rapids_singlecell.tl.leiden

rapids_singlecell.tl.leiden(adata, resolution=1.0, *, random_state=0, restrict_to=None, key_added='leiden', adjacency=None, n_iterations=100, use_weights=True, neighbors_key=None, obsp=None, copy=False)

Performs Leiden clustering using cuGraph, which implements the method described in:

Traag, V.A., Waltman, L., & van Eck, N.J. (2019). From Louvain to Leiden: guaranteeing well-connected communities. Sci. Rep., 9(1), 5233. DOI: 10.1038/s41598-019-41695-z

Parameters:

adata AnnData

annData object

resolution float (default: 1.0)

A parameter value controlling the coarseness of the clustering. (called gamma in the modularity formula). Higher values lead to more clusters.

random_state int | None (default: 0)

Change the initialization of the optimization. Defaults to 0.

restrict_to tuple[str, Sequence[str]] | None (default: None)

Restrict the clustering to the categories within the key for sample annotation, tuple needs to contain (obs_key, list_of_categories).

key_added str (default: 'leiden')

adata.obs key under which to add the cluster labels.

adjacency spmatrix | None (default: None)

Sparse adjacency matrix of the graph, defaults to neighbors connectivities.

n_iterations int (default: 100)

This controls the maximum number of levels/iterations of the Leiden algorithm. When specified, the algorithm will terminate after no more than the specified number of iterations. No error occurs when the algorithm terminates early in this manner.

use_weights bool (default: True)

If True, edge weights from the graph are used in the computation (placing more emphasis on stronger edges).

neighbors_key str | None (default: None)

If not specified, leiden looks at .obsp['connectivities'] for neighbors connectivities. If specified, leiden looks at .obsp[.uns[neighbors_key]['connectivities_key']] for neighbors connectivities.

obsp str | None (default: None)

Use .obsp[obsp] as adjacency. You can’t specify both obsp and neighbors_key at the same time.

copy bool (default: False)

Whether to copy adata or modify it in place.

Return type:

AnnData | None