Add plot directives

[rwhitt2049]

Checklist to go through for (potentially) replacing python code + png import with the plot directive. This is just a project management issue to give contributors some direction.

Quickstart

http://www.scikit-yb.org/en/latest/quickstart.html quickstart.rst

• [x] bikeshare_rank2d.png
• [x] temp_feelslike_jointplot.png
• [x] bikeshare_ols_residuals.png
• [x] bikeshare_ridge_alphas.png
• [x] bikeshare_ridge_prediction_error.png

Gallery

… lots to do and figure out here …

update: we've made the gallery independent and created a script to generate the gallery docs (the plot directive didn't work well in the gallery). See #732

Tutorial

update: this has been updated to use the new datasets module (see #818) but we've opted not to do the plot directive because it disrupts the flow of the tutorial and makes the docs take a long time to build

~Lot's of split code here, so I'll need to know how the team wants it formatted~

~http://www.scikit-yb.org/en/latest/tutorial.html# tutorial.rst~

~- [ ] modelselect_linear_svc.png~ ~- [ ] modelselect_nu_svc.png~ ~- [ ] modelselect_svc.png~ ~- [ ] modelselect_sgd_classifier.png~ ~- [ ] modelselect_kneighbors_classifier.png~ ~- [ ] modelselect_logistic_regression_cv.png~ ~- [ ] modelselect_logistic_regression.png~ ~- [ ] modelselect_bagging_classifier.png~ ~- [ ] modelselect_extra_trees_classifier.png~ ~- [ ] modelselect_random_forest_classifier.png~

API

• [ ] Anscombe's quartet: anscomb.png

Radviz

• [x] Features\radviz radviz.png

Rankd

• [x] Features\rankd rank1d_shapiro.png
• [x] Features\rankd rank2d_pearson.png
• [x] Features\rankd rank2d_covariance.png

Pcoords

• [x] Features\pcoords parallel_coordinates.png
• [x] Features\pcoords normalized_sampled_parallel_coordinates.png
• [x] Features\pcoords fast_vs_slow_parallel_coordinates.png
• [x] Features\pcoords fast_parallel_coordinates_speedup.png

PCA

• [x] Features\pca pca_projection_2d.png
• [x] Features\pca pca_projection_3d.png
• [x] Features\pca pca_biplot_2d.png
• [x] Features\pca pca_biplot_3d.png

Manifold

*update: we have opted not to use the plot directive for manifold because it makes the docs take a long time to build

~- [ ] Features\manifold concrete_tsne_manifold.png (this one has no accompanying code in rst)~ ~- [ ] Features\manifold occupancy_select_k_best_isomap_manifold.png~ ~- [ ] Features\manifold concrete_isomap_manifold.png~

Importances

• [x] Features\importances feature_importances.png
• [x] Features\importances feature_importances_coef.png
• [x] Features\importances feature_importances_stacked.png

RFECV

*update: we have opted not to use the plot directive for RFEVC because it makes the docs take a long time to build

~- [ ] Features\rfecv rfecv_sklearn_example.png~ ~- [ ] Features\rfecv rfecv_credit.png~

Joint plot

Note: Joint Plot documentation is updated in #728

Text Visualizers

DispersionPlot

• [x] Text\dispersionplot dispersion_docs.png

Note that the docs/api/text/images/dispersion_docs.png image was not removed because it is being used in the gallery.

[bbengfort]

Thank you so much for compiling this @rwhitt2049!

[rebeccabilbro]

Per #709 - when we update quickstart.rst to auto-gen the images, let's double check that the 45 degree line appears on the prediction error plot.

[rebeccabilbro]

Per #703 - when we update quickstart.rst to auto-gen the images, let's double-check that we're using fit_transform for the joint plot.

[bbengfort]

@rebeccabilbro for #709 and #703 should we just update the quickstart.rst in this PR rather than in an additional PR?

[rebeccabilbro]

@bbengfort - yep!

[bbengfort]

er ... sorry I thought that was a comment on the review for PR #446 (too many windows open); however, I am happy to make those changes in #446 if that will make the review easier.

[rebeccabilbro]

@bbengfort nah, I say we stick with keeping #446 nice and focused on the POC with the feature importances and k-elbow docs. So excited to be moving forward with this docs refresh!!

[bbengfort]

719 handles the quickstart documentation.

[bbengfort]

Note that the cleanup is going to require the gallery to be updated to use the plot directive relatively soon - the gallery uses many of the static images that we'd like to delete throughout this documentation process!

[bbengfort]

Note - we had to use the :context: close-figs on all of our plot directives to ensure they rendered correctly. I'm still looking into this, but it's something to be aware of as you're working on these files!

[rebeccabilbro]

One of things that @lwgray and @Kautumn06 identified as part of #669 is that when we updated theUMAPVisualizer to use the plot directive, the images don't show up in the ReadtheDocs version (but they do show up when you build locally). The reason for this is that we don't have the main dependency of UMAPVisualizer, an optional dependency umap-learn, in our requirements.txt. Since I don't think we want to require umap-learn, we might have to move back to using static images in the docs for the UMAPVisualizer — unless anyone has another suggestion?

[lwgray]

no other suggestions from me.

[rebeccabilbro]

Going to go ahead and mark this one complete! 🎉 Thanks for all the hard work to everyone who contributed to this massive but very worthwhile effort, with special thanks to @Kautumn06 @lwgray @pdamodaran for reviewing the large majority of the resulting PRs!