Inline example plots in docs

[ivirshup]

Meta-issue for tracking the addition of rendered plots in the examples sections of the API docs (initial functionality implemented in #1632).

We now allow code samples which generate plots in our docs. See the examples sections of calculate_qc_metrics and dotplot for examples of what this looks like. There is a short section in the dev docs with more information on how to make these: Plots in docstring

Here is a checklist of the functions which should have rendered examples. This list is not exclusive and can definitely be expanded.

Functions in sc.pl

• Embedding plots (these may deserve their own prose section)
  • sc.pl.embedding
  • sc.pl.draw_graph add various inline examples #1809 @AnnaChristina
  • sc.pl.diffmap add various inline examples #1809 @AnnaChristina
  • sc.pl.pca Add example PCA plots #1813 @lazappi
  • sc.pl.tsne add various inline examples #1809 @AnnaChristina
  • sc.pl.umap add inline examples #1830 @mayarali
  • sc.pl.embedding_density @ivirshup
• PCA specific
  • sc.pl.pca_loadings added example for PCA loadings plot #1815 @bio-la
  • sc.pl.pca_overview Added example plot for pca overview #1812 @MxMstrmn
  • sc.pl.pca_scatter
  • sc.pl.pca_variance_ratio docs: add inline example plot to sc.pl.pca_variance_ratio #4056 @Ekin-Kahraman
• PAGA
  • sc.pl.paga Inline example paga #1811 @le-ander
  • sc.pl.paga_adjacency
  • sc.pl.paga_compare
  • sc.pl.paga_path
• DPT pseudotime
  • sc.pl.dpt_groups_pseudotime
  • sc.pl.dpt_timeseries
• Groupby
  • sc.pl.dotplot @ivirshup
  • sc.pl.matrixplot Plot documentation for matrixplot #1808 @mbuttner
  • sc.pl.clustermap More inline example plots in docs #2509 @giuliafrrn
  • sc.pl.heatmap add various inline examples #1809 @AnnaChristina
  • sc.pl.dendrogram add various inline examples #1809 @AnnaChristina
  • sc.pl.stacked_violin More inline example plots in docs #2509 @giuliafrrn
  • sc.pl.tracksplot More inline example plots in docs #2509 @giuliafrrn
  • sc.pl.violin add violin plot example #1814 @Hrovatin
• Preprocessing
  • sc.pl.filter_genes_dispersion
  • sc.pl.highest_expr_genes docs(plotting): add inline plot example for highest_expr_genes #4025 @haoyu-haoyu
  • sc.pl.highly_variable_genes docs: add inline example plot to sc.pl.highly_variable_genes #4032 @Ekin-Kahraman
• DE
  • sc.pl.rank_genes_groups add inline examples #1830 @mayarali
  • sc.pl.rank_genes_groups_dotplot Add example plots to sc.pl.rank_genes_groups_dotplot docstring #1810 @LouisK92 new options to rank_genes_groups plots #1529 @fidelram
  • sc.pl.rank_genes_groups_heatmap add inline examples #1830 @mayarali
  • sc.pl.rank_genes_groups_matrixplot new options to rank_genes_groups plots #1529 @fidelram
  • sc.pl.rank_genes_groups_stacked_violin docs: add inline example plot to sc.pl.rank_genes_groups_stacked_violin #4057 @Ekin-Kahraman
  • sc.pl.rank_genes_groups_tracksplot
  • sc.pl.rank_genes_groups_violin docs: add inline example plot to sc.pl.rank_genes_groups_violin #4058 @Ekin-Kahraman
• Misc/ to be classified
  • sc.pl.ranking
  • sc.pl.scatter
  • sc.pl.sim
  • sc.pl.correlation_matrix docs: add inline example plot to sc.pl.correlation_matrix #4059 @Ekin-Kahraman
  • sc.pl.matrix
• Time series (???)
  • sc.pl.timeseries
  • sc.pl.timeseries_as_heatmap
  • sc.pl.timeseries_subplot

Other functions

• sc.pp.calculate_qc_metrics @ivirshup (?)
• sc.tl.embedding_density @ivirshup (?)
• sc.get.obs_df
• sc.get.rank_genes_groups_df