squidpy.gr.interaction_matrix

squidpy.gr.interaction_matrix(adata, cluster_key, connectivity_key=None, normalized=False, copy=False, weights=False)

Compute interaction matrix for clusters.

Parameters:

• adata (AnnData | SpatialData) – Annotated data object.

• cluster_key (str) – Key in anndata.AnnData.obs where clustering is stored.

• connectivity_key (Optional[str]) – Key in anndata.AnnData.obsp where spatial connectivities are stored. Default is: anndata.AnnData.obsp ['spatial_connectivities'].

• normalized (bool) – If True, each row is normalized to sum to 1.

• copy (bool) – If True, return the result, otherwise save it to the adata object.

• weights (bool) – Whether to use edge weights or binarize.

Return type:

Optional[ndarray[Any, dtype[Any]]]

Returns:

: If copy = True, returns the interaction matrix.

Otherwise, modifies the adata with the following key:

• anndata.AnnData.uns ['{cluster_key}_interactions'] - the interaction matrix.