smftools.tools.calculate_leiden

smftools.tools.calculate_leiden(adata, *, resolution=0.1, key_added='leiden', connectivities_key='connectivities')

Compute Leiden clusters from a connectivity graph.

Parameters:

• adata (AnnData) -- AnnData object with obsp[connectivities_key] set.

• resolution (float (default: 0.1)) -- Resolution parameter for Leiden clustering.

• key_added (str (default: 'leiden')) -- Column name to store cluster assignments in adata.obs.

• connectivities_key (str (default: 'connectivities')) -- Key in adata.obsp containing a sparse adjacency matrix.

Return type:

AnnData

Returns:

Updated AnnData object with Leiden labels in adata.obs.