).
main Title for the plot.
xlim,ylim Explicit x and y limits for the plot.
xlab,ylab Labels for the x and y axes.
xat,yat Where to place the ticks and tick labels on the axes.
xaxlab,yaxlab Tick labels for the x and y axes.
xcex,ycex Character expansions for the axis tick labels.
xlas,ylas Orientation for the axis tick labels (see ‘par’).
xgrid,ygrid Whether to display a grid along the x or y direction.
size_n_color 177

mar Margins for the plot (see Details).

boxit Whether to draw a box around the plot.
add Whether to draw a new plot (FALSE) or add symbols to an existing plot (TRUE).
... Additional arguments passed to ‘plot’.

Details
‘size_n_color’ plots circles centered on the ‘x’ and ‘y’ coordinates. The size and color of the
circles may also be specified individually, allowing four dimensions of variation to be displayed on
the plot.
‘size_n_color’ may also be used to display a "visual table" as in the second example. Here the
x and y coordinates are used to associate the symbols with two categorical variables, underlying
cause of death and year of observation. If the x values are not passed to the function, it will try
to space out the circles evenly in a representation of the matrix. If the matrix is not square, use a
plotting device that has about the same proportion of height and width as the matrix.

Value
nil

Author(s)
Jim Lemon

See Also
plot, points, par

Examples
meantemp<-c(19,22,25,29,21,20,16,27,23,26)
totalrain<-c(174,152,196,120,177,183,92,153,161,85)
numpumpkin<-c(53,47,61,63,38,42,48,71,66,29)
meanwt<-c(1.5,2.3,2.8,1.9,2.4,1.8,2.6,2.2,1.7)
size_n_color(meantemp,totalrain,meanwt/5,NA,xlim=c(15,30),
color.scale(numpumpkin,c(0.8,0),c(0.8,1),0),
xlab="Temperature (degrees C)",ylab="Rainfall (mm)",
main="Number and weight of pumpkins by temperature and rainfall",
xat=seq(15,30,by=5),yat=seq(80,200,by=20))
color.legend(15,55,18.5,60,seq(40,70,by=10),
rect.col=color.scale(seq(40,70,by=10),c(0.8,0),c(0.8,1),0))
points(15:18,rep(126,4),cex=seq(1.5,3.0,by=0.5))
text(15:19,rep(134,5),c("1.5","2.0","2.5","3.0","kg"))
par(xpd=TRUE)
text(13.5,60,"Number of\npumpkins")
par(xpd=FALSE)
# now display a "visual table" of delayed registrations by underlying cause of
# death and year of observation. The sizes of the circles represent the log of
# the number of deaths and the colors represent the percentage of deaths that
# occurred in the year prior to registration or earlier
178 sliceArray

data(death_reg)
size_n_color(x=matrix(rep(1996:2010,each=22),nrow=22),
y=matrix(rep(1:22,15),nrow=22),size=t(death_reg[[1]])/200,
col=color.scale(t(death_reg[[2]]),c(0,0.8,1),c(1,0.2,0),0),
ylim=c(1,22),main="Delayed registrations by ICD chapter",
xlab="Year",xaxlab=1996:2010,xat=1996:2010,xcex=0.8,
yaxlab=colnames(death_reg[[1]]),ycex=0.8,ygrid=TRUE,mar=c(5,6,4,2))
color.legend(1994,-3.5,2000,-2.5,seq(0,50,by=10),cex=0.8,
rect.col=color.scale(seq(0,50,by=10),c(0,0.8,1),c(1,0.2,0),0))
par(xpd=TRUE)
text(1993.4,-2.5,"Pct.\nslow",cex=0.8)
par(xpd=FALSE)

sliceArray Slice an array

Description
Slices one dimension from an array by taking one element from the first dimension.

Usage
sliceArray(x,slice)

Arguments
x An array
slice The index of the slice to take from the first dimension of the array.

Details
‘sliceArray’ builds an extractor string containing the value of ‘slice’ as the first element and as
many commas as needed to match the dimensions of the array. It then applies the extractor function
to ‘x’ and returns the result. Note how the array "slice" swaps dimensions in the example.

Value
The desired slice of the array.

Author(s)
Jim Lemon

See Also
array
smoothColors 179

Examples
a1<-array(1:27,dim=c(3,3,3))
a1
sliceArray(a1,2)

smoothColors Build a vector of color values

Description
‘smoothColors’ calculates a sequence of colors. If two color names in the arguments are separated
by a number, that number of interpolated colors will be inserted between the two color endpoints.
Any number of color names and integers may be passed, but the last argument must be a color
name. If more than one integer appears between two color names, only the first will be used in the
interpolation and the others will be ignored.

Usage
smoothColors(...,alpha=NA)

Arguments
... an arbitrary sequence of color names and integers beginning and ending with a
color name.
alpha optional ‘alpha’ (transparency) value.

Value
A vector of hexadecimal color values as used by ‘col’.

Note
For more R functions that transform numeric values into colors or produce colors that can be used
to represent values, see the colourschemes package.

Author(s)
Barry Rowlingson

See Also
color.gradient,rgb

Examples
plot(1:10,main="Test opaque colors",type="n",axes=FALSE)
box()
rect(1:7,1:7,3:9,3:9,col=smoothColors("red",2,"green",2,"blue"))
180 soil.texture

soil.texture Soil texture triangle plot

Description
Display a USDA soil texture triangle with optional grid, labels and soil texture points.

Usage
soil.texture(soiltexture=NULL, main="", at=seq(0.1, 0.9, by=0.1),
axis.labels=c("percent sand", "percent silt",
"percent clay"),
tick.labels=list(l=seq(10, 90, by=10), r=seq(10, 90, by=10),
b=seq(10, 90, by=10)),
show.names=TRUE, show.lines=TRUE, col.names="gray",
bg.names=par("bg"), show.grid=FALSE, col.axis="black",
col.lines="gray", col.grid="gray", lty.grid=3,
show.legend=FALSE, label.points=FALSE, point.labels=NULL,
col.symbols="black", pch=par("pch"), ...)

Arguments
soiltexture Matrix of soil textures where each row is a soil sample and three columns contain
the proportions of the components sand, silt and clay in the range 0 to 1 or
percentages in the range 0 to 100.
main The title of the soil texture plot. Defaults to nothing.
at Positions on the three axes where ticks will be drawn.
axis.labels Labels for the axes.
tick.labels The tick labels for the three axes.
show.names Logical - whether to show the names of different soil types within the soil trian-
gle.
show.lines Logical - whether to show the boundaries of the different soil types within the
soil triangle.
col.names Color of the soil names. Defaults to gray.
bg.names Color to use when drawing a blank patch for the names of soil types.
show.grid Logical - whether to show grid lines at each 10 level of each soil component.
col.axis Color of the triangular axes, ticks and labels.
col.lines Color of the boundary lines. Defaults to gray.
col.grid Color of the grid lines. Defaults to gray.
lty.grid Type of line for the grid. Defaults to dashed.
show.legend Logical - whether to display a legend.
label.points Logical - whether to call thigmophobe.labels to label the points.
soil.texture 181

point.labels Optional labels for the points or legend.

col.symbols Color of the symbols representing each value.
pch Symbols to use in plotting values.
... Additional arguments passed to triax.points and then ‘points’.

Details
‘soil.texture’ displays a triangular plot area on which soil textures defined as proportions of
sand, silt and clay can be plotted. Optional grid, vertex labels, soil type divisions and names may
also be displayed. If a matrix of soil textures is present, these will be plotted.

Value
If ‘soiltexture’ was included, a list of the ‘x,y’ positions of the soil types plotted. If not, nil.

Note
This is now a special case of ‘triax.plot’.

Author(s)
Sander Oom, Jim Lemon, and Michael Toews

References
U.S. Department of Agriculture, Natural Resources Conservation Service, 2007. National Soil Sur-
vey Handbook, title 430-VI.// http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/
survey/class/taxonomy/?cid=nrcs142p2_053577
U.S. Department of Agriculture, Natural Resources Conservation Service, 2007. Soil Texture Calcu-
lator// http://www.nrcs.usda.gov/wps/portal/nrcs/detail/soils/survey/class/taxonomy/
?cid=nrcs142p2_053577

See Also
get.soil.texture, triax.plot

Examples
data(soils)
soil.texture(main="NO DATA")
soil.texture(soils, main="DEFAULT", pch=2)
soil.texture(soils, main="LINES AND NAMES", show.lines=TRUE,
show.names=TRUE, pch=3)
soiltex.return<-soil.texture(soils[1:6,], main="GRID AND LEGEND",
show.grid=TRUE, pch=4, col.symbols=1:6, show.legend=TRUE)
par(soiltex.return$oldpar)
182 soil.texture.uk

soil.texture.uk Soil texture triangle plot using UK conventions

Description
Display a UK style soil texture triangle with optional grid, labels and soil texture points.

Usage
soil.texture.uk(soiltexture = NULL, main = "",at = seq(0.1, 0.9, by = 0.1),
axis.labels = c("percent sand", "percent silt", "percent clay"),
tick.labels = list(l = seq(10, 90, by = 10), r = seq(10, 90, by = 10),
b = seq(10, 90, by = 10)), show.names = TRUE,
show.lines = TRUE, col.names = "gray", bg.names = par("bg"),
show.grid = FALSE, col.axis = "black", col.lines = "gray",
col.grid = "gray", lty.grid = 3, show.legend = FALSE, label.points = FALSE,
point.labels = NULL, col.symbols = "black", pch = par("pch"),
h1 = NA, h3 = NA, t1 = NA, t3 = NA, lwduk = 2, xpos = NA, ypos = NA,
snames = NA, cexuk = 1.1, ...)

Arguments
soiltexture Matrix of soil textures where each row is a soil sample and three columns con-
taining the percentages of the components sand, silt and clay in the range 0 to
100.
main The title of the soil texture plot. Defaults to nothing.
at Positions on the three axes where ticks will be drawn.
axis.labels Labels for the axes.
tick.labels The tick labels for the three axes.
show.names Logical - whether to show the names of different soil types within the soil trian-
gle.
show.lines Logical - whether to show the boundaries of the different soil types within the
soil triangle.
col.names Color of the soil names. Defaults to gray.
bg.names Color to use when drawing a blank patch for the names of soil types.
show.grid Logical - whether to show grid lines at each 10 level of each soil component.
col.axis Color of the triangular axes, ticks and labels.
col.lines Color of the boundary lines. Defaults to gray.
col.grid Color of the grid lines. Defaults to gray.
lty.grid Type of line for the grid. Defaults to dashed.
show.legend Logical - whether to display a legend.
label.points Logical - whether to call thigmophobe.labels to label the points.
soil.texture.uk 183

point.labels Optional labels for the points or legend.

col.symbols Color of the symbols representing each value.
pch Symbols to use in plotting values.
h1,h3,t1,t3 Points used in drawing boundaries for soil types.
lwduk Line width for the boundaries
xpos,ypos Positions for the soil type labels.
snames Soil type labels.
cexuk Character expansion for the soil type labels.
... Additional arguments passed to triax.points and then ‘points’.

Details
‘soil.texture.uk’ displays a triangular plot area on which soil textures defined as proportions of
sand, silt and clay can be plotted. It is similar to the ‘soil.texture’ function but uses the UK
display conventions.

Value
If ‘soiltexture’ was included, a list of the ‘x,y’ positions of the soil types plotted. If not, nil.

Author(s)
Julian Stander

See Also
triax.plot

Examples
soils.sw.percent<-data.frame(
Sand=c(67,67,66,67,36,25,24,59,27,9,8,8,20,
45,50,56,34,29,39,41,94,98,97,93,96,99),
Silt=c(17,16,9,8,39,48,54,27,46,70,68,68,66,
34,30,24,48,53,46,48,2,2,2,4,1,1),
Clay=c(16,17,25,25,25,27,22,14,27,21,24,24,
14,21,20,20,18,18,15,11,4,0,1,3,3,0))
soils.sw.cols <- c(1, 1, 1, 1, 2, 2, 2, 2, 2, 3, 3,
3, 3, 4, 4, 4, 5, 5, 5, 5, 6, 6, 6, 6, 6, 6)
soils.sw.names <- c("Ardington","Astrop","Atrim",
"Banbury","Beacon","Beckfoot")
soil.texture.uk(soils.sw.percent,
main = "Ternary Diagram for Some Soils from South West England",
col.lines = "black", col.names = "black", show.grid = TRUE,
col.grid = "blue", lty.grid = 2, pch = 16, cex = 1.0,
col.symbols = soils.sw.cols, h1 = NA, h3 = NA, t1 = NA,
t3 = NA , lwduk = 2, xpos = NA, ypos = NA,
snames = NA, cexuk = 1.1)
legend("topleft", legend = soils.sw.names, col = 1:max(soils.sw.cols),
pch = 16, cex = 1.1, title = "Location", bty = "n")
184 spread.labels

soils Soil texture data from 125 soils

Description
A set of 125 soil texture measurements from soils from various parts of the world.

Usage
data(soils)

Source
T.H. Skaggs, L.M. Arya, P.J. Shouse and B.P. Mohanty (2001) Estimating Particle-Size Distribution
from Limited Soil Texture Data. Soil Science Society of America Journal 65:1038-1044.

spread.labels Spread labels for irregularly spaced values

Description
Places labels for irregularly spaced values in a regular staggered order

Usage
spread.labels(x,y,labels=NULL,ony=NA,offsets=NA,between=FALSE,
linecol=par("fg"),srt=0,...)

Arguments
x,y x and y data values
labels text strings
ony Whether to force the labels to be spread horizontally (FALSE) or vertically
(TRUE). Defaults to whichever way the points are most spread out.
offsets How far away from the data points to place the labels. Defaults to one quarter
of the plot span for all, staggered on each side.
between Whether to place the labels between two sets of points.
linecol Optional colors for the lines drawn to the points.
srt Rotation of the labels in degrees.
... additional arguments passed to ‘text’.
spread.labels 185

Details
This function is mainly useful when labeling irregularly spaced data points that are "spread out"
along one dimension. It places the labels regularly spaced and staggered on the long dimension of
the data, drawing lines from each label to the point it describes.
If ‘between’ is TRUE, the function expects two points for each label and will attempt to place the
labels between two vertical lines of points. Lines will be drawn from the ends of each label to the
two corresponding points.
If spreading labels horizontally, the user may wish to rotate the labels by 90 degrees (‘srt=90’). If
long labels run off the edge of the plot, increase the ‘xlim’ for extra room.

Value
nil

Author(s)
Jim Lemon

References
Cooke, L.J. & Wardle, J. (2005) Age and gender differences in children’s food preferences. British
Journal of Nutrition, 93: 741-746.

See Also
‘text’, ‘spread.lab (TeachingDemos)’

Examples
# spread labels out in the x dimension using defaults
x<-sort(rnorm(10))
y<-rnorm(10)/10
plot(x,y,ylim=c(-1,1),type="p")
nums<-c("one","two","three","four","five","six","seven","eight","nine","ten")
spread.labels(x,y,nums)
# food preferences of children by sex (Cooke & Wardle, 2005)
fpkids<-data.frame(Food=c("Fatty/sugary","Fruit","Starchy","Meat",
"Proc.meat","Eggs","Fish","Dairy","Vegetables"),
Female=c(4.21,4.22,3.98,3.57,3.55,3.46,3.34,3.26,3.13),
Male=c(4.35,4.13,4.02,3.9,3.81,3.64,3.45,3.27,2.96))
plot(rep(1,9),fpkids$Female,xlim=c(0.8,2.2),
ylim=range(c(fpkids$Female,fpkids$Male)),xlab="Sex",xaxt="n",
ylab="Preference rating",main="Children's food preferences by sex",
col="red")
axis(1,at=1:2,labels=c("Female","Male"))
points(rep(2,9),fpkids$Male,col="blue",pch=2)
spread.labels(rep(1:2,each=9),c(fpkids$Female,fpkids$Male),
fpkids$Food,between=TRUE,linecol=c("red","blue"))
186 spreadout

spreadout Spread out a vector of numbers to a minimum interval

Description
Spread out a vector of numbers so that there is a minimum interval between any two numbers when
in ascending or descending order.

Usage
spreadout(x,mindist)

Arguments
x A numeric vector which may contain NAs.
mindist The minimum interval between any two values when in ascending or descending
order.

Details
‘spreadout’ starts at or near the middle of the vector and increases the intervals between the ordered
values. NAs are preserved. ‘spreadout’ first tries to spread groups of values with intervals less than
‘mindist’ out neatly away from the mean of the group. If this doesn’t entirely succeed, a second
pass that forces values away from the middle is performed.
‘spreadout’ is currently used to avoid overplotting of axis tick labels where they may be close
together.

Value
On success, the spread out values. If there are less than two valid values, the original vector is
returned.

Author(s)
Jim Lemon

Examples
spreadout(c(1,3,3,3,3,5),0.2)
spreadout(c(1,2.5,2.5,3.5,3.5,5),0.2)
spreadout(c(5,2.5,2.5,NA,3.5,1,3.5,NA),0.2)
# this will almost always invoke the brute force second pass
spreadout(rnorm(10),0.5)
stackpoly 187

stackpoly Display the columns of a matrix or data frame as stacked polygons

Description

Plot one or more columns of numeric values as the top edges of polygons instead of lines.

Usage

stackpoly(x,y=NULL,main="",xlab="",ylab="",xat=NA,xaxlab=NA,
xlim=NA,ylim=NA,lty=1,lwd=1,border=NA,col=NULL,staxx=FALSE,stack=FALSE,
axis2=TRUE,axis4=TRUE,padj=0,...)

Arguments

x A numeric data frame or matrix with the ‘x’ values. If ‘y’ is NULL, these
will become the ‘y’ values and the ‘x’ positions will be the integers from 1 to
dim(x)[1].
y The ‘y’ values.
main The title for the plot.
xlab,ylab x and y axis labels for the plot.
xat Where to put the optional xaxlabs.
xaxlab Optional labels for the x positions.
xlim Optional x limits.
ylim Optional y limits.
lty Line type for the polygon borders.
lwd Line width for the polygon borders.
border Color for the polygon borders.
col Color to fill the polygons. If NULL, ‘rainbow’ will be called to generate the
colors. If NA, the polygons will not be filled.
staxx Whether to call ‘staxlab’ to stagger the x axis labels.
stack Whether to stack the successive values on top of each other.
axis2 Whether to display the left ordinate on the plot.
axis4 Whether to display the right ordinate on the plot.
padj Vertical justfication of the x axis labels, defaulting to "top". Can be a vector with
an element for each label.
... Additional arguments passed to ‘plot’.
188 stackpoly

Details

‘stackpoly’ is similar to a line plot with the area under the lines filled with color(s). Ideally, each
successive set of y values is greater than the values in the previous set so that the polygons form
a rising series of crests. If ‘stack’ is TRUE, this is not a problem unless some values of ‘x’ are
negative.
If ‘x’ or ‘y’ is a vector, not a matrix or list, the values will be displayed as a "waterfall plot".
The options for ‘axis2’ and ‘axis4’ can be used to produce panel plots. See the last example.

Value

nil

Author(s)

Jim Lemon and Thomas Petzoldt (waterfall plot option) - thanks to Phil Novack-Gottshall for the
mismatched x and y fix

See Also

polygon

Examples

testx<-matrix(abs(rnorm(100)),nrow=10)
stackpoly(matrix(cumsum(testx),nrow=10),main="Test Stackpoly I",
xaxlab=c("One","Two","Three","Four","Five",
"Six","Seven","Eight","Nine","Ten"),border="black",staxx=TRUE)
stackpoly(testx,main="Test Stackpoly II",
xaxlab=c("One","Two","Three","Four","Five",
"Six","Seven","Eight","Nine","Ten"),border="black",
staxx=TRUE,stack=TRUE)
layout(matrix(1:2,nrow=1))
oldmar<-par(mar=c(5,4,4,0))
stackpoly(rev(sort(testx-mean(testx))),
main="Waterfall Plot (x-mean)",xat=seq(10,90,by=10),
xlab="Index",ylab="Value",lwd=3,col="green",border="black",
axis4=FALSE)
ylim<-par("usr")[3:4]
par(mar=c(5,0,4,4))
stackpoly(rev(sort((testx-mean(testx))/sd(as.vector(testx)))),
ylim=ylim,main="Waterfall Plot ((x-mean)/sd)",xat=seq(10,90,by=10),
xlab="Index",lwd=3,col="lightblue",border="black",axis2=FALSE)
par(oldmar)
staircase.plot 189

staircase.plot Display a staircase plot

Description

Displays a plot showing a sequence of changing totals and increments as successive linked bars.

Usage

staircase.plot(heights,totals=NA,labels=NULL,halfwidth=0.3,main="",
mar=NA,total.col="blue",inc.col=NA,bg.col=NA,direction="e",las=1,
display.height=TRUE,stagger=FALSE,cex=par("cex"),prefix="",suffix="",...)

Arguments

heights vector of numeric values or a matrix or data frame with at least two columns.
The first column must be numeric and the second may be numeric or logical.
totals A vector of logicals or zero/non-zero values indicating whether the correspond-
ing height is a total (TRUE) or an increment (FALSE).
labels An optional vector of labels for the bars.
halfwidth Half of the width of a bar as a proportion. See Details.
main A title for the plot.
mar Margins for the plot. Defaults to 10 on the baseline axis, 3 on the top and 1 on
the other two sides.
total.col Color(s) for the bars representing successive totals.
inc.col Color(s) for the bars representing increments.
bg.col The background color for the plot.
direction Direction in which the bars should be presented. See Details.
las Orientation for the bar labels. See ‘par’.
display.height Whether to display the totals and increments at the upper ends of the bars. De-
faults to TRUE.
stagger Whether to stagger the labels to avoid overlap.
cex The usual character expansion value.
prefix A prefix to the numbers displayed next to the bars (e.g. $).
suffix A suffix as for prefix (e.g. %).
... arguments passed to ‘plot’.
190 staircase.plot

Details

Displays a plot representing successive changes in counts or values. For example, if a research
study attempts to contact a certain number of people and some cannot be contacted, some decline
to participate, some are ineligible, the final sample will be smaller than the initial contact list. The
first value will be the total of attempts, there will be a number of decrements, and the last value will
be the actual sample. There may be intermediate totals specified. This produces a visual display of
the sampling procedure. See the example.
The bars are placed at integer values on the axis representing the succession of counts or values. The
width of the bars is determined by the argument ‘halfwidth’. This defaults to 0.3, meaning that
the bar extends 0.3 to each side, so that the proportion of bar to space is 0.6 to 0.4. The succession
of bars is determined by the ‘direction’ argument. The default is "e" (east), meaning that the first
bar is at the left of the plot and subsequent bars are placed to the right. The other three possibilities
follow the conventional compass layout.
The ‘prefix’ and ‘suffix’ arguments allow the user to specify units for the numbers displayed
next to the bars. If a single value is passed, all numbers will get the same prefix or suffix. Different
prefixes or suffixes for each number can be passed as vectors.
The ‘getFigCtr’ function is called to center the plot title in the figure region as the plot area is
typically off center.

Value

nil

Author(s)

Jim Lemon

See Also

plot, getFigCtr

Examples

sample_size<-c(500,-72,428,-94,334,-45,289)
totals<-c(TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE)
labels<-c("Contact list","Uncontactable","","Declined","","Ineligible",
"Final sample")
staircase.plot(sample_size,totals,labels,
main="Acquisition of the sample (staircase.plot)",
total.col="gray",inc.col=2:4,bg.col="#eeeebb",direction="s")
staircasePlot 191

staircasePlot Display a staircase plot

Description

Displays a plot showing a sequence of changing totals and increments as successive linked bars.

Usage

staircasePlot(heights,totals=NA,labels=NULL,halfwidth=0.3,main="",mar=NA,
stair.info=list(total.col="blue",inc.col=NA,border=par("fg")),bg.col=NA,
direction="e",las=1,display.height=TRUE,stagger=FALSE,cex=par("cex"),
prefix="",suffix="",...)

Arguments

heights vector of numeric values or a matrix or data frame with at least two columns.
The first column must be numeric and the second may be numeric or logical.
totals A vector of logicals or zero/non-zero values indicating whether the correspond-
ing height is a total (TRUE) or an increment (FALSE).
labels An optional vector of labels for the bars.
halfwidth Half of the width of a bar as a proportion. See Details.
main A title for the plot.
mar Margins for the plot. Defaults to 10 on the baseline axis, 3 on the top and 1 on
the other two sides.
stair.info A list of arguments for the bars including color(s) for the bars representing suc-
cessive totals, and increments and the border color.
bg.col The background color for the plot.
direction Direction in which the bars should be presented. See Details.
las Orientation for the bar labels. See ‘par’.
display.height Whether to display the totals and increments at the upper ends of the bars. De-
faults to TRUE.
stagger Whether to stagger the labels to avoid overlap.
cex The usual character expansion value.
prefix A prefix to the numbers displayed next to the bars (e.g. $).
suffix A suffix as for prefix (e.g. %).
... arguments passed to ‘plot’.
192 staircasePlot

Details

Displays a plot representing successive changes in counts or values. For example, if a research
study attempts to contact a certain number of people and some cannot be contacted, some decline
to participate, some are ineligible, the final sample will be smaller than the initial contact list. The
first value will be the total of attempts, there will be a number of decrements, and the last value will
be the actual sample. There may be intermediate totals specified. This produces a visual display of
the sampling procedure. See the example.
The bars are placed at integer values on the axis representing the succession of counts or values. The
width of the bars is determined by the argument ‘halfwidth’. This defaults to 0.3, meaning that
the bar extends 0.3 to each side, so that the proportion of bar to space is 0.6 to 0.4. The succession
of bars is determined by the ‘direction’ argument. The default is "e" (east), meaning that the first
bar is at the left of the plot and subsequent bars are placed to the right. The other three possibilities
follow the conventional compass layout.
The ‘prefix’ and ‘suffix’ arguments allow the user to specify units for the numbers displayed
next to the bars. If a single value is passed, all numbers will get the same prefix or suffix. Different
prefixes or suffixes for each number can be passed as vectors.
The ‘getFigCtr’ function is called to center the plot title in the figure region as the plot area is
typically off center.

Value

nil

Author(s)

Jim Lemon

See Also

plot, getFigCtr

Examples

sample_size<-c(500,-72,428,-94,334,-45,289)
totals<-c(TRUE,FALSE,TRUE,FALSE,TRUE,FALSE,TRUE)
labels<-c("Contact list","Uncontactable","","Declined","","Ineligible",
"Final sample")
staircasePlot(sample_size,totals,labels,
main="Acquisition of the sample (staircasePlot)",
total.col="gray",inc.col=2:4,bg.col="#eeeebb",direction="s")
starPie 193

starPie A pie-like graphic object

Description
Display a polygon with each sector proportional to a vector of numeric values.

Usage
starPie(x,y,radext,values,maxval=NA,border=par("fg"),col=NA,prop.area=FALSE,
label="",labelpos=1)

Arguments
x,y The coordinate position for the center of the starPie.
radext The maximum distance from the center of the starPie to one vertex of the poly-
gon.
values A vector of numeric values.
maxval A maximum value for scaling the values to the radius. If NA, the maximum
value in ‘values’ will be used.
border The color to use for the borders of the polygon sectors.
col The color(s) to use for the fills of the polygon.
prop.area Whether to scale the values to the area (TRUE) or the radial extent (FALSE) of
the polygon sectors.
label Optional text labels for the starPies.
labelpos Positions of the labels relative to the starPies.

Details
‘starPie’ displays a polygon centered on the ‘x,y’ position having sectors of equal angular ex-
tent. The radial extent of each sector is proportional to the values in the numeric vector ‘lengths’.
If the ‘prop.area’ argument is TRUE, the proportion is based on the area of the sector, and if
‘prop.area’ is FALSE, the proportion is on the radial extent. As the function is intended to ex-
aggerate the differences between different starPies, the default produces sectors proportional to the
squares of the ‘lengths’.
‘starPie’ is intended to display a visual analog of the relative value of matched attributes of a
number of similar objects or groups. Thus objects having similar attributes will produce similar
looking starPies. When constructing such a matrix, it is necessary for ‘maxval’ to be specified,
usually as the overall maximum value in any of the attribute value vectors. If ‘maxval’ is not
specified in such a situation, only the relative values within each vector will determine the radial
extents of each starPie. There appears to be no reason to have different sector colors for different
objects, but the user can display more than one set of starPies on a plot with different sector colors
if necessary.
‘starPie’ calls ‘getYmult’ to automatically adjust for both the aspect and coordinate ratio of the
plot.
194 staxlab

Value
nil

Author(s)
Jim Lemon

Examples
date_mat<-data.frame(sex=rep(c("M","F"),each=10),
names=c("Abe","Bob","Col","Dave","Eddie","Frank","Geoff","Harry","Igor","Jack",
"Alice","Betty","Clare","Dora","Eva","Fran","Grace","Hilda","Iris","Joan"),
eating=sample(0:100,20),dancing=sample(0:100,20),movies=sample(0:100,20),
reading=sample(0:100,20),travel=sample(0:100,20))
plot(0,xlim=c(0.5,10.5),ylim=c(0,3),type="n",axes=FALSE,xlab="",ylab="Sex",
main="Date matching matrix")
par(xpd=TRUE)
legend(0.7,-0.3,c("Eat out","Dance","Movies","Read","Travel"),fill=rainbow(5),
ncol=5)
par(xpd=FALSE)
box()
axis(2,at=c(0.9,2.4),labels=c("Male","Female"))
starPie(x=rep(1:10,2),y=rep(c(0.9,2.4),each=10),radext=0.5,
values=as.matrix(date_mat[,3:7]),label=as.character(date_mat[["names"]]))

staxlab Place staggered or angled labels on an axis

Description
Places labels on an axis in a regular staggered order or at an angle

Usage
staxlab(side=1,at,labels,nlines=2,top.line=0.5,line.spacing=0.8,
srt=NA,ticklen=0.03,adj=1,...)

Arguments
side axis on which to place the labels, as in ‘axis’
at where to place the labels in user units, as in ‘axis’
labels text strings
nlines How many lines to use to stagger the labels.
top.line Distance from the axis to place the first line of text.
line.spacing Spacing between lines of text labels.
srt Text rotation.
std.error 195

ticklen Proportion of plot height in user units to place text below the plot.
adj horizontal adjustment of the labels.
... Additional arguments to be passed to ‘mtext’ or ‘text’.

Value
nil

Note
This function is mainly useful when either long axis labels or a large number of labels are to be
placed without overlapping. It staggers the labels along the axis specified. The user may wish to
increase the space beneath the plot using ‘mar’ before calling ‘staxlab’. It is probably only useful
on the bottom or left side of the plot.
If ‘srt’ is not NA, the labels will be rotated ‘srt’ degrees and placed below the plot. This method
will only place labels at the bottom. Note that this option only works on the lower and left axes.

Author(s)
Jim Lemon (thanks to Tim Elwell-Sutton for the log axis fix)

See Also
mtext

Examples
x<-rnorm(12)
plot(x,axes=FALSE)
box()
months<-c("January","February","March","April","May","June",
"July","August","September","October","November","December")
staxlab(1,1:12,months)
plot(x,axes=FALSE)
box()
staxlab(1,1:12,months,srt=45)
ylabels<-round(seq(min(x),max(x),length.out=10),3)
staxlab(2,ylabels,ylabels,srt=45)

std.error Calculate standard error of the mean

Description
Calculates the standard error of the mean.

Usage
std.error(x,na.rm)
196 sumbrk

Arguments
x A vector of numerical observations.
na.rm Dummy argument to match other functions.

Details
‘std.error’ will accept a numeric vector.

Value
The conventional standard error of the mean = sd(x)/sqrt(sum(!is.na(x)))

Author(s)
Jim Lemon

See Also
sd

sumbrk Count specified values in a vector

Description
Counts the number of values in a vector that are equal to a specified value.

Usage
sumbrk(x,trueval=TRUE,na.rm=TRUE)

Arguments
x a character, factor or numeric vector.
trueval the value to be matched in ‘x’.
na.rm whether to remove NA values.

Details
‘sumbrk’ counts the values in ‘x’ matching a specified value. It is mainly to allow these sums to be
calculated in the ‘brkdnNest’ function.

Value
nil
sumDendrite 197

Author(s)
Jim Lemon

See Also
brkdnNest

Examples
sumbrk(sample(LETTERS,100,TRUE),trueval="M")

sumDendrite Sum the counts in the top level of a dendrite object

Description
Find the sum of the counts that are the first elements of each list in the top level of a dendrite object.

Usage
sumDendrite(x)

Arguments
x A list with a numeric value as the first element in each of its toplevel elements.

Details
A ‘dendrite’ object is a possibly nested list of lists that contain the counts and pointers to sublists
in each list. Such an object describes the attributes of objects that can take on mutually exclusive
attributes (that is, belong to disjunct sets). ‘sumDendrite’ is a convenience function to get the total
number of objects that are so classified.

Value
The sum of the counts in the top level of lists.

Author(s)
Jim Lemon

See Also
plot.dendrite
198 symbolbarplot

symbolbarplot barplot filled with symbols

Description
Produces a barplot where each piece of the barplot is filled with the number of symbols equal to the
size of the bar

Usage
symbolbarplot(height,width=1,space=NULL,names.arg=NULL,
legend.text=NULL,beside=FALSE,horiz=FALSE,col=heat.colors(NR),
border=par("fg"),main=NULL,sub=NULL,xlab=NULL,ylab=NULL,xlim=NULL,
ylim=NULL,axes=TRUE,axisnames=TRUE,inside=TRUE,plot=TRUE,rel.width=0.8,
symbol="circles",symbbox=TRUE,debug=FALSE,...)

Arguments
height numeric vector or matrix of barplot heights
width width of bars
space space between bars
names.arg vector of names
legend.text vector of legend text
beside (logical) plot bars beside each other?
horiz (logical) horizontal barplot?
col vector of colors
border plot border?
main main title
sub subtitle
xlab x axis label
ylab y axis label
xlim x limits
ylim y limits
axes draw axes?
axisnames label horizontal axis?
inside draw lines dividing adjacent bars?
plot produce plot?
rel.width relative width of symbols
symbol which symbol to use
symbbox draw boxes for symbol boxes?
debug debug output?
... further arguments to multsymbolbox
symbolbox 199

Value
Nil

Note
This is a mostly a hack of barplot()

Author(s)
Ben Bolker

Examples
set.seed(1001)
bvals <- matrix(rpois(12,20),nrow=3)
b <- symbolbarplot(bvals)

symbolbox Draw a box filled with symbols

Description
Draws a box on the current figure that is filled with symbols representing individual counts

Usage
symbolbox(x1,y1,x2,y2,tot,relw=0.5,fg=par("fg"),bg=par("bg"),box=TRUE,
debug = TRUE,...)

Arguments
x1 left side of box
y1 bottom side of box
x2 right side of box
y2 top side of box
tot total number of symbols to put in the box
relw relative width (relative to height) of symbols
fg foreground color
bg background color
box (logical) draw box border?
debug debug output?
... additional arguments to polygon() for drawing box
200 tab.title

Details
tries to automatically figure out appropriate scaling to fit symbols into the box

Value
none; draws on the current figure

Author(s)
Ben Bolker

See Also
multsymbolbox

Examples
plot(1:10,1:10,type="n")
symbolbox(2,5,3,7,tot=20)
symbolbox(6,2,10,6,tot=50,fg="blue",bg="magenta")

tab.title Display the title of a plot as a colored tab

Description
Display the title of a plot as a colored tab.

Usage
tab.title(label,text.col=par("fg"),tab.col=par("bg"),border=par("fg"),
lwd=par("lwd"),cex=1.5,pad.mult=1.6,radius=0)

Arguments
label The title for the plot.
text.col The color for the title text.
tab.col The color for the tab fill.
border The color for the tab border.
lwd The line width for the border.
cex Character expansion for the title.
pad.mult How much higher to make the tab relative to the label.
radius What proportion of the tab corners to round off.
taylor.diagram 201

Details
‘tab.title’ displays the plot title in a colored tab. The tab can be rounded at the upper corners by
specifying the proportion of the tab height to be rounded as a number between 0 and 1. If the tab is
too high to fit on the figure region, a warning will be displayed and the tab will still be shown.

Value
nil

Author(s)
Jim Lemon

See Also
polygon

Examples
testx<-matrix(cumsum(rnorm(30)^2)+1,nrow=10)
stackpoly(testx,main="",
xaxlab=c("One","Two","Three","Four","Five",
"Six","Seven","Eight","Nine","Ten"),staxx=TRUE)
tab.title("Three Squiggly Lines",tab.col="yellow",radius=0.5)

taylor.diagram Taylor diagram

Description
Display a Taylor diagram

Usage
taylor.diagram(ref,model,add=FALSE,col="red",pch=19,pos.cor=TRUE,
xlab="",ylab="",main="Taylor Diagram",show.gamma=TRUE,ngamma=3,
gamma.col=8,sd.arcs=0,ref.sd=FALSE,sd.method="sample",
grad.corr.lines=c(0.2,0.4,0.6,0.8,0.9),
pcex=1,cex.axis=1,normalize=FALSE,mar=c(5,4,6,6),...)

Arguments
ref numeric vector - the reference values.
model numeric vector - the predicted model values.
add whether to draw the diagram or just add a point.
col the color for the points displayed.
pch the type of point to display.
202 taylor.diagram

pos.cor whether to display only positive (‘TRUE’) or all values of correlation (‘FALSE’).
xlab,ylab plot axis labels.
main title for the plot.
show.gamma whether to display standard deviation arcs around the reference point (only for
‘pos.cor=TRUE’).
ngamma the number of gammas to display (default=3).
gamma.col color to use for the gamma arcs (only with pos.cor=TRUE).
sd.arcs whether to display arcs along the standard deviation axes (see Details).
ref.sd whether to display the arc representing the reference standard deviation.
sd.method Whether to use the sample or estimated population SD.
grad.corr.lines
the values for the radial lines for correlation values (see Details).
pcex character expansion for the plotted points.
cex.axis character expansion for the axis text.
normalize whether to normalize the models so that the reference has a standard deviation
of 1.
mar margins - only applies to the ‘pos.cor=TRUE’ plot.
... Additional arguments passed to ‘plot’.

Details
The Taylor diagram is used to display the quality of model predictions against the reference values,
typically direct observations.
A diagram is built by plotting one model against the reference, then adding alternative model points.
If ‘normalize=TRUE’ when plotting the first model, remember to set it to ‘TRUE’ when plotting
additional models.
Two displays are available. One displays the entire range of correlations from -1 to 1. Setting
‘pos.cor’ to ‘FALSE’ will produce this display. The -1 to 1 display includes a radial grid for the
correlation values. When ‘pos.cor’ is set to ‘TRUE’, only the range from 0 to 1 will be displayed.
The ‘gamma’ lines and the arc at the reference standard deviation are optional in this display.
Both the standard deviation arcs and the gamma lines are optional in the ‘pos.cor=TRUE’ version.
Setting ‘sd.arcs’ or ‘grad.corr.lines’ to zero or FALSE will cause them not to be displayed. If
more than one value is passed for ‘sd.arcs’, the function will try to use the values passed, otherwise
it will call ‘pretty’ to calculate the values.

Value
The values of ‘par’ that preceded the function. This allows the user to add points to the diagram,
then restore the original values. This is only necessary when using the 0 to 1 correlation range.

Author(s)
Olivier Eterradossi with modifications by Jim Lemon
textbox 203

References
Taylor, K.E. (2001) Summarizing multiple aspects of model performance in a single diagram. Jour-
nal of Geophysical Research, 106: 7183-7192.

Examples
# fake some reference data
ref<-rnorm(30,sd=2)
# add a little noise
model1<-ref+rnorm(30)/2
# add more noise
model2<-ref+rnorm(30)
# display the diagram with the better model
oldpar<-taylor.diagram(ref,model1)
# now add the worse model
taylor.diagram(ref,model2,add=TRUE,col="blue")
# get approximate legend position
lpos<-1.5*sd(ref)
# add a legend
legend(lpos,lpos,legend=c("Better","Worse"),pch=19,col=c("red","blue"))
# now restore par values
par(oldpar)
# show the "all correlation" display
taylor.diagram(ref,model1,pos.cor=FALSE)
taylor.diagram(ref,model2,add=TRUE,col="blue")

textbox Add text box

Description
Add text to plot, justified, in a box

Usage
textbox(x, y, textlist, justify=c('l','c','r'), cex=1, leading=0.5, box=TRUE,
adj=c(0,0), font=NULL, vfont=NULL, col=NULL, border=NULL, fill=NA, density=NULL,
angle=45, lty=par("lty"), lwd=par("lwd"), margin=0)

Arguments
x x position: a vector with min. and max. x-position
y y position: location of the top of the box
textlist a vector of text strings
justify x alignment: ’l’=left, ’c’=center, ’r’=right.
cex character expansion
leading inter-line spacing
204 textbox

box whether to draw a box around the text

adj adjustment for x and y position, default is no adjustment, see Details
font text font, see Details
vfont text font, see Details
col text color
border box border color
fill box fill color
density box shading line density, see Details
angle box shading line angle, see Details
lty box border and shading line types, see Details
lwd box border and shading line width, see Details
margin amount to adjust box border in or out. See Details

Details
Draws text in the box by pasting the textlist vector together, splitting it into words, and then adding
words to the current line until the line is wide enough before moving on to the next line.
‘margin’ may be a vector of 1, 2, or 4 values, corresponding to adjustment of all borders (1 value),
top/bottom and left/right borders (2 values), or bottom/left/top/right borders (4 values). A positive
value moves text inwards from specified (x,y) position with border remaining at (x,y), and a negative
value moves the border outwards from (x,y) with the text remaining at (x,y).
The ‘density’ and ‘angle’ arguments have the same behavior as in the ‘rect’ function. The
‘adj, font’ and vfont arguments have the same behavior as in the ‘text’ function. The ‘lty’ and
‘lwd’ arguments have the same behavior as in the ‘lines’ function.

Value
y-position of bottom line of box, or y-position of next line if there is no box.

Author(s)
Ben Bolker. Improvements by Ted Toal.

Examples
plot.new()
textbox(c(0,0.2), 1, c("many words","more words","why not?",
"keep going",rep("and going",10)))
textbox(c(0.3,0.5), 1, c("keep going",rep("and going",10)), cex=0.45,
col="blue", border="red", fill="#00FFEE80", density=25, angle=60)
textbox(c(0.6,0.8), 1, c("keep going",rep("and going",10)), justify='c', cex=0.6,
leading=1, font=4, border="gold", lty=2, lwd=4, margin=0.025)
textbox(c(0.6,0.8), 0.5, c("keep going",rep("and going",10)), justify='r', cex=0.7,
col="purple", font=3, border="green", margin=-0.025)
lines(c(0,1), c(1,1), col="red", lty=2)
lines(c(0,1), c(0.5,0.5), col="red", lty=2)
thigmophobe 205

thigmophobe Find the direction away from the closest point

Description

Find the direction away from the closest point

Usage

thigmophobe(x,y,plot.span=par("usr"),xlog=par("xlog"),ylog=par("ylog"))

Arguments

x,y Numeric data vectors. Typically the x/y coordinates of plotted points. If arrays
are passed, they will be silently coerced to numeric vectors.
plot.span The extent of the plot in user units.
xlog,ylog Flags for logarithmic axes. See Note.

Details

‘thigmophobe’ returns the direction (as 1|2|3|4 - see pos= in ‘text’) away from the nearest point to
each of the points described by ‘x’ and ‘y’.

Value

A vector of directions away from the point nearest to each point.

Note

‘thigmophobe’ is typically used to get the offset to automatically place labels on a scatterplot or
similar using ‘thigmophobe.labels’ to avoid overlapping labels. The name means "one who fears
being touched".
The ‘plot.span’, ‘xlog’ and ‘ylog’ arguments were added to allow ‘thigmophobe’ to be used
outside of base graphics.

Author(s)

Jim Lemon - thanks to Gustaf Rydevik for the "names" bug fix, Steve Ellison for the suggestion
about arrays and Duncan Murdoch for the additional arguments.

See Also

thigmophobe.labels
206 thigmophobe.labels

Examples
x<-rnorm(10)
y<-rnorm(10)
thigmophobe(x,y)

thigmophobe.labels Place labels away from the nearest point

Description
‘thigmophobe.labels’ places labels adjacent to each point, offsetting each label in the direction
returned by ‘thigmophobe’.

Usage
thigmophobe.labels(x,y,labels=NULL,text.pos=NULL,...)

Arguments
x,y Numeric data vectors or a list with two components. Typically the x/y coordi-
nates of plotted points.
labels A vector of strings that will be placed adjacent to each point. Defaults to the
indices of the coordinates.
text.pos An optional vector of text positions (see text).
... additional arguments are passed to ‘text’.

Details
Typically used to automatically place labels on a scatterplot or similar to avoid overlapping labels.
‘thigmophobe.labels’ will sometimes place a label off the plot or fail to separate labels in clusters
of points. The user can manually adjust the errant labels by running ‘thigmophobe’ first and saving
the returned vector. Then modify the position values to place the labels properly and pass the edited
vector to ‘thigmophobe.labels’ as the ‘text.pos’ argument. This takes precedence over the
positions calculated by ‘thigmophobe’.
‘thigmophobe’ will fail with only two labels, as it can’t figure out the nearest neighbors. If you
really want to use this with two labels, just eyeball the plot and work out in which direction the
labels will go. Then pass the directions to ‘thigmophobe.labels’ as the ‘text.pos’ argument.
When all else fails, look to sampplaceLabels.
Both ‘pointLabel’ in the maptools package and ‘spread.labs’ in the TeachingDemos package
use more sophisticated algorithms to place the labels and are worth a try if ‘thigmophobe’ just
won’t get it right.

Value
A vector of directions away from the point nearest to each point.
triax.abline 207

Author(s)
Jim Lemon (thanks to Stephen Milborrow for finding the single point bug and Erik Aronesty for
finding the two point problem.)

See Also
thigmophobe, text

Examples
x<-rnorm(20)
y<-rnorm(20)
xlim<-range(x)
xspace<-(xlim[2]-xlim[1])/20
xlim<-c(xlim[1]-xspace,xlim[2]+xspace)
ylim<-range(y)
yspace<-(ylim[2]-ylim[1])/20
ylim<-c(ylim[1]-yspace,ylim[2]+yspace)
plotlabels<-
c("one","two","three","four","five","six","seven","eight","nine","ten",
"eleven","twelve","thirteen","fourteen","fifteen","sixteen","seventeen",
"eighteen","nineteen","twenty")
plot(x=x,y=y,xlim=xlim,ylim=ylim,main="Test thigmophobe.labels")
# skip the almost invisible yellow label, make them bold
thigmophobe.labels(x,y,plotlabels,col=c(2:6,8:12),font=2)

triax.abline Lines for triangle plot

Description
Display lines on a triangle plot.

Usage
triax.abline(b=NULL,r=NULL,l=NULL,col=par("col"),lty=par("lty"),
cc.axes=FALSE)

Arguments
b Lines relating to the bottom axis.
r Lines relating to the right axis.
l Lines relating to the left axis.
col Color(s) of the lines.
lty Type(s) of the lines.
cc.axes Clockwise/counterclockwise axes and ticks.
208 triax.fill

Details

‘triax.abline’ displays one or more lines on a triangle plot. Lines are oriented in the conventional
way, horizontal for the left axis, slanting up to the right for the right axis and up to the left for the
bottom axis. If ‘cc.axes’ is TRUE, the orientation is up-left for the left axis, horizontal for the
right axis and up-right for the bottom axis.
Remember to call ‘triax.plot’ with ‘no.add=FALSE’ and restore the graphics parameters as in the
example or the lines will not be placed properly.

Value

nil

Author(s)

Jim Lemon

See Also

triax.plot

Examples
triax.return<-triax.plot(data.frame(bottom=0.4,right=0.3,left=0.3),
main="Triax ablines",no.add=FALSE)
triax.abline(l=0.3,col="red")
triax.abline(r=0.3,col="green")
triax.abline(b=0.4,col="blue")
par(triax.return$oldpar)

triax.fill Triangle plot fill

Description

Fill a triangle plot with smaller triangles.

Usage

triax.fill(col)

Arguments

col List of colors (see Details).

triax.frame 209

Details
In order for ‘triax.fill’ to fill an existing plot that has been created by a call to ‘triax.plot’, the
user must supply a list of fill colors. The first element of the list must begin with at least one value
that can be interpreted as a color. The second element must begin with at least three such values,
and so on, adding two values for each element of the list. Each list element will be displayed as a
row of colored triangles starting at the top of the plot. The number of elements in the list determines
the number of rows that will be displayed.

Value
nil

Author(s)
Jim Lemon

See Also
triax.plot,color.scale

Examples
# the data will be something like response at different proportions
fillval<-list(0,c(0,0.1,0),c(0,0.1,0.2,0.1,0),
c(0,0.1,0.2,0.3,0.2,0.1,0),c(0,0.1,0.2,0.3,0.4,0.3,0.2,0.1,0),
c(0,0.1,0.2,0.3,0.4,0.5,0.4,0.3,0.2,0.1,0),
c(0,0,0.1,0.2,0.3,0.4,0.5,0.4,0.3,0.2,0.1,0,0),
c(0,0,0,0.1,0.1,0.2,0.3,0.4,0.3,0.2,0.1,0.1,0,0,0))
# use some method of converting values to colors
fillcol<-sapply(fillval,function(x) {x*10+1} )
oldpar<-triax.plot(main="Test of triax.fill function")
triax.fill(fillcol)
par(oldpar)

triax.frame Triangle plot frame

Description
Display a three axis frame with optional grid.

Usage
triax.frame(at=seq(0.1,0.9,by=0.1),axis.labels=NULL,
tick.labels=NULL,col.axis="black",cex.axis=1,cex.ticks=1,
align.labels=TRUE,show.grid=FALSE,col.grid="gray",lty.grid=par("lty"),
cc.axes=FALSE)
210 triax.frame

Arguments

at The tick positions on the three axes.

axis.labels Labels for the three axes in the order bottom, right left. Defaults to the column
names.
tick.labels The tick labels for the axes. Defaults to argument ‘at’ (proportions).
col.axis Color of the triangular axes, ticks and labels.
cex.axis Character expansion for axis labels.
cex.ticks Character expansion for the tick labels.
align.labels Logical - whether to align axis and tick labels with the axes.
show.grid Whether to display grid lines at the ticks.
col.grid Color of the grid lines. Defaults to gray.
lty.grid Type of line for the grid.
cc.axes Whether to align the axes clockwise or counterclockwise.

Details

‘triax.frame’ displays a triangular plot area on which proportions or percentages may be dis-
played. An optional grid may also be displayed. If ‘cc.axes’ is TRUE, both the axes and axis ticks
will be in reverse order.

Value

nil

Author(s)

Jim Lemon

See Also

triax.points,triax.abline,triax.fill

Examples

triax.plot(main="DEFAULT")
triax.plot(main="Clockwise axes",cc.axes=TRUE)
triax.plot 211

triax.plot Triangle plot

Description
Display a triangle plot with optional grid.

Usage
triax.plot(x=NULL,main="",at=seq(0.1,0.9,by=0.1),
axis.labels=NULL,tick.labels=NULL,col.axis="black",cex.axis=1,
cex.ticks=1,
align.labels=TRUE,show.grid=FALSE,col.grid="gray",lty.grid=par("lty"),
cc.axes=FALSE,show.legend=FALSE,label.points=FALSE,point.labels=NULL,
col.symbols="black",pch=par("pch"),mar=c(5,2,4,2),no.add=TRUE,...)

Arguments
x Matrix where each row is three proportions or percentages that must sum to 1 or
100 respectively.
main The title of the triangle plot. Defaults to nothing.
at The tick positions on the three axes.
axis.labels Labels for the three axes in the order left, right, bottom. Defaults to the column
names.
tick.labels The tick labels for the three axes as a list with three components l, r and b (left,
right and bottom). Defaults to argument ‘at’ (proportions).
col.axis Color of the triangular axes, ticks and labels.
cex.axis Character expansion for axis labels.
cex.ticks Character expansion for the tick labels.
align.labels Logical - whether to align axis and tick labels with the axes.
show.grid Whether to display grid lines at the ticks.
col.grid Color of the grid lines. Defaults to gray.
lty.grid Type of line for the grid.
cc.axes Whether axes and axis ticks should be clockwise or counterclockwise.
show.legend Logical - whether to display a legend.
label.points Logical - whether to call ‘thigmophobe.labels’ to label the points.
point.labels Optional labels for the points and/or legend.
col.symbols Color of the symbols representing each value.
pch Symbols to use in plotting values.
mar Margins for the triangle plot.
no.add Whether to restore the previous plotting parameters (‘TRUE’) or leave them, al-
lowing more points to be added.
... Additional arguments passed to ‘points’.
212 triax.plot

Details

‘triax.plot’ displays a triangular plot area on which proportions or percentages are displayed. A
grid or legend may also be displayed.

Value

A list containing ‘xypos’ (the ‘x,y’ positions plotted) and ‘oldpar’ (the plotting parameters at the
time ‘triax.plot’ was called).

Note

A three axis plot can only properly display one or more sets of three proportions that each sum to
1 (or percentages that sum to 100). Other values may be scaled to proportions (or percentages), but
unless each set of three sums to 1 (or 100), they will not plot properly and ‘triax.points’ will
complain appropriately. Note also that ‘triax.plot’ will only display properly in a square plot,
which is forced by ‘par(pty="s")’.
In case the user does want to plot values with different sums, the axis tick labels can be set to
different ranges to accomodate this. ‘triax.points’ will still complain, but it will plot the values.
If planning to add points with ‘triax.points’ call ‘triax.plot’ with ‘no.add=FALSE’ and restore
plotting parameters after the points are added.

Author(s)

Jim Lemon - thanks to Ben Daughtry for the info on counterclockwise axes.

See Also

triax.points, triax.abline, thigmophobe.labels

Examples

data(soils)
triax.plot(soils[1:10,],main="DEFAULT")
triax.plot(soils[1:10,],main="PERCENTAGES (Counterclockwise axes)",
tick.labels=list(l=seq(10,90,by=10),r=seq(10,90,by=10),b=seq(10,90,by=10)),
pch=3,cc.axes=TRUE)
triax.return<-triax.plot(soils[1:6,],main="GRID AND LEGEND",
show.grid=TRUE,show.legend=TRUE,col.symbols=1:6,pch=4)
# triax.plot changes a few parameters
par(triax.return$oldpar)
triax.points 213

triax.points Triangle plot points

Description
Display points on a triangle plot.

Usage
triax.points(x,show.legend=FALSE,label.points=FALSE,
point.labels=NULL,col.symbols=par("fg"),pch=par("pch"),
bg.symbols=par("bg"),cc.axes=FALSE,...)

Arguments
x Matrix or data frame where each row is three proportions or percentages that
must sum to 1 or 100 respectively.
show.legend Logical - whether to display a legend.
label.points Logical - whether to call ‘thigmophobe.labels’ to label the points.
point.labels Optional labels for the points and/or legend.
col.symbols Color of the symbols representing each value.
pch Symbols to use in plotting values.
bg.symbols Background color for plotting symbols.
cc.axes Clockwise or counterclockwise axes and ticks.
... Additional arguments passed to ‘points’.

Details
In order for ‘triax.points’ to add points to an existing plot, the argument ‘no.add’ in the initial
call to ‘triax.plot’ must be set to ‘FALSE’. Failing to do this will result in the points being plotted
in the wrong places. It is then up to the user to call ‘par’ as in the example below to restore plotting
parameters altered during the triangle plot.
‘triax.points’ displays each triplet of proportions or percentages as a symbol on the triangle
plot. Unless each triplet sums to 1 (or 100), they will not plot properly and ‘triax.points’ will
complain appropriately.

Value
A list of the ‘x,y’ positions plotted.

Author(s)
Jim Lemon
214 tsxpos

See Also
triax.plot,thigmophobe.labels

Examples
data(soils)
triax.return<-triax.plot(soils[1:10,],
main="Adding points to a triangle plot",no.add=FALSE)
triax.points(soils[11:20,],col.symbols="green",pch=3)
par(triax.return$oldpar)

tsxpos Calculate equispaced x positions.

Description
Calculate equispaced x positions of values that have been plotted with the plot command.

Usage
tsxpos(x,xlim,nint)

Arguments
x A vector of numeric values or a time series object created with the ts function.
xlim Explicit x limits for the x positions.
nint The number of intervals between x positions.

Details
‘tsxpos’ calculates equispaced x positions for a vector of values or a time series created with the
‘ts’ command from the stats package. It assumes that the default x limits have been used in the
existing plot. It adds the appropriate padding if ‘par("xaxs")’ is "r". It is mainly useful when x
axis labels or some other markers are to be added to a time series plot.
A plot device must be open. If the user wishes to specify explicit x limits or the number of intervals
(not values), these will override the calculations from the x values.

Value
The calculated x positions in user units.

Author(s)
Jim Lemon (thanks to Prof J.C. Nash for the idea)
twoord.plot 215

Examples
# create a vector of numbers
y<-rnorm(28)
par(mfrow=c(2,1),mar=c(6,4,4,2))
plot(y,main="Plot of the values")
# convert it into a time series object
yt<-ts(y,start=2011,frequency=12)
# don't use the default axis
plot(yt,main="Plot of the time series",xaxt="n",xlab="Month")
labelpos<-tsxpos(yt)
# display an axis showing the months only
staxlab(1,labelpos,rep(month.abb,length.out=28))
par(mfrow=c(1,1),mar=c(5,4,4,2))

twoord.plot Plot with two ordinates

Description
Two sets of values are displayed on the same plot with different ordinate scales on the left and right.

Usage
twoord.plot(lx,ly,rx,ry,data=NULL,main="",xlim=NULL,lylim=NULL,rylim=NULL,
mar=c(5,4,4,4),lcol=1,rcol=2,xlab="",lytickpos=NA,ylab="",ylab.at=NA,
rytickpos=NA,rylab="",rylab.at=NA,lpch=1,rpch=2,
type="b",xtickpos=NULL,xticklab=NULL,halfwidth=0.4,axislab.cex=1,
do.first=NULL,...)

Arguments
lx,ly,rx,ry y and optional x values for the plot
data an optional data frame from which to obtain the above values
main Title for the plot
xlim optional x limits as in ‘plot’
lylim,rylim optional y limits for the left and right axes respectively
mar optional margin adjustment, defaults to ‘c(5,4,4,4)’
lcol,rcol colors to distinguish the two sets of values
xlab X axis label as in ‘plot’
lytickpos Optional positions for the left axis tick labels.
ylab Left Y axis label as in ‘plot’
ylab.at Optional position for the left Y axis label
rytickpos Optional positions for the right axis tick labels.
rylab Right Y axis label
216 twoord.plot

rylab.at Optional position for the right Y axis label

lpch,rpch plot symbols to distinguish the two sets of values
type as in ‘plot’
xtickpos Optional positions for x-axis tick labels.
xticklab Optional labels for x-axis. Useful for things like dates.
halfwidth Half the width of the bars in user units. The bars are centered on successive
integers if no ‘x’ values are supplied.
axislab.cex Character expansion for the axis labels and tick labels.
do.first Optional command(s) that will be executed immediately after the blank plot is
displayed.
... additional arguments passed to ‘plot’ and ‘points’.

Details
‘twoord.plot’ automates the process of displaying two sets of values that have different ranges on
the same plot. It is principally useful in illustrating some relationship between the values across
the observations. It is assumed that the ‘lx’ and ‘rx’ values are at least adjacent, and probably
overlapping.
It is best to pass all the arguments ‘lx, ly, rx, ry’, but the function will attempt to substitute
sensible x values if one or two are missing.
If at least one of the ‘type’ arguments is "bar", bars will be plotted instead of points or lines. It is
best to plot the bars first (i.e. relative to the left axis) if the other type is points or lines, as the bars
will usually obscure at least some of the points or lines. Using NA for the color of the bars will
partially correct this. If both types are to be bars, remember to pass somewhat different x values or
the bars will be overplotted.
Note that more values can be added to the plot using ‘points’ or ‘lines’, but remember that these
will be plotted relative to the left ordinate.
The ‘do.first’ argument is useful for adding a background color or grid to the plot as shown in
the first two examples.

Value
nil

Note
There are many objections to the use of plots with two different ordinate scales, and some of them
are even sensible and supported by controlled observation. Many of the objections rest on assertions
that the spatial arrangement of the values plotted will override all other evidence. Here are two:
The viewer will assume that the vertical position of the data points indicates a quantitative relation-
ship.
To some extent. It is probably not a good idea to have the spatial relationship of the points opposed
to their numerical relationship. That is to say, if one set of values is in the range of 0-10 and the
other 20-100, it is best to arrange the plot so that the latter values are not plotted below the former.
twoord.plot 217

See the second example, which illustrates a method for separating the two series and offsetting the
axes.
The viewer will assume that an intersection of lines indicates an intersection of values.
If the visual elements representing values can be arranged to avoid intersections, so much the better.
Many people have no trouble distinguishing which visual elements are linked to which axis as long
as they are both coded similarly, usually with colors and/or symbols. In the special case where there
is an underlying relationship between the two such as the probability of that value occurring under
some conditions, it may help to mark the point(s) where this occurs.
It may be useful to consider ‘gap.plot’ or separate plots as an alternative.

Author(s)
Jim Lemon (thanks to Christophe Dutang for the idea of using bars and lines in the same plot, Clair
Crossupton for pointing out that dates on the x-axis weren’t very good, Jacob Kasper for the axis
character expansion and Ye Lin for finally motivating me to add the do.first argument.)

See Also
plot

Examples
xval1 <- seq.Date(as.Date("2017-01-02"),
as.Date("2017-01-10"), by="day")
xval2 <- seq.Date(as.Date("2017-01-01"),
as.Date("2017-01-15"), by="day")
going_up<-seq(3,7,by=0.5)+rnorm(9)
going_down<-rev(60:74)+rnorm(15)
twoord.plot(2:10,going_up,1:15,going_down,xlab="Sequence",
ylab="Ascending values",rylab="Descending values",lcol=4,
main="Plot with two ordinates - points and lines",
do.first="plot_bg();grid(col=\"white\",lty=1)")
axis.Date(1,xval2)
# now separate the lines
twoord.plot(2:10,going_up,1:15,going_down,xlab="Sequence",
lylim=range(going_up)+c(-1,10),rylim=range(going_down)+c(-10,2),
ylab="Ascending values",ylab.at=5,rylab="Descending values",
rylab.at=65,lcol=4,main="Plot with two ordinates - separated lines",
lytickpos=3:7,rytickpos=seq(55,75,by=5),
do.first="plot_bg();grid(col=\"white\",lty=1)")
twoord.plot(2:10,going_up,1:15,going_down,xlab="Sequence",
lylim=range(going_up)+c(-1,10),rylim=range(going_down)+c(-10,2),
type=c("bar","l"),ylab="Ascending values",ylab.at=5,
rylab="Descending values",rylab.at=65,
main="Bars on left axis, lines on right axis",
lytickpos=3:7,rytickpos=seq(55,75,by=5),
lcol=3,rcol=4,do.first="plot_bg()")
twoord.plot(2:10,going_up,1:15,going_down,xlab="Sequence",
lylim=c(-3,8),rylim=c(50,100),type=c("l","bar"),
ylab="Ascending values",rylab="Descending values",
lytickpos=3:7,rytickpos=seq(55,75,by=5),ylab.at=5,rylab.at=65,
218 twoord.stackplot

main="Lines on left axis, bars on right axis",

lcol=3,rcol=4,do.first="plot_bg(\"yellow\")")
# histogram with density curve superimposed
xhist<-hist(rnorm(100),plot=FALSE)
xdens<-dnorm(seq(-3,3,by=0.05))
twoord.plot(xhist$mids,xhist$counts,seq(-3,3,by=0.05),
xdens,type=c("bar","l"),lcol=4,rcol=2,ylab="Counts",
rylab="Density",main="Histogram and density curve",
halfwidth=0.2,lylim=c(0,max(xhist$counts)+1),rylim=c(0,0.45),lwd=2)

twoord.stackplot Multiple (stack) plot with two ordinates

Description
Two set of data are plotted on two different ordinate scales.

Usage
twoord.stackplot(lx, rx, ldata, rdata, lcol, rcol, ltype, rtype,
border, rylab, lylab, xlab, ..., incrylim=NULL,
halfwidth=0.4, leftfront=FALSE, mar = c(5, 4, 4, 4))

Arguments
lx,rx x-values for left/right data.
ldata,rdata data on the left/right y-axes.
lcol, rcol colors to be used for left/right data.
ltype, rtype line types to be used for left/right data, see details.
border color for the border of barplot
rylab,lylab labels for the left/right y-axes.
xlab labels for the x-axis.
... further arguments to be passed to ‘plot’.
incrylim a number to increase the limits of y-axes.
halfwidth half the width of the bars in user units. The bars are centered on successive
integers if no x values are supplied
leftfront if ‘TRUE’, plot the left data on the front layer.
mar optional margin adjustment, defaults to c(5,4,4,4).

Details
‘twoord.stackplot’ works in the same way as ‘twoord.plot’ on which it is heavily inspired. The
functions let the user plot multiple curve/point or bar plots on the same graph with two different
axes. The line type can be one of the following ‘"l"’ for lines, ‘"p"’ for points, ‘"b"’ for both
points and line, ‘"o"’ for overplotted, ‘"bar"’ for barplot.
twoord.stackplot 219

Value
nil

Author(s)
Christophe Dutang

See Also
twoord.plot

Examples
# plot data
#

time <- 0:25

A <- 1+1/2*sin(time/2)
B <- A + rnorm(length(A), sd=1/10)
B <- B + rnorm(length(A), sd=1/10)

sizeA <- floor(450*(1 + 1/4*sin(time/2+2))*(1+.1))

sizeB <- 1000-sizeA

C <- (A*sizeA + B*sizeB)/(sizeA+sizeB)

#typical usage
#

twoord.stackplot(lx=time, rx=time, ldata=cbind(sizeA, sizeB),

rdata=cbind(A, B, C), lcol=c("grey80", "white"),
rcol=c("blue", "red","black"), ltype="bar", rtype=c("l","p","o"),
border="grey80", lylab="Size", rylab="A,B,C", xlab="Time",
main="a plot", incrylim=2/100)

#add a legend
#

par(xpd=TRUE) #extend the area of plotting

par(new=TRUE) #to add new graph "layers"
plot(0:1, 0:1, type="n", xlab="",ylab="", axes=FALSE) #redo the x/y limits

#first legend
legend(-0.18, 1.2, leg=c("Size A", "Size B"), fill=c("grey80", "white"))
#second legend
legend(.97, -0.08, leg=c("A", "B", "C"), col=c("blue", "red","black"),
pch=c(NA, 19, 19), lty=c(1,NA,1))

par(xpd=FALSE, new=FALSE) #default setting

220 valid.n

#reverse the order of plotting

twoord.stackplot(lx=time, rx=time, ldata=cbind(sizeA, sizeB),
rdata=cbind(A, B, C), lcol=c("grey80", "white"),
rcol=c("blue", "red","black"), ltype="bar", rtype=c("l","p","o"),
border="grey80", lylab="Size", rylab="A,B,C", xlab="Time",
main="a plot", incrylim=2/100, leftfront=TRUE)

valid.n Find the number of valid (not NA) values

Description

Finds the number of valid (not NA) or total values in an object.

Usage

valid.n(x,na.rm=TRUE)

Arguments

x An object.
na.rm Whether to count all values (FALSE) or only those not NA.

Details

‘valid.n’ finds the number of valid values of the object if ‘na.rm=TRUE’.

Value

The number of valid values or the length of the object.

Author(s)

Jim Lemon
vectorField 221

vectorField Display magnitude/direction vectors

Description
Display magnitude/direction vectors as arrows on an existing plot.

Usage

vectorField(u,v,xpos=NA,ypos=NA,scale=1,headspan=0.1,
vecspec=c("lonlat","rad","deg"),col=par("fg"))

Arguments
u,v x (longitude) and y (latitude) offsets OR orientation and magnitude in either
radians or degrees. See details.
xpos,ypos The centers of the vectors in user units.
scale The proportion of each cell that the maximal vector will fill. See details.
headspan The extent of the heads of the arrows as a proportion of cell size.
vecspec How the vectors are described. See details
col Color(s) for the arrows.

Details
‘vectorField’ displays arrows on an existing plot. Each arrow is specified by a position on the plot
‘xpos,ypos’ and either x/y offsets or orientation and magnitude. The default is x/y offsets, and the
user must specify whether radians or degrees are used if the orientation/magnitude option is used.
If the first four arguments are matrices, there must be no missing values. If these arguments are
vectors, the calculation of the scaling of the magnitudes and length of the arrowheads may be
slightly different.

Value
nil

Author(s)
Jim Lemon (original code by Robin Hankin and Brian Ripley)

See Also
arrows
222 violin_plot

Examples

## Not run:
# this requires the maps package, and just wouldn't pass check
require(maps)
map("world",xlim=c(110,155),ylim=c(-40,-10))
par(xpd=TRUE)
text(132,-5,"Approximate magnetic deviation - Australia",cex=1.5)
par(xpd=FALSE)
long<-rep(seq(117.5,152.5,by=5),6)
lat<-rep(c(-12.5,-17.5,-22.5,-27.5,-32.5,-37.5),each=8)
# just show the direction, don't have a magnitude difference
mag<-rep(1,48)
devdeg<-c(110,98,85,65,65,65,65,65,
115,100,90,80,72,66,63,55,
130,100,90,82,72,67,62,54,
122,111,95,86,70,67,56,48,
118,116,110,87,74,68,62,45,
128,115,107,90,78,66,53,45)
vectorField(devdeg,mag,long,lat,scale=0.7,vecspec="deg")

## End(Not run)
# do a magnitude/direction plot with radians
plot(1:10,type="n",main="Random vectors")
mag<-runif(100)+1
dir<-runif(100)*2*pi
xpos<-rep(1:10,10)
ypos<-rep(1:10,each=10)
vectorcol<-sample(colors(),100)
vectorField(dir,mag,xpos,ypos,scale=0.8,vecspec="rad",col=vectorcol)

violin_plot Display a "violin" plot

Description

Displays violin plots (rotated kernel density plots on each side of boxplots).

Usage

violin_plot(X=rnorm(50),at,add=FALSE,na.rm=TRUE,bw,violin_width,
violin_end_width=0.005,equal_width=TRUE,show_box=TRUE,box_width=0.01,
box_col="black",show_outliers=TRUE,outlier_pch=NA,range=1.5,xlim,ylim,
axes=TRUE,ann=TRUE,xlab="",ylab="",x_axis_labels,main="Violin Plot",
col="red",median_col="white",show_mean=FALSE,mean_pch=19,
mean_pch_col="yellow",...)
violin_plot 223

Arguments
X A vector or matrix or data frame of numeric values.
at Horizontal position(s) for the violin plot(s).
add Whether this violin should be added to an existing plot.
na.rm Remove NA values. Passed to functions such as ‘boxplot’ or ‘density’.
bw Vector or bandwidth values for ‘density’. Will be recycled. If not provided
then will be calculated using ‘bw.nrd0’.
violin_width Multiplier to scale the width of the ‘violin’.
violin_end_width
Multiplier to scale the width of the ends of the violin.
equal_width Should all violin widths be equal?
show_box Whether to display the box.
box_width Multiplier for the width of internal boxes.
box_col Fill color for the internal rectangle.
show_outliers Whther to display outliers as points.
outlier_pch Symbol for displaying outliers.
range Passed to ‘boxplot’.
xlim,ylim Explicitly set the plot limits.
axes Logical value indicating whether both axes should be drawn on the plot.
ann Annotate the plots with axis titles and overall titles.
xlab,ylab Labels for the X and Y axes.
x_axis_labels Labels for the violins.
main Title for the violin plot.
col Fill color for the violin(s). Will be recycled.
median_col Fill color for the median mark.
show_mean Whether to plot the mean as well as the median.
mean_pch Symbol to use for the mean.
mean_pch_col Fill color for the mean symbol.
... Extra arguments passed to ‘polygon’ used for representing violin(s).

Details
‘violin_plot’ displays one or more violin plots by drawing rotated kernel density curves on each
side of box plots.

Value
nil

Author(s)
Darshan Baral
224 weighted.hist

Examples
# plotting a data frame
violin_plot(mtcars)

set.seed(42)
normvar<-c(rnorm(49),-3)
unifvar<-runif(50,-2,2)
normvar2<-rnorm(45)

# plotting a matrix
violin_plot(matrix(c(normvar,unifvar),ncol=2),
main="Default Plot",x_axis_labels=c("Normal","Uniform"))

# plotting with different colors and with at specified

violin_plot(matrix(c(normvar,unifvar),ncol=2),at=1:3,
main="Different colors and extra space",
x_axis_labels=c("Normal","Uniform","Normal"),
show_outliers=TRUE,col=c("blue","red"),median_col="lightgray",
pch=6)

# adding a violin to existing plot

violin_plot(normvar2,at=3,add=TRUE,col="green",violin_width=1)

weighted.hist Display a weighted histogram

Description
Calculate the counts of the weighted values in specified bins and optionally display either a fre-
quency or density histogram.

Usage
weighted.hist(x,w,breaks="Sturges",col=NULL,plot=TRUE,
freq=TRUE,ylim,ylab=NULL,xaxis=TRUE,...)

Arguments
x A vector of numeric values
w A vector of weights at least as long as x.
breaks The endpoints of the ranges into which to count the weighted values.
col An optional vector of colors for the bars of the histogram.
plot Whether to plot a histogram.
freq Whether to plot counts or densities.
ylim The limits of the plot ordinate.
ylab Label for the ordinate.
xaxis Whether to display the default x axis.
... Additional arguments passed to barplot.
zoomInPlot 225

Details
‘weighted.hist’ calculates the weighted counts of values falling into the ranges specified by
‘breaks’. Instead of counting each value as 1, it counts the corresponding value in ‘w’ (the weight).
‘breaks’ may be specified by a monotonically increasing vector of numbers that are interpreted as
the endpoints of the ranges, a single number representing the number of ranges desired or the name
of the function to calculate the ranges (see hist). If a vector of numbers is passed that does not
include all values in ‘x’, the user is warned. If the ranges are not equal, a warning will be displayed
if ‘freq’ is TRUE or the heights of the bars will be adjusted to display areas approximately equal
to the counts if ‘freq’ is FALSE.

Value
A list containing:
breaks - The endpoints of the intervals
counts - The weighted counts
density - The weighted counts divided by their sum.
mids - The midpoints of the intervals and the bars displayed.
xname - the name of ‘x’.
equidist - Whether the intervals differ by less than the total range/1000.

Author(s)
Jim Lemon and Hadley Wickham - thanks to Ben Graf for asking for a custom x axis option

See Also
hist

Examples
testx<-sample(1:10,300,TRUE)
testw<-seq(1,4,by=0.01)
weighted.hist(testx,testw,breaks=1:10,main="Test weighted histogram")

zoomInPlot Display a plot with a rectangular section expanded in an adjacent plot

Description
Display one plot on the left half of a device and an expanded section of that plot on the right half of
the device with connecting lines showing the expansion.

Usage
zoomInPlot(x,y=NULL,xlim=NULL,ylim=NULL,rxlim=xlim,rylim=ylim,xend=NA,
zoomtitle=NULL,titlepos=NA,...)
226 zoomInPlot

Arguments
x,y numeric data vectors. If ‘y’ is not specified, it is set equal to ‘x’ and ‘x’ is set to
‘1:length(y)’.
xlim,ylim Limits for the initial plot.
rxlim,rylim Limits for the expanded plot. These must be within the above.
xend Where to end the segments that indicate the expansion. Defaults to just left of
the tick labels on the left ordinate.
zoomtitle The title of the plot, display in the top center.
titlepos The horizontal position of the title in user units of the zoomed plot.
... additional arguments passed to ‘plot’.

Details
‘zoomInPlot’ sets up a two column layout in the current device and calls ‘plot’ to display a plot
in the left column. It then draws a rectangle corresponding to the ‘rxlim’ and ‘rylim’ arguments
and displays a second plot of that rectangle in the right column. It is currently very simple and will
probably become more flexible in future versions.
It just has. If ‘rxlim’ is set to NA, ‘locator’ will be called and the user can define the zoomed
rectangle by clicking on each corner. This is a shameless ripoff of a suggestion by Greg Snow on
the help list. Thanks, Greg.

Value
nil

Author(s)
Jim Lemon

See Also
plot

Examples
zoomInPlot(rnorm(100),rnorm(100),rxlim=c(-1,1),rylim=c(-1,1),
zoomtitle="Zoom In Plot",titlepos=-1.5)
Index

∗Topic \textasciitildekwd1 brkdnNest, 33

ehplot, 72 bumpchart, 35
∗Topic \textasciitildekwd2 categoryReshape, 36
ehplot, 72 centipede.plot, 37
∗Topic aplot clock24.plot, 40
ablineclip, 6 clplot, 41
corner.label, 54 cluster.overplot, 42
ladderplot, 112 clustered.dotplots, 43
multsymbolbox, 125 color.axis, 44
symbolbox, 199 color.gradient, 45
textbox, 203 color.legend, 47
∗Topic color color.scale, 48
color.id, 46 color.scale.lines, 50
∗Topic design color2D.matplot, 51
multivari, 122 count.overplot, 55
∗Topic hplot cylindrect, 56
dotplot.mtb, 62 death_reg, 57
multhist, 121 dendroPlot, 57
multivari, 122 diamondplot, 59
plotCI, 140 dispersion, 60
revaxis, 170 do.first, 61
sizeplot, 173 draw.arc, 63
symbolbarplot, 198 draw.circle, 64
∗Topic misc draw.ellipse, 66
addtable2plot, 9 draw.radial.line, 67
arctext, 11 draw.tilted.sector, 68
axis.break, 12 drawNestedBars, 69
axis.mult, 13 drawSectorAnnulus, 71
barlabels, 15 election, 73
barNest, 16 emptyspace, 74
barp, 19 fan.plot, 75
battleship.plot, 22 feather.plot, 77
bin.wind.records, 24 fill.corner, 78
binciW, 25 floating.pie, 79
binciWl, 26 fullaxis, 80
binciWu, 27 furc, 82
box.heresy, 28 gantt.chart, 83
boxed.labels, 29 gap.barplot, 85
brkdn.plot, 31 gap.boxplot, 86

227
228 INDEX

gap.plot, 88 radial.grid, 153

get.breaks, 90 radial.pie, 154
get.gantt.info, 91 radial.plot, 156
get.segs, 92 radial.plot.labels, 159
get.soil.texture, 93 radialtext, 161
get.tablepos, 94 rectFill, 168
get.triprop, 95 rescale, 169
get_axispos3d, 99 ruginv, 171
getFigCtr, 96 seats, 172
getIntersectList, 96 size_n_color, 176
getMarginWidth, 98 sizetree, 174
getYmult, 99 sliceArray, 178
gradient.rect, 100 smoothColors, 179
hexagon, 101 soil.texture, 180
histStack, 102 soil.texture.uk, 182
intersectDiagram, 103 soils, 184
jiggle, 106 spread.labels, 184
joyPlot, 107 spreadout, 186
kiteChart, 108 stackpoly, 187
labbePlot, 111 staircase.plot, 189
legendg, 114 staircasePlot, 191
lengthKey, 116 starPie, 193
listDepth, 117 staxlab, 194
makeDendrite, 117 std.error, 195
sumbrk, 196
makeIntersectList, 118
sumDendrite, 197
maxEmptyRect, 120
tab.title, 200
mtext3d, 121
taylor.diagram, 201
oz.windrose, 126
thigmophobe, 205
oz.windrose.legend, 127
thigmophobe.labels, 206
p2p_arrows, 128
triax.abline, 207
panes, 129
triax.fill, 208
pasteCols, 131
triax.frame, 209
paxis3d, 132
triax.plot, 211
perspx, 133 triax.points, 213
pie.labels, 134 tsxpos, 214
pie3D, 135 twoord.plot, 215
pie3D.labels, 137 twoord.stackplot, 218
placeLabels, 138 valid.n, 220
plot.dendrite, 139 vectorField, 221
plot_bg, 144 violin_plot, 222
plotH, 142 weighted.hist, 224
polar.plot, 145 zoomInPlot, 225
polygon.shadow, 146 ∗Topic package
print.brklist, 147 plotrix-package, 5
propbrk, 148 ∗Topic programming
psegments3d, 149 clean.args, 39
ptext3d, 150
pyramid.plot, 150 abline, 7
INDEX 229

ablineclip, 6 cylindrect, 21, 56

add.ps, 7, 165
addtable2plot, 9, 94 death_reg, 57
approx, 46 dendroPlot, 57
arctext, 11, 162 diamondplot, 59
array, 178 dispbars (dispersion), 60
arrows, 61, 116, 129, 141, 221 dispersion, 33, 60
axis, 12, 14, 81 do.first, 61, 89
axis.break, 12, 86, 87, 89 dotchart, 62
axis.mult, 13 dotplot.mtb, 62
draw.arc, 63
barlabels, 15 draw.circle, 64, 99, 112, 127
barNest, 16 draw.ellipse, 66
barp, 19 draw.radial.line, 67
barplot, 21, 122, 143, 224 draw.tilted.sector, 68, 136, 137
battleship.plot, 22 drawNestedBars, 18, 69, 70
bin.wind.records, 24, 127 drawSectorAnnulus, 71
binciW, 25
binciWl, 25, 26, 27 ehplot, 58, 72
binciWu, 25, 26, 27 election, 73, 172
box, 171 emptyspace, 74
box.heresy, 28
boxed.labels, 15, 29, 80, 135 fan.plot, 75
boxplot, 29, 87, 141 feather.plot, 77
brkdn.plot, 31 fill.corner, 53, 78
brkdnNest, 18, 33, 70, 148, 149, 197 floating.pie, 79, 135
bumpchart, 35 fullaxis, 80
by, 34 furc, 82, 140

categoryReshape, 36, 104, 105 gantt.chart, 83, 91

centipede.plot, 37, 92 gap.barplot, 85, 86, 88, 89
clean.args, 39 gap.boxplot, 86
clip, 7 gap.plot, 13, 88, 88
clock24.plot, 40, 158 get.breaks, 90
clplot, 41 get.gantt.info, 83, 84, 91
cluster.overplot, 42, 44, 55 get.segs, 38, 39, 92
clustered.dotplots, 43 get.soil.texture, 93, 181
col2rgb, 46, 49 get.tablepos, 94
color.axis, 44 get.triprop, 93, 95
color.gradient, 45, 48, 179 get_axispos3d, 99
color.id, 46 getFigCtr, 96, 190, 192
color.legend, 47 getIntersectList, 96, 105
color.scale, 46, 48, 51, 53, 154, 209 getMarginWidth, 98
color.scale.lines, 50 getYmult, 99
color2D.matplot, 51, 102 gradient.rect, 21, 47, 48, 57, 100
colors, 46
corner.label, 54 hexagon, 101
count.overplot, 42, 43, 55 hist, 91, 103, 122, 225
cut, 57 histStack, 102
230 INDEX

image, 53 plotmath, 165

interaction.plot, 124 plotrix (plotrix-package), 5
intersectDiagram, 97, 103, 119 plotrix-package, 5
points, 113, 141, 163, 165, 169, 177
jiggle, 106 polar.plot, 41, 145, 158
jitter, 163 polygon, 65, 66, 110, 147, 171, 188, 201
joyPlot, 107 polygon.shadow, 80, 146
print.brklist, 147
kiteChart, 108 propbrk, 148
labbePlot, 111 psegments3d, 149
ladderplot, 35, 112 ptext3d, 150
layout, 130 pyramid.plot, 150
legend, 10, 103, 115, 165
radial.grid, 153
legendg, 94, 114
radial.pie, 71, 154
lengthKey, 116
radial.plot, 40, 41, 59, 145, 155, 156
lines, 61, 68, 113, 165
radial.plot.labels, 159
listDepth, 117
radialtext, 161
makeDendrite, 117 raw.means.plot, 8, 124, 162
makeIntersectList, 37, 97, 105, 118, 131 raw.means.plot2, 8
matplot, 36 raw.means.plot2 (raw.means.plot), 162
maxEmptyRect, 120 rect, 152, 169
mtext, 14, 47, 195 rectFill, 168
mtext3d, 121 remove.args (clean.args), 39
multhist, 121 rescale, 46, 49, 169
multivari, 122 revaxis, 170
multsymbolbox, 125, 200 rgb, 179
rug, 171
oz.windrose, 24, 126, 128 ruginv, 171
oz.windrose.legend, 127, 127
sd, 196
p2p_arrows, 128 seats, 74, 172
panes, 129 segments, 61, 116
par, 130, 164, 165, 170, 171, 177 size_n_color, 176
parcoord, 112, 113 sizeplot, 42, 43, 55, 173
pasteCols, 119, 131 sizetree, 174
paxis3d, 132 sliceArray, 178
perspx, 133 smoothColors, 49, 179
pie.labels, 80, 134 soil.texture, 93, 95, 180
pie3D, 69, 135, 137 soil.texture.uk, 182
pie3D.labels, 136, 137 soils, 184
placeLabels, 138 spread.labels, 30, 78, 139, 184
plot, 23, 29, 42, 59, 108, 143, 164, 165, 171, spreadout, 135, 186
175, 177, 190, 192, 217, 226 stackpoly, 108, 187
plot.default, 141 staircase.plot, 189
plot.dendrite, 82, 117, 118, 139, 197 staircasePlot, 191
plot_bg, 144 starPie, 193
plotCI, 140 staxlab, 20, 21, 23, 32, 194
plotH, 142 std.error, 195
INDEX 231

stripchart, 113
strptime, 83, 91
sumbrk, 196
sumDendrite, 197
symbolbarplot, 198
symbolbox, 199
symbols, 173

t.test, 8
tab.title, 200
taylor.diagram, 201
text, 12, 47, 160, 162, 206, 207
textbox, 203
thigmophobe, 205, 207
thigmophobe.labels, 30, 139, 180, 182, 205,
206, 212, 214
triax.abline, 207, 210, 212
triax.fill, 208, 210
triax.frame, 209
triax.plot, 95, 181, 183, 208, 209, 211, 214
triax.points, 181, 183, 210, 212, 213
tsxpos, 214
twoord.plot, 215, 219
twoord.stackplot, 218

valid.n, 220
vectorField, 221
violin_plot, 222

weighted.hist, 224

xy.coords, 30, 138

zoomInPlot, 225