bento.tl.coloc_quotient

bento.tl.coloc_quotient(sdata, points_key='transcripts', instance_key='cell_boundaries', feature_key='feature_name', shapes=['cell_boundaries'], radius=20, min_points=10, min_cells=0)

Calculate pairwise gene colocalization quotient in each cell.

Parameters:

  • sdata (SpatialData) – Spatial formatted SpatialData object.

  • points_key (str) – Key that specifies transcript points in sdata.

  • instance_key (str) – Key that specifies cell_boundaries instance in sdata.

  • feature_key (str) – Key that specifies genes in sdata.

  • shapes (list) – Specify which shapes to compute colocalization separately.

  • radius (int) – Unit distance to count neighbors, default 20

  • min_points (int) – Minimum number of points for sample to be considered for colocalization, default 10

  • min_cells (int) – Minimum number of cells for gene to be considered for colocalization, default 0

Returns:

sdata – .table.uns[‘clq’]: Pairwise gene colocalization similarity within each cell formatted as a long dataframe.

Return type:

SpatialData