pyXenium.contour.summarize_contour_composition

summarize_contour_composition(sdata, *, contour_key, contour_query=None, cell_type_key=None, cell_query=None, genes=None, gene_sets=None, transcript_query=None, feature_key='gene_name')

Summarize cell-type and gene/program composition inside each contour.

The returned dictionary contains long-form tables for cell composition, gene-level transcript composition, program-level transcript composition, and one contour-level summary table. Membership is based on cell centroids or transcript coordinates intersecting each contour polygon.

Parameters:

• sdata (XeniumSlide)

• contour_key (str)

• contour_query (str | None)

• cell_type_key (str | None)

• cell_query (str | None)

• genes (str | Sequence[str] | None)

• gene_sets (Mapping[str, Sequence[str]] | None)

• transcript_query (str | None)

• feature_key (str)

Return type:

dict[str, DataFrame]