Doc: Adding annotated heatmap example by ImportanceOfBeingErnest · Pull Request #11017 · matplotlib/matplotlib

ImportanceOfBeingErnest · 2018-04-10T12:11:42Z

PR Summary

PR #10956 suggested to provide a function to draw annotated categorical heatmaps in matplotlib. The discussion to this concluded that such a function is not necessary given that those are easily produced from imshow plots. It would however be useful to have an example in the gallery showing how to do this.

This PR creates such example.

PR Checklist

This is an example
Code is PEP 8 compliant
Documentation is sphinx and numpydoc compliant

ImportanceOfBeingErnest · 2018-04-10T14:29:32Z

Link to the created example.

jklymak · 2018-04-10T14:36:32Z

Wow! Very nice!

I’m personally not opposed to adding a method like this to the core axes class so long as the API is thought out. I think these sorts of plots get used a fair bit in some fields.

ImportanceOfBeingErnest · 2018-04-10T14:46:28Z

The line

# sphinx_gallery_thumbnail_number = 2

renders like this:

Does anyone have an idea how to set the thumbnail number without it appearing in the output?

I'm not convinced that this should be a built-in function. This is just one possible implementation. I think it's better to show users how to adjust stuff to their liking instead of providing a closed function and let them fight with all the possible arguments etc.

jklymak · 2018-04-10T17:14:54Z

+# which defines the data to color code. We then also need two lists or arrays
+# of categories; of course the number of elements in those lists
+# need to match the data along the respective axes.
+# The heatmap itself is an :meth:`imshow <matplotlib.axes.Axes.imshow>` plot


`~.Axes.imshow`

Will give you the same thing I am 98% sure as this long string (including the :meth:)

jklymak · 2018-04-10T17:17:55Z

+# As discussed in the :ref:`Coding styles <coding_styles>`
+# one might want to reuse such code to create some kind of heatmap
+# for different input data and/or on different axes.
+# We might hence create a function which takes the data and the row and


"We might hence" is pretty verbose. -> "we create a..."

Usually only use "which" after a comma. "which"->"that"

Suggest: "We create a function that takes the data and the row and column labels as input, and allows arguments that are used to customize the plot"

jklymak

This is great. Some comments in the text that you can take or leave as they are just english suggestions.

QuLogic

Some typos. A nice set of examples, otherwise.

QuLogic · 2018-04-10T23:51:42Z

+Creating annotated heatmaps
+===========================
+
+It is often desireable to show data which depends on two independent


QuLogic · 2018-04-10T23:52:04Z

+===========================
+
+It is often desireable to show data which depends on two independent
+variables as a colorcoded image plot. This is often referred to as a


color coded

QuLogic · 2018-04-10T23:52:28Z

+heatmap. If the data is categorical, this would be called a categorical
+heatmap.
+Matplotlib's :meth:`imshow <matplotlib.axes.Axes.imshow>` function makes
+production of such plot particularly easy.


"such a plot" / "such plots"

QuLogic · 2018-04-10T23:54:12Z

+#
+# Here, in addition to the above we also want to create a colorbar and
+# position the labels above of the heatmap instead of below it.
+# The annotations shall


Early line break.

QuLogic · 2018-04-10T23:56:55Z

+        data = im.get_array()
+
+    # Normalize the threshold to the images color range.
+    if not threshold and threshold != 0.0:


if threshold is not None: seems to be the same intent?

QuLogic · 2018-04-10T23:58:14Z

+    texts = []
+    for i in range(data.shape[0]):
+        for j in range(data.shape[1]):
+            kw.update(dict(color=textcolors[im.norm(data[i, j]) > threshold]))


kw['color'] = ...; no need for the extra dict.

QuLogic · 2018-04-10T23:59:15Z

+# Replicate the above example with a different font size and colormap.
+
+im, _ = heatmap(harvest, vegetables, farmers, ax=ax,
+                   cmap="Wistia", cbarlabel="harvest [t/year]")


Misaligned.

ImportanceOfBeingErnest · 2018-04-11T07:45:01Z

Thanks @jklymak and @QuLogic for your input. That is very useful.

I'm still stuggeling with where to put the line # sphinx_gallery_thumbnail_number = 2. I tried several places by now; in the current version it would just appear as text:

although it does take effect and the thumbnail image is indeed the second one.

jklymak · 2018-04-11T14:15:25Z

I’d just have it as a comment up in the import section. Yes a naive user may include it but it doesn’t hurt anything.

ImportanceOfBeingErnest · 2018-04-11T15:17:06Z

Ok, that's what I did now. Apart, it looks all good, doesn't it?

Backport PR #11017 on branch v2.2.2-doc

ImportanceOfBeingErnest force-pushed the doc-heatmap-example branch 3 times, most recently from 0e012a4 to e0b81c4 Compare April 10, 2018 14:27

ImportanceOfBeingErnest mentioned this pull request Apr 10, 2018

Examples not shown in API docs for many methods. #10974

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jklymak reviewed Apr 10, 2018

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jklymak approved these changes Apr 10, 2018

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QuLogic reviewed Apr 11, 2018

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ImportanceOfBeingErnest force-pushed the doc-heatmap-example branch from e0b81c4 to da9aee0 Compare April 11, 2018 07:16

add example: annotated heatmap

c8b6231

ImportanceOfBeingErnest force-pushed the doc-heatmap-example branch from da9aee0 to c8b6231 Compare April 11, 2018 14:27

jklymak added this to the v2.2-doc milestone Apr 12, 2018

jklymak merged commit 2825fe2 into matplotlib:master Apr 12, 2018

lumberbot-app Bot pushed a commit that referenced this pull request Apr 12, 2018

Backport PR #11017: Doc: Adding annotated heatmap example

fd9ac3e

lumberbot-app Bot mentioned this pull request Apr 12, 2018

Backport PR #11017 on branch v2.2.2-doc #11037

Merged

jklymak added a commit that referenced this pull request Apr 12, 2018

Merge pull request #11037 from matplotlib/auto-backport-of-pr-11017

97e8f2f

Backport PR #11017 on branch v2.2.2-doc

ImportanceOfBeingErnest mentioned this pull request Apr 14, 2018

Feature Request: Add annotations to heatmaps (imshow or pcolor*) #10956

Closed

ImportanceOfBeingErnest deleted the doc-heatmap-example branch April 14, 2018 17:51

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ImportanceOfBeingErnest commented Apr 11, 2018

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ImportanceOfBeingErnest commented Apr 10, 2018 •

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