Inline example plots in docs #1664
Labels
Area - Documentation 📒
Area - Plotting 🌺
Enhancement ✨
good first issue
easy first issue to get started in OSS community contribution!
Milestone
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
anddotplot
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 docstringHere 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
sc.pl.embedding
sc.pl.draw_graph
add various inline examples #1809 @AnnaChristinasc.pl.diffmap
add various inline examples #1809 @AnnaChristinasc.pl.pca
Add example PCA plots #1813 @lazappisc.pl.tsne
add various inline examples #1809 @AnnaChristinasc.pl.umap
add inline examples #1830 @mayaralisc.pl.spatial
sc.pl.embedding_density
@ivirshupsc.pl.pca_loadings
added example for PCA loadings plot #1815 @bio-lasc.pl.pca_overview
Added example plot for pca overview #1812 @MxMstrmnsc.pl.pca_scatter
sc.pl.pca_variance_ratio
sc.pl.paga
Inline example paga #1811 @le-andersc.pl.paga_adjacency
sc.pl.paga_compare
sc.pl.paga_path
sc.pl.dpt_groups_pseudotime
sc.pl.dpt_timeseries
sc.pl.dotplot
@ivirshupsc.pl.matrixplot
Plot documentation for matrixplot #1808 @mbuttnersc.pl.clustermap
More inline example plots in docs #2509 @giuliafrrnsc.pl.heatmap
add various inline examples #1809 @AnnaChristinasc.pl.dendrogram
add various inline examples #1809 @AnnaChristinasc.pl.stacked_violin
More inline example plots in docs #2509 @giuliafrrnsc.pl.tracksplot
More inline example plots in docs #2509 @giuliafrrnsc.pl.violin
add violin plot example #1814 @Hrovatinsc.pl.filter_genes_dispersion
sc.pl.highest_expr_genes
sc.pl.highly_variable_genes
sc.pl.rank_genes_groups
add inline examples #1830 @mayaralisc.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 @fidelramsc.pl.rank_genes_groups_heatmap
add inline examples #1830 @mayaralisc.pl.rank_genes_groups_matrixplot
new options to rank_genes_groups plots #1529 @fidelramsc.pl.rank_genes_groups_stacked_violin
sc.pl.rank_genes_groups_tracksplot
sc.pl.rank_genes_groups_violin
sc.pl.ranking
sc.pl.scatter
sc.pl.sim
sc.pl.correlation_matrix
sc.pl.matrix
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
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