MEP12 improvments for statistics plots by phobson · Pull Request #7331 · matplotlib/matplotlib

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

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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

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