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MEP28: fix rst syntax for code blocks #7309

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Oct 20, 2016
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MEP28: fix rst syntax for code blocks #7309

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59 changes: 51 additions & 8 deletions doc/devel/MEP/MEP28.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ Status
..
.. MEPs go through a number of phases in their lifetime:

- **Discussion**
**Discussion**
..
.. - **Progress**: Consensus was reached on the mailing list and
.. implementation work has begun.
Expand Down Expand Up @@ -95,6 +95,44 @@ This will be achieved in the following way:
3. Outdated parameters from ``Axes.boxplot`` will be deprecated and
later removed.

Importance
----------

Since the limits of the whiskers are computed arithmetically, there
is an implicit assumption of normality in box and whisker plots.
This primarily affects which data points are classified as outliers.

Allowing transformations to the data and the results used to draw
boxplots will allow users to opt-out of that assumption if the
data are known to not fit a normal distribution.

Below is an example of how ``Axes.boxplot`` classifies outliers of lognormal
data differently depending one these types of transforms.

.. plot::
:include-source: true

import numpy as np
import matplotlib.pyplot as plt
from matplotlib import cbook
np.random.seed(0)

fig, ax = plt.subplots(figsize=(4, 6))
ax.set_yscale('log')
data = np.random.lognormal(-1.75, 2.75, size=37)

stats = cbook.boxplot_stats(data, labels=['arimetic'])
logstats = cbook.boxplot_stats(np.log(data), labels=['log-transformed'])

for lsdict in logstats:
for key, value in lsdict.items():
if key != 'label':
lsdict[key] = np.exp(value)

stats.extend(logstats)
ax.bxp(stats)
fig.show()

Implementation
==============

Expand Down Expand Up @@ -209,7 +247,6 @@ This MEP can be divided into a few loosely coupled components:
#. Removing redundant statistical options in ``Axes.boxplot``
#. Shifting all styling parameter processing from ``Axes.boxplot`` to ``Axes.bxp``.


With this approach, #2 depends and #1, and #4 depends on #3.

There are two possible approaches to #2. The first and most direct would
Expand All @@ -222,7 +259,8 @@ value of ``statfxn`` would be ``cbook.boxplot_stats``, but users could
pass their own function. Then ``transform_in`` and ``tranform_out`` would
then be passed as elements of the ``statfxn_args`` parameter.

.. python:
.. code:: python

def boxplot_stats(data, ..., transform_in=None, transform_out=None):
if transform_in is None:
transform_in = lambda x: x
Expand Down Expand Up @@ -256,7 +294,8 @@ then be passed as elements of the ``statfxn_args`` parameter.

Both cases would allow users to do the following:

.. python:
.. code:: python

fig, ax1 = plt.subplots()
artists1 = ax1.boxplot_optionX(data, transform_in=np.log,
transform_out=np.exp)
Expand All @@ -268,22 +307,25 @@ whiskers set differently depending on some attribute of the data.

This is available under the current API:

.. python:
.. code:: python

fig, ax1 = plt.subplots()
my_stats = my_box_stats(data, bootstrap_method='BCA',
whisker_method='dynamic')
ax1.bxp(my_stats)

And would be more concise with Option Two

.. python:
.. code:: python

fig, ax = plt.subplots()
statopts = dict(transform_in=np.log, transform_out=np.exp)
ax.boxplot(data, ..., **statopts)

Users could also pass their own function to compute the stats:

.. python:
.. code:: python

fig, ax1 = plt.subplots()
ax1.boxplot(data, statfxn=my_box_stats, bootstrap_method='BCA',
whisker_method='dynamic')
Expand All @@ -293,7 +335,8 @@ but in the context of downstream libraries like seaborn, its advantage
is more apparent as the following would be possible without any patches
to seaborn:

.. python:
.. code:: python

import seaborn
tips = seaborn.load_data('tips')
g = seaborn.factorplot(x="day", y="total_bill", hue="sex", data=tips,
Expand Down