monkeybread.calc.shortest_distances

monkeybread.calc.shortest_distances(adata, groupby, group1, group2, basis='X_spatial')

Calculates the distance from each cell in one group to the nearest cell in another group.

Parameters:

  • adata (AnnData) – Annotated data matrix.

  • groupby (str) – A categorical column in adata.obs to classify groups.

  • group1 (Union[str, List[str]]) – Either one value or a list of values from adata.obs[groupby].

  • group2 (Union[str, List[str]]) – Either one value or a list of values from adata.obs[groupby].

  • basis (Optional[str] (default: 'X_spatial')) – Coordinates in adata.obsm[{basis}] to use. Defaults to spatial.

Return type:

DataFrame

Returns:

: A dataframe, indexed by cells in group1. The dataframe has two columns, distance and nearest_cell, corresponding to the distance to the nearest cell in group2 and the index of that cell respectively.