squidpy.gr.interaction_matrix

squidpy.gr.interaction_matrix(adata, cluster_key, connectivity_key=None, normalized=False, copy=False, weights=False, *, table_key=None)[source]

Compute interaction matrix for clusters.

Parameters:

adata (AnnData | SpatialData) – Annotated data object.
table_key (str | None) – Key in spatialdata.SpatialData.tables where the table is stored. Required when adata is a spatialdata.SpatialData object and ignored otherwise.
cluster_key (str) – Key in anndata.AnnData.obs where clustering is stored.
connectivity_key (str | None) – 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:

ndarray[tuple[Any, ...], dtype[Any]] | None

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.