docs(plotting): add inline example plots for 4 sc.pl functions (#1664)#4103
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…ing, paga_compare (scverse#1664) Adds Examples sections with `.. plot::` directives to four public plotting functions that lacked rendered examples in the API reference: - sc.pl.embedding: UMAP coloured by cell-type, plus a multi-panel example - sc.pl.scatter: obs-vs-obs, gene-vs-gene, and basis-driven panels - sc.pl.ranking: top-3 PC loadings, with and without the lowest values - sc.pl.paga_compare: PAGA graph next to the UMAP embedding All examples use the bundled sc.datasets.pbmc68k_reduced() so the docs build stays self-contained and deterministic. Refs scverse#1664.
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Summary
Adds inline example plots to four
sc.pl.*functions still unchecked on the issue #1664 checklist:sc.pl.embedding— top of the list; the generic embedding plottersc.pl.scatter— daily-driver basic scatter (currently in "Misc")sc.pl.ranking— small example showing thepl.pca_loadings-style usagesc.pl.paga_compare— closes a gap in the PAGA sectionEach new Examples section uses one or more
.. plot:: :context: close-figsblocks and the bundledsc.datasets.pbmc68k_reduced()dataset, no network downloads, deterministic across CI runs. The matplotlibplot_directiveis already wired up indocs/conf.py, so no Sphinx config changes were needed.For
sc.pl.ranking, the example subsets toadata[:, adata.var["highly_variable"]]becausepbmc68k_reducedcarries PCA loadings only for the highly-variable subset (the rest areNaN); without subsetting,argsortpulls the NaNs tothe top and
set_ylimraises. Subsetting in the example also reads as a useful hint for users.I confirmed none of these functions overlap with @Ekin-Kahraman's recently-merged PRs (#4056-#4059).
Refs #1664.
Why this issue
scanpy's plotting API is the daily workhorse for single-cell exploratory analysis. Embedding example plots directly under each function's docstring closes the loop between API reference and visual output, exactly the "honest reporting + high-impact dashboard" principle I bring to data work.
Test plan
sc.pl.dotplot,sc.pl.umap, etc.)