ENH Add kwargs to format ICE and PD lines separately in partial dependence plots #19428

mhham · 2021-02-10T13:47:14Z

This PR implements the feature specified in #18976 :

Add two keyword arguments to sklearn/inspection/_plot/partial_dependence.py:plot_partial_dependence : ice_lines_kw and pd_line_kw. They take priority over line_kw when not None and allow to format the ICE (individual) lines and the PD (average) line separately

Example:

from sklearn.ensemble import RandomForestRegressor
from sklearn.datasets import fetch_california_housing
from sklearn.inspection import plot_partial_dependence

X, y = fetch_california_housing(return_X_y=True, as_frame=True)
features = ['MedInc', 'AveOccup', 'HouseAge', 'AveRooms', 'AveOccup']
est = RandomForestRegressor(n_estimators=10)
est.fit(X, y)
display = plot_partial_dependence(
       est, X, features, kind="both", subsample=100,
       n_jobs=3, grid_resolution=20, random_state=0,
       line_kw={"color": "g", "linewidth": 5},
       pd_line_kw={"color": "r"},
       ice_lines_kw={"linewidth": 0.5, "color":"b", "alpha": 0.3},
)

Which outputs:

…dence plot

glemaitre · 2021-02-10T16:35:46Z

Please add an entry to the change log at doc/whats_new/v*.rst. Like the other entries there, please reference this pull request with :pr: and credit yourself (and other contributors if applicable) with :user:.

We would also need some test to check the behaviour. These tests are located in test_partial_dependence.py. We will have to check that setting the line will change the the plot. We can inspect the matplotlib axis for such checking.

What would be important is to check that if the new keywords are used, they takeover the previous available keyword.
We should also raise a warning if all keyword are set or maybe an error since it would not give a reasonable output.

…e_lines_kw

glemaitre

Let's also use the keyword in the documentation: https://scikit-learn.org/stable/auto_examples/inspection/plot_partial_dependence.html#sphx-glr-auto-examples-inspection-plot-partial-dependence-py to highlight the average line in a different color than blue.

sklearn/inspection/_plot/partial_dependence.py

sklearn/inspection/_plot/tests/test_plot_partial_dependence.py

Co-authored-by: Guillaume Lemaitre <[email protected]>

cmarmo · 2021-02-24T18:16:30Z

Hi @mhham thanks for your work so far! Do you mind synchronizing with upstream? Thanks!

cmarmo

Thanks @mhham for your work and your patience!
Do you mind modifying the example to show the enhancement you implemented? This is quite an improvement in the visualization!
Also, in the meanwhile some conflicts arose...

sklearn/inspection/_plot/partial_dependence.py

Co-authored-by: Chiara Marmo <[email protected]>

…lines

mhham · 2021-04-07T09:03:41Z

Thanks @mhham for your work and your patience!
Do you mind modifying the example to show the enhancement you implemented? This is quite an improvement in the visualization!
Also, in the meanwhile some conflicts arose...

All done 👍

glemaitre · 2021-04-09T08:33:32Z

I will review this PR shortly

glemaitre

I am finally back on the PDP feature. I merge the master changes into this PR. I made a couple of comments with a bit of cosmetic for the rendering but the core code looks fine.

examples/inspection/plot_partial_dependence.py

sklearn/inspection/_plot/partial_dependence.py

sklearn/inspection/_plot/tests/test_plot_partial_dependence.py

glemaitre

LGTM

jjerphan

Thanks for this contribution @mhham!

I have a suggestion to prevent irrelevant warnings to be raised.

sklearn/inspection/_plot/partial_dependence.py

examples/inspection/plot_partial_dependence.py

thomasjpfan

Thank you for the PR @mhham !

sklearn/inspection/_plot/partial_dependence.py

mhham · 2021-08-02T10:08:46Z

Thank you all for the subsequent work 👍 !

jjerphan

LGTM!

Thanks @mhham; this helps better interpreting partial dependencies plots. 👍

thomasjpfan

Minor comments on the docstrings, otherwise LGTM.

sklearn/inspection/_plot/partial_dependence.py

Co-authored-by: Julien Jerphanion <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

glemaitre · 2021-08-16T12:38:54Z

examples/inspection/plot_partial_dependence.py

-ax = Axes3D(fig)
-surf = ax.plot_surface(XX, YY, Z, rstride=1, cstride=1,
-                       cmap=plt.cm.BuPu, edgecolor='k')
+ax = Axes3D(fig, auto_add_to_figure=False)


AttributeError: Unknown property auto_add_to_figure

So it does not seem to be supported in all matplotlib version?

…dence plots (scikit-learn#19428) Co-authored-by: Guillaume Lemaitre <[email protected]> Co-authored-by: Chiara Marmo <[email protected]> Co-authored-by: Julien Jerphanion <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

Add parameters to format ICE and PD lines separately in partial depen…

f8ca2fd

…dence plot

github-actions bot added the module:inspection label Feb 10, 2021

glemaitre changed the title ~~Add kwargs to format ICE and PD lines separately in partial dependence plots~~ ENH Add kwargs to format ICE and PD lines separately in partial dependence plots Feb 10, 2021

mhham added 3 commits February 10, 2021 18:53

Add warning when line_kw is used in conjunction with pd_line_kw or ic…

3b71e0d

…e_lines_kw

Add test to check line formatting behavior in partial dependence plot

e35187d

Add PR info to whats_new

69c33fe

glemaitre reviewed Feb 11, 2021

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mhham and others added 5 commits February 11, 2021 11:01

Add call to action to silence line_kw warning

6a21afa

Co-authored-by: Guillaume Lemaitre <[email protected]>

Add comment to explain what test does

b2b5d74

Co-authored-by: Guillaume Lemaitre <[email protected]>

Add partial dependence line kwargs to documentation

41ede4d

Add line_kw ice_lines_kw pd_line_kw warnings test

281ad24

Formatting + pytest check UserWarning instead of Warning

8ff4183

cmarmo added Enhancement Waiting for Reviewer labels Feb 24, 2021

Merge branch 'main' into feature/pdp-ice-pd-lines

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mhham and others added 3 commits April 7, 2021 10:52

Apply suggestions from code review: versionadded

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Co-authored-by: Chiara Marmo <[email protected]>

Add ICE and PDP line formatting to example

6c2d85f

Merge remote-tracking branch 'upstream/main' into feature/pdp-ice-pd-…

61cca2e

…lines

glemaitre self-requested a review April 9, 2021 08:33

glemaitre added 2 commits June 29, 2021 18:11

Merge remote-tracking branch 'origin/main' into pr/mhham/19428

7839d7e

fix whats new

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black

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solve issue warning

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Merge remote-tracking branch 'origin/main' into pr/mhham/19428

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avoid warning

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Co-authored-by: Julien Jerphanion <[email protected]> Co-authored-by: Thomas J. Fan <[email protected]>

Merge remote-tracking branch 'origin/main' into pr/mhham/19428

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Update plot_partial_dependence.py

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glemaitre merged commit 696ca3d into scikit-learn:main Aug 16, 2021

madhuracj mentioned this pull request May 17, 2022

Make it easy to use different color for mean in plot_partial_dependence #18976

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ENH Add kwargs to format ICE and PD lines separately in partial dependence plots #19428

ENH Add kwargs to format ICE and PD lines separately in partial dependence plots #19428

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