bento.tl.comp_diff

bento.tl.comp_diff(sdata, points_key, shape_names, groupby, ref_group) → SpatialData

Calculate the average difference in gene composition for shapes across batches of cells.

Uses the Wasserstein distance to compare compositions.

Parameters:

  • sdata (SpatialData) – SpatialData object.

  • points_key (str) – Key for points DataFrame in sdata.points.

  • shape_names (List[str]) – Names of shapes to calculate compositions for.

  • groupby (str) – Key in sdata.points[points_key] to group cells by.

  • ref_group (str) – Reference group to compare other groups to.

Returns:

Updated SpatialData object with composition statistics for each group stored in sdata.tables[“table”].uns[“{groupby}_comp_stats”].

Return type:

SpatialData