MEP12 improvments for statistics plots #7331

phobson · 2016-10-22T16:29:41Z

This isn't ready yet -- but I noticed a lot of MEP12 PRs, so I wanted to get this up sooner to avoid duplicate efforts

NelleV · 2016-10-22T17:04:35Z

I've added those as being "done" on #7206.

phobson · 2016-10-22T17:18:09Z

@NelleV cool, I'll update it as I go.

QuLogic · 2016-10-22T20:39:20Z

Can you add the titling =s while you're here?

phobson · 2016-10-22T22:52:15Z

@QuLogic I don't follow.

NelleV · 2016-10-22T23:28:21Z

@phobson if the title is written in restructured text format, it will be rendered as so with sphinx-gallery. It is not requirement for the examples to be parsed properly, but it does look much nicer.

QuLogic

Are all the plots PEP8-good now?

QuLogic · 2016-10-23T01:12:19Z

examples/statistics/boxplot_demo.py

+mean is the only value not shown by default). The second
+figure demonstrates how the styles of the artists of can
+be customized. It also demonstrates how to set the limit
+if the whiskers to specific percentiles (lower right axes)


if -> of.
Missing period at end of sentence.

Also, is there a reason for wrapping lines so early?

QuLogic · 2016-10-23T01:13:58Z

examples/statistics/bxp_demo.py

+statistics to the box plot drawer. The first figure demostrates
+how to remove and add individual components (note that the
+mean is the only value not shown by default). The second
+figure demonstrates how the styles of the artists of can


Remove second 'of'.

QuLogic · 2016-10-23T01:14:32Z

examples/statistics/customized_violin_demo.py

+The first plot shows the default style by providing only
+the data. The second plot first limits what matplotlib draws
+with additional kwargs. Then a simplified representation of
+a box plot in drawn on top. Lastly, the styles of arists


arists -> artists

QuLogic · 2016-10-23T01:16:38Z

examples/statistics/customized_violin_demo.py

+for ax in [ax1, ax2]:
+    ax.get_xaxis().set_tick_params(direction='out')
+    ax.xaxis.set_ticks_position('bottom')
+    ax.set_xticks([x + 1 for x in range(len(lab))])


You could maybe replace this with np.arange(1, ...) instead.

QuLogic · 2016-10-23T01:16:53Z

examples/statistics/errorbar_demo.py

+Demo of the errorbar function
+=============================
+
+This exhibits the most basic use of of the error bar method.


Double 'of'.

QuLogic · 2016-10-23T01:43:27Z

examples/statistics/multiple_histograms_side_by_side.py

 Demo of how to produce multiple histograms side by side
+=======================================================
+
+This example plots horizonal histograms of different samples along


horizonal -> horizontal

QuLogic · 2016-10-23T01:45:18Z

examples/statistics/violinplot_demo.py

+Violin plots are similar to histograms and box plots in that they show
+an abstract representation of the probability distribution of the
+sample. Rather than showing counts of data points that fall into bins
+or order statistics, violin plots use kernal density estimation (KDE) to


kernal -> kernel

QuLogic · 2016-10-23T01:46:22Z

examples/statistics/violinplot_demo.py

+or order statistics, violin plots use kernal density estimation (KDE) to
+compute an emperical distribution of the sample. That computation
+is controlled by several parameters. This example demostrates how to
+modify the number of points at the KDE is evaluated (``points``) and


at -> at which (or maybe "for which", depending on the exact meaning.)

QuLogic · 2016-10-23T01:46:45Z

examples/statistics/violinplot_demo.py

+compute an emperical distribution of the sample. That computation
+is controlled by several parameters. This example demostrates how to
+modify the number of points at the KDE is evaluated (``points``) and
+how to modify the band-width of the kde (``bw_method``).


kde -> KDE
for consistency.

QuLogic · 2016-10-23T01:47:30Z

examples/statistics/violinplot_demo.py

+an abstract representation of the probability distribution of the
+sample. Rather than showing counts of data points that fall into bins
+or order statistics, violin plots use kernal density estimation (KDE) to
+compute an emperical distribution of the sample. That computation


emperical -> empirical

NelleV

This looks good.
I've underlined a couple of typos, but this is a huge improvements in our examples. Thanks for the work put into this!

NelleV · 2016-10-23T04:05:32Z

examples/statistics/boxplot_demo.py

+=========================================
+
+This example demonstrates how to use the various kwargs
+to fully customize box plots. The first figure demostrates


typo: demostrates -> demonstrates

NelleV · 2016-10-23T04:06:09Z

examples/statistics/boxplot_demo.py

+to fully customize box plots. The first figure demostrates
+how to remove and add individual components (note that the
+mean is the only value not shown by default). The second
+figure demonstrates how the styles of the artists of can


type: there is an extra of

NelleV · 2016-10-23T04:06:42Z

examples/statistics/bxp_demo.py

+===================================
+
+This example demonstrates how to pass pre-computed box plot
+statistics to the box plot drawer. The first figure demostrates


typo: demostrates -> demonstrates

NelleV · 2016-10-23T04:07:19Z

examples/statistics/customized_violin_demo.py

+The first plot shows the default style by providing only
+the data. The second plot first limits what matplotlib draws
+with additional kwargs. Then a simplified representation of
+a box plot in drawn on top. Lastly, the styles of the artists


typo: in -> is

NelleV · 2016-10-23T04:08:29Z

examples/statistics/errorbars_and_boxes.py

+called `make_error_boxes`. Close inspection of this function will reveal
+the preferred pattern in writing functions for matplotlib:
+
+  1. an `Axes` object is passed directly to the function


NelleV · 2016-10-23T04:09:12Z

examples/statistics/histogram_demo_cumulative.py

+A couple of other options to the ``hist`` function are demonstrated.
+Namely, we use the ``normed`` parameter to normalize the histogram and
+a couple of different options to the `cumulative` parameter. Normalizing
+a histogram means that the heights bins are scaled such that


"heights bins" or "height bins"? I never know…

Neither: "bin heights"

NelleV · 2016-10-23T04:10:54Z

examples/statistics/violinplot_demo.py

+modify the number of points at which the KDE is evaluated (``points``)
+and how to modify the band-width of the KDE (``bw_method``).
+
+For more information on violin plots and KDE, the scikit-learn docs


👍 (I am of course totally biased…)

QuLogic · 2016-10-23T04:28:10Z

examples/statistics/customized_violin_demo.py

+for ax in [ax1, ax2]:
+    ax.get_xaxis().set_tick_params(direction='out')
+    ax.xaxis.set_ticks_position('bottom')
+    ax.set_xticks([x for x in np.arange(1, len(lab) + 1)])


You don't need the list comprehension now.

phobson · 2016-10-23T15:58:21Z

@QuLogic -- I never answered your question about PEP8. Yes. The pep8 that I ran locally w/o any exceptions didn't complain at all and Travis was happy with the last pass at them.

QuLogic · 2016-10-24T00:32:37Z

@phobson phobson changed the title from MEP12 improvments for statistics plots to [MRG+1]MEP12 improvments for statistics plots 2 hours ago

You can't +1 your own PR 😛

QuLogic

One minor tweak.

QuLogic · 2016-10-24T00:38:40Z

examples/statistics/histogram_demo_cumulative.py

+
+A couple of other options to the ``hist`` function are demonstrated.
+Namely, we use the ``normed`` parameter to normalize the histogram and
+a couple of different options to the `cumulative` parameter. Normalizing


Missed on set of backticks.

QuLogic · 2016-10-24T00:39:51Z

examples/statistics/histogram_demo_cumulative.py

+Namely, we use the ``normed`` parameter to normalize the histogram and
+a couple of different options to the `cumulative` parameter. Normalizing
+a histogram means that the bin heights are scaled such that
+the total area is 1. Since we're showing a normalized and


I still feel there's one sentence missing between here explaining what the cumulative argument does, or maybe the "Since..." sentence can go after the next paragraph.

@QuLogic I took another stab at this. Let me know what you think.

QuLogic · 2016-10-24T22:37:14Z

examples/statistics/histogram_demo_cumulative.py

+
+Since we're showing a normalized and cumulative histogram, these curves
+are effectively the cumulative distribution functions (CDFs) of the
+samples. In engineering, empirical CDFs where are sometimes called


An extra 'where' in this sentence.

phobson · 2016-10-25T14:04:03Z

Let me know if y'all want me to squash all of this (I'm inclined to do so).

NelleV · 2016-10-25T14:16:46Z

@phobson Whatever you prefer. Let me know, else I am going to merge.

phobson · 2016-10-25T15:36:53Z

@NelleV I'll squash -- one sec

NelleV · 2016-10-25T15:57:11Z

I'll wait until the checks finish running before merging :)

phobson · 2016-10-25T18:13:34Z

Cool. I'll take a stab at that soon.

On Sunday, October 23, 2016, Elliott Sales de Andrade <
notifications@github.com> wrote:

@QuLogic commented on this pull request.

One minor tweak.

In examples/statistics/histogram_demo_cumulative.py
#7331 (review)
:

@@ -1,29 +1,72 @@
"""
-Demo of the histogram (hist) function used to plot a cumulative distribution.
+==========================================================
+Demo of using histograms to plot a cumulative distribution
+==========================================================
+
+This shows how to plot a cumulative, normalized histogram as a
+step function in order to visualize the empirical cumulative
+distribution function (CDF) of a sample. We also use the mlab
+module to show the theoretical CDF.
+
+A couple of other options to the hist function are demonstrated.
+Namely, we use the normed parameter to normalize the histogram and
+a couple of different options to the cumulative parameter. Normalizing

Missed on set of backticks.

In examples/statistics/histogram_demo_cumulative.py
#7331 (review)
:

@@ -1,29 +1,72 @@
"""
-Demo of the histogram (hist) function used to plot a cumulative distribution.
+==========================================================
+Demo of using histograms to plot a cumulative distribution
+==========================================================
+
+This shows how to plot a cumulative, normalized histogram as a
+step function in order to visualize the empirical cumulative
+distribution function (CDF) of a sample. We also use the mlab
+module to show the theoretical CDF.
+
+A couple of other options to the hist function are demonstrated.
+Namely, we use the normed parameter to normalize the histogram and
+a couple of different options to the cumulative parameter. Normalizing
+a histogram means that the bin heights are scaled such that
+the total area is 1. Since we're showing a normalized and

I still feel there's one sentence missing between here explaining what the
cumulative argument does, or maybe the "Since..." sentence can go after
the next paragraph.

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
#7331 (review),
or mute the thread
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.

Sent from my sorry. Sorry about the typos.

phobson · 2016-10-25T18:23:27Z

Ha. Sorry. That was a response to the approval.

On Sunday, October 23, 2016, Elliott Sales de Andrade <
notifications@github.com> wrote:

@phobson https://github.com/phobson phobson changed the title from
MEP12 improvments for statistics plots to [MRG+1]MEP12 improvments for
statistics plots 2 hours ago

You can't +1 your own PR 😛

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
#7331 (comment),
or mute the thread
https://github.com/notifications/unsubscribe-auth/ABHCo5Z04c0HdOZ2Vo4ru9cmzhjs7PbGks5q2_yogaJpZM4Kd5xr
.

Sent from my sorry. Sorry about the typos.

NelleV · 2016-10-25T18:33:36Z

So… the backport doesn't apply cleanly and I got distracted by something else.
@tacaswell do you mind doing it?

MEP12 improvments for statistics plots

QuLogic · 2016-10-25T21:56:41Z

Backported to v2.x via 58cc83d.

phobson added Documentation MEP: MEP12 gallery and examples improvements labels Oct 22, 2016

phobson added this to the 2.0.1 (next bug fix release) milestone Oct 22, 2016

phobson self-assigned this Oct 22, 2016

phobson force-pushed the MEP12-statistic-plots branch from 5aadd99 to bb8143a Compare October 22, 2016 19:26

phobson changed the title ~~(WIP) MEP12 improvments for statistics plots~~ MEP12 improvments for statistics plots Oct 22, 2016

phobson added the status: needs review label Oct 22, 2016

QuLogic reviewed Oct 23, 2016

View reviewed changes

NelleV approved these changes Oct 23, 2016

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QuLogic reviewed Oct 23, 2016

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phobson force-pushed the MEP12-statistic-plots branch from 146a417 to a47556a Compare October 23, 2016 15:39

phobson force-pushed the MEP12-statistic-plots branch from 0a00e9a to 8e0323b Compare October 23, 2016 16:01

phobson changed the title ~~MEP12 improvments for statistics plots~~ [MRG+1]MEP12 improvments for statistics plots Oct 23, 2016

QuLogic reviewed Oct 24, 2016

View reviewed changes

QuLogic changed the title ~~[MRG+1]MEP12 improvments for statistics plots~~ [MRG]MEP12 improvments for statistics plots Oct 24, 2016

NelleV changed the title ~~[MRG]MEP12 improvments for statistics plots~~ [MRG+1] MEP12 improvments for statistics plots Oct 24, 2016

QuLogic reviewed Oct 24, 2016

View reviewed changes

DOC: MEP12 docstring for the statistics examples

076b98c

phobson force-pushed the MEP12-statistic-plots branch from 7c7d1c7 to 076b98c Compare October 25, 2016 15:38

NelleV merged commit 3127815 into matplotlib:master Oct 25, 2016

QuLogic pushed a commit that referenced this pull request Oct 25, 2016

Merge pull request #7331 from phobson/MEP12-statistic-plots

58cc83d

MEP12 improvments for statistics plots

QuLogic changed the title ~~[MRG+1] MEP12 improvments for statistics plots~~ MEP12 improvments for statistics plots Oct 25, 2016

phobson deleted the MEP12-statistic-plots branch October 25, 2016 23:29

QuLogic removed the status: needs review label Nov 24, 2016

QuLogic modified the milestones: 2.0.1 (next bug fix release), 2.0 (style change major release) Dec 7, 2016

MEP12 improvments for statistics plots #7331

MEP12 improvments for statistics plots #7331

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phobson commented Oct 22, 2016

NelleV commented Oct 22, 2016

phobson commented Oct 22, 2016

QuLogic commented Oct 22, 2016

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phobson commented Oct 25, 2016

NelleV commented Oct 25, 2016

phobson commented Oct 25, 2016

NelleV commented Oct 25, 2016

phobson commented Oct 25, 2016

One minor tweak.

Missed on set of backticks.

phobson commented Oct 25, 2016

NelleV commented Oct 25, 2016

QuLogic commented Oct 25, 2016