harpy.tb.nhood_enrichment

harpy.tb.nhood_enrichment(sdata, labels_name, table_name, output_table_name, celltype_column='annotation', seed=0, overwrite=False)

Calculate the nhood enrichment using squidpy via squidpy.gr.spatial_neighbors() and squidpy.gr.nhood_enrichment().

Parameters:

• sdata (SpatialData) – Input spatialdata.SpatialData object containing spatial data.

• labels_name (list[str]) – The labels element(s) of sdata used to select the cells via the region key in sdata.tables[table_name].obs. Note that if output_table_name is equal to table_name and overwrite is True, cells in sdata.tables[table_name] linked to other labels_name (via the region key), will be removed from sdata.tables[table_name] (also from the backing zarr store if it is backed).

• table_name (str) – The table element in sdata.

• output_table_name (str) – The output table element in sdata.

• celltype_column (str (default: 'annotation')) – This will be passed to cluster_key of squidpy.gr.nhood_enrichment().

• seed (int (default: 0)) – seed

• overwrite (bool (default: False)) – If True, overwrites the output_table_name if it already exists in sdata.

Return type:

SpatialData

Returns:

: The updated spatialdata.SpatialData object.