[WIP] Modify pairplot to include jointplot and cornerplot like features #1079

agustinaarroyuelo · 2020-02-18T18:50:16Z

The motivation behind this PR is that plots that are currently made with plot_joint can be made with plot_pair. Also, the point_estimate key word argument and scatter_kde kind will allow pair plots similar to fairly used cornerplots.
Here are some examples:

I will really appreciate suggestions, especially on function testing.

Checklist

Follows official PR format
Includes a sample plot to visually illustrate the changes (only for plot-related functions)
New features are properly documented (with an example if appropriate)?
Includes new or updated tests to cover the new feature
Code style correct (follows pylint and black guidelines)
Changes are listed in changelog

ahartikainen · 2020-02-18T18:52:25Z

Looks good. Not needed for this PR, but it could be interesting to have this property for bokeh, but for any point that is selected.

OriolAbril

Thanks a lot! This is a kind of plot that has been missing far too much time.

I have commented on some aspects of the code, my main motivations being reusing code when possible (it's less code to maintain on the long run), using sensible default while letting users customize most if not all features and last but not least things I happened to see by chance that I missed in the past. Feel free to not follow all of them. I can help with testing too afterwards.

Also, general note, I'd be great if a second pair of eyes could confirm (either you or another reviewer), the **kwargs in plot_kde are passed to the backend but NOT accepted by neither of them. It looks safe to delete (it actually feels safer than having it like this).

arviz/plots/backends/bokeh/distplot.py

arviz/plots/plot_utils.py

arviz/plots/pairplot.py

arviz/plots/backends/matplotlib/pairplot.py

agustinaarroyuelo · 2020-02-19T13:02:04Z

Thanks Oriol for your comments! I am going through them 👍

OriolAbril

github marks the changes in a very strange way, I think I commented on green things that have been on the code for quite a long time, there is no need to fix all these extra comments.

CHANGELOG.md

arviz/data/io_pymc3.py

arviz/plots/backends/bokeh/pairplot.py

ahartikainen · 2020-02-27T14:12:48Z

I recommend that you rebase your branch.

First update your master against arviz master.

Then go to your branch

git rebase -i master

And then you can remove unneeded commits and keep only your.

rebase -i should open a text editor (vim for example) and then you can edit commits as needed.

agustinaarroyuelo · 2020-02-27T20:30:50Z

Thank you Ari for your help.
I did what you suggested and removed the commits that were previous to rebasing. This commits were duplicated. When I tried to push this to my branch, the tip was behind its remote counterpart. Git suggested git pull ..., but pulling from my branch would have reverted the changes made by git rebase -i master. Therefore I forced the push, using --force-with-lease just in case. Let me know if it is ok.

ahartikainen · 2020-02-27T22:02:57Z

git push -f is needed, I forgot to add that.

aloctavodia · 2020-03-02T22:15:20Z

arviz/plots/pairplot.py

@@ -68,13 +76,29 @@ def plot_pair(
        Matplotlib axes or bokeh figures.
    divergences_kwargs : dicts, optional
        Additional keywords passed to ax.scatter for divergences
-    plot_kwargs : dicts, optional
-        Additional keywords passed to ax.plot, az.plot_kde or ax.hexbin
+    scatter_kwargs:


Given the changes parts of the docstring are outdated. For example

kind : str Type of plot to display (scatter, kde or hexbin)

is not an "or" but and/or. And probably we should explicitly indicate the overlaying feature.

Instead of
Plot a scatter or hexbin matrix of the sampled parameters.

we should have something like:

Scatter, kde and/or hexbin matrix with (optional) marginals on the diagonal

Also the examples need to be updated. It's OK for me if we do that in another PR (but we should open and issue so we do not forget).

fix pylint issues fix hover feature fix hover feature minor fixes

run pylint

OriolAbril · 2020-03-03T22:00:27Z

Changelog should be updated to list changes in unreleased version, not 0.7.0

OriolAbril

I think we can merge and work on several issues/ideas that came up thanks to this in other PRs, I'll try to create some issues so we don't forget. Thanks for the PR!

agustinaarroyuelo · 2020-03-05T15:25:32Z

Thanks everyone for your comments and help!

…es (#1079) * add jointplot features into pairplot * add scatter_kde kind for pairplot * add point_estimate arguments * bokeh backend * fix None argument for color in kdeplot bokeh backend * run black, pylint and pytest * remove scatter_kde kind among several other changes * minor changes * run pytest * add plot width and height to backend_kwargs fix pylint issues fix hover feature fix hover feature minor fixes * update docstring run pylint * update changelog

* [WIP] Modify pairplot to include jointplot and cornerplot like features (#1079) * add jointplot features into pairplot * add scatter_kde kind for pairplot * add point_estimate arguments * bokeh backend * fix None argument for color in kdeplot bokeh backend * run black, pylint and pytest * remove scatter_kde kind among several other changes * minor changes * run pytest * add plot width and height to backend_kwargs fix pylint issues fix hover feature fix hover feature minor fixes * update docstring run pylint * update changelog * add true_values argument for plot_pair remove whitespace * change argument name to reference_values change argument name to reference_values * update tests Co-authored-by: Ari Hartikainen <ahartikainen@users.noreply.github.com>

* [WIP] Modify pairplot to include jointplot and cornerplot like features (#1079) * add jointplot features into pairplot * add scatter_kde kind for pairplot * add point_estimate arguments * bokeh backend * fix None argument for color in kdeplot bokeh backend * run black, pylint and pytest * remove scatter_kde kind among several other changes * minor changes * run pytest * add plot width and height to backend_kwargs fix pylint issues fix hover feature fix hover feature minor fixes * update docstring run pylint * update changelog * fix jointplot with bokeh * To transform colors in plotting functions to hex (#1084) * Transform colors to hex in plot_khat * Reformatted with black * Added hex conversion to khatplot.py and vectorized_to_hex to plot_utils.py * Black changes * Added keep_alpha parameter and list comprehension * Pydocstyle changes * More pydocstyle changes * generalised vectorized_to_hex * Black changes * Black changes * Modified khatplot hline_kwargs, vectorized_to_hex and test for vectorized_to_hex * Black changes * Rewrote tests and modified vectorized_to_hex * lint and minor fixes Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com> * [WIP] Modify pairplot to include jointplot and cornerplot like features (#1079) * add jointplot features into pairplot * add scatter_kde kind for pairplot * add point_estimate arguments * bokeh backend * fix None argument for color in kdeplot bokeh backend * run black, pylint and pytest * remove scatter_kde kind among several other changes * minor changes * run pytest * add plot width and height to backend_kwargs fix pylint issues fix hover feature fix hover feature minor fixes * update docstring run pylint * update changelog * fix jointplot with bokeh * update changelog * fixed changelog Co-authored-by: Ari Hartikainen <ahartikainen@users.noreply.github.com> Co-authored-by: amukh18 <45681148+amukh18@users.noreply.github.com> Co-authored-by: Oriol (ZBook) <oriol.abril.pla@gmail.com>

OriolAbril reviewed Feb 18, 2020

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OriolAbril reviewed Feb 22, 2020

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OriolAbril mentioned this pull request Feb 24, 2020

[WIP]Add de-aliaser function for plots #1073

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aloctavodia reviewed Mar 2, 2020

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agustinaarroyuelo added 10 commits March 3, 2020 16:53

add jointplot features into pairplot

3db74ad

add scatter_kde kind for pairplot

e93b9ce

add point_estimate arguments

94d51d7

bokeh backend

3ddf152

fix None argument for color in kdeplot bokeh backend

3c393a8

run black, pylint and pytest

fd8db2d

remove scatter_kde kind among several other changes

ec0d252

minor changes

70b8933

run pytest

e06ef29

add plot width and height to backend_kwargs

9020567

fix pylint issues fix hover feature fix hover feature minor fixes

agustinaarroyuelo mentioned this pull request Mar 3, 2020

New example pairplots #1105

Closed

update docstring

9881715

run pylint

update changelog

5a479b7

aloctavodia approved these changes Mar 4, 2020

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OriolAbril approved these changes Mar 4, 2020

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ahartikainen merged commit 3081799 into arviz-devs:master Mar 5, 2020

agustinaarroyuelo deleted the pairplot_jointplot branch March 5, 2020 12:13

hectormz mentioned this pull request Mar 6, 2020

Easily plot and compare multiple marginal posteriors #662

Open

agustinaarroyuelo mentioned this pull request Mar 6, 2020

[WIP] add new examples for plot_pair #1110

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[WIP] Modify pairplot to include jointplot and cornerplot like features #1079

[WIP] Modify pairplot to include jointplot and cornerplot like features #1079

agustinaarroyuelo commented Feb 18, 2020 •

edited by aloctavodia

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agustinaarroyuelo commented Mar 5, 2020

[WIP] Modify pairplot to include jointplot and cornerplot like features #1079

[WIP] Modify pairplot to include jointplot and cornerplot like features #1079

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agustinaarroyuelo commented Feb 18, 2020 • edited by aloctavodia Loading

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agustinaarroyuelo commented Feb 18, 2020 •

edited by aloctavodia

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