Skip to content

MEP12-on-arrow_demo.py #4660

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 2 commits into from
Jul 19, 2015
Merged

MEP12-on-arrow_demo.py #4660

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
0fa4b94
pylab to plt and np
Jul 11, 2015
b26a521
pep8
Jul 17, 2015
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
56 changes: 29 additions & 27 deletions examples/pylab_examples/arrow_demo.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,10 +9,12 @@


"""
from pylab import *
import matplotlib.pyplot as plt
import numpy as np

rates_to_bases = {'r1': 'AT', 'r2': 'TA', 'r3': 'GA', 'r4': 'AG', 'r5': 'CA', 'r6': 'AC',
'r7': 'GT', 'r8': 'TG', 'r9': 'CT', 'r10': 'TC', 'r11': 'GC', 'r12': 'CG'}
rates_to_bases = {'r1': 'AT', 'r2': 'TA', 'r3': 'GA', 'r4': 'AG', 'r5': 'CA',
'r6': 'AC', 'r7': 'GT', 'r8': 'TG', 'r9': 'CT', 'r10': 'TC',
'r11': 'GC', 'r12': 'CG'}
numbered_bases_to_rates = dict([(v, k) for k, v in rates_to_bases.items()])
lettered_bases_to_rates = dict([(v, 'r' + v) for k, v in rates_to_bases.items()])

Expand Down Expand Up @@ -45,17 +47,17 @@ def make_arrow_plot(data, size=4, display='length', shape='right',
linewidth and edgecolor.
"""

xlim(-0.5, 1.5)
ylim(-0.5, 1.5)
gcf().set_size_inches(size, size)
xticks([])
yticks([])
plt.xlim(-0.5, 1.5)
plt.ylim(-0.5, 1.5)
plt.gcf().set_size_inches(size, size)
plt.xticks([])
plt.yticks([])
max_text_size = size*12
min_text_size = size
label_text_size = size*2.5
text_params = {'ha': 'center', 'va': 'center', 'family': 'sans-serif',
'fontweight': 'bold'}
r2 = sqrt(2)
r2 = np.sqrt(2)

deltas = {
'AT': (1, 0),
Expand Down Expand Up @@ -103,13 +105,13 @@ def make_arrow_plot(data, size=4, display='length', shape='right',
}

def do_fontsize(k):
return float(clip(max_text_size*sqrt(data[k]),
return float(np.clip(max_text_size*np.sqrt(data[k]),
min_text_size, max_text_size))

A = text(0, 1, '$A_3$', color='r', size=do_fontsize('A'), **text_params)
T = text(1, 1, '$T_3$', color='k', size=do_fontsize('T'), **text_params)
G = text(0, 0, '$G_3$', color='g', size=do_fontsize('G'), **text_params)
C = text(1, 0, '$C_3$', color='b', size=do_fontsize('C'), **text_params)
A = plt.text(0, 1, '$A_3$', color='r', size=do_fontsize('A'), **text_params)
T = plt.text(1, 1, '$T_3$', color='k', size=do_fontsize('T'), **text_params)
G = plt.text(0, 0, '$G_3$', color='g', size=do_fontsize('G'), **text_params)
C = plt.text(1, 0, '$C_3$', color='b', size=do_fontsize('C'), **text_params)

arrow_h_offset = 0.25 # data coordinates, empirically determined
max_arrow_length = 1 - 2*arrow_h_offset
Expand All @@ -119,7 +121,7 @@ def do_fontsize(k):
max_head_length = 2*max_arrow_width
arrow_params = {'length_includes_head': True, 'shape': shape,
'head_starts_at_zero': head_starts_at_zero}
ax = gca()
ax = plt.gca()
sf = 0.6 # max arrow size represents this in data coords

d = (r2/2 + arrow_h_offset - 0.5)/r2 # distance for diags
Expand Down Expand Up @@ -179,7 +181,7 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):

x_scale, y_scale = deltas[pair]
x_pos, y_pos = positions[pair]
arrow(x_pos, y_pos, x_scale*length, y_scale*length,
plt.arrow(x_pos, y_pos, x_scale*length, y_scale*length,
fc=fc, ec=ec, alpha=alpha, width=width, head_width=head_width,
head_length=head_length, **arrow_params)

Expand All @@ -192,24 +194,24 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):

where = label_positions[pair]
if where == 'left':
orig_position = 3*array([[max_arrow_width, max_arrow_width]])
orig_position = 3*np.array([[max_arrow_width, max_arrow_width]])
elif where == 'absolute':
orig_position = array([[max_arrow_length/2.0, 3*max_arrow_width]])
orig_position = np.array([[max_arrow_length/2.0, 3*max_arrow_width]])
elif where == 'right':
orig_position = array([[length - 3*max_arrow_width,
orig_position = np.array([[length - 3*max_arrow_width,
3*max_arrow_width]])
elif where == 'center':
orig_position = array([[length/2.0, 3*max_arrow_width]])
orig_position = np.array([[length/2.0, 3*max_arrow_width]])
else:
raise ValueError("Got unknown position parameter %s" % where)

M = array([[cx, sx], [-sx, cx]])
coords = dot(orig_position, M) + [[x_pos, y_pos]]
x, y = ravel(coords)
M = np.array([[cx, sx], [-sx, cx]])
coords = np.dot(orig_position, M) + [[x_pos, y_pos]]
x, y = np.ravel(coords)
orig_label = rate_labels[pair]
label = '$%s_{_{\mathrm{%s}}}$' % (orig_label[0], orig_label[1:])

text(x, y, label, size=label_text_size, ha='center', va='center',
plt.text(x, y, label, size=label_text_size, ha='center', va='center',
color=labelcolor or fc)

for p in positions.keys():
Expand Down Expand Up @@ -302,11 +304,11 @@ def draw_arrow(pair, alpha=alpha, ec=ec, labelcolor=labelcolor):
display = 'length'

size = 4
figure(figsize=(size, size))
plt.figure(figsize=(size, size))

make_arrow_plot(d, display=display, linewidth=0.001, edgecolor=None,
normalize_data=scaled, head_starts_at_zero=True, size=size)

draw()
plt.draw()

show()
plt.show()