cellcharter.gr.remove_intra_cluster_links

cellcharter.gr.remove_intra_cluster_links(adata, cluster_key, connectivity_key=None, distances_key=None, copy=False)

Remove links between cells that belong to the same cluster.

Used in cellcharter.gr.nhood_enrichment() to consider only interactions between cells of different clusters.

Parameters:

• adata (AnnData) – Annotated data object.

• cluster_key (str) – Key in anndata.AnnData.obs of the cluster labeling to consider.

• connectivity_key (Optional[str] (default: None)) – Key in anndata.AnnData.obsp where spatial connectivities are stored. Default is: anndata.AnnData.obsp ['spatial_connectivities'].

• distances_key (Optional[str] (default: None)) – Key in anndata.AnnData.obsp where spatial distances are stored. Default is: anndata.AnnData.obsp ['{{Key.obsp.spatial_dist()}}'].

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

Return type:

tuple[csr_matrix, csr_matrix] | None

Returns:

If copy = True, returns a tuple with the new spatial connectivities and distances matrices.

Otherwise, modifies the adata with the following keys:

• anndata.AnnData.obsp ['{{connectivity_key}}'] - the new spatial connectivities.

• anndata.AnnData.obsp ['{{distances_key}}'] - the new spatial distances.