sparrow.pl.nhood_enrichment

sparrow.pl.nhood_enrichment#

sparrow.pl.nhood_enrichment(sdata, table_layer, celltype_column='annotation', output=None)#

Plot the neighborhood enrichment across cell-type annotations.

Enrichment is shown in a hierarchically clustered heatmap. Each entry in the heatmap indicates if the corresponding cluster pair (or cell-type pair) is over-represented or over-depleted for node-node interactions in the spatial connectivity graph.

Parameters:

  • sdata (SpatialData) – The SpatialData object containing the data for analysis.

  • table_layer (str) – The table layer in sdata to visualize.

  • celltype_column (str (default: 'annotation')) – The column name in the SpatialData object’s table that specifies the cell type annotations. The default value is _ANNOTATION_KEY.

  • output (Optional[str] (default: None)) – If provided, the plot will be displayed and also saved to a file with the specified filename. If None, the plot will be displayed directly without saving.

Return type:

None

Returns:

: None

Notes

See https://www.nature.com/articles/s41592-021-01358-2 for details on the permutation-based neighborhood enrichment score.

See also

sparrow.tb.nhood_enrichment

Calculate neighborhood enrichment.

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