nichepca.clustering.leiden_unique

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nichepca.clustering.leiden_unique#

nichepca.clustering.leiden_unique(adata, use_rep=None, resolution=1.0, n_neighbors=15, key_added='leiden', flavor='igraph', n_iterations=2, **kwargs)#

Perform Leiden clustering with duplicate embeddings.

Parameters:

  • adata (AnnData) – Anndata object with the graph information.

  • use_rep (str | None (default: None)) – The embedding to use for clustering, by default None.

  • resolution (float (default: 1.0)) – The resolution parameter for the Leiden algorithm, by default 1.0.

  • n_neighbors (int (default: 15)) – The number of neighbors to use for the Leiden algorithm, by default 15.

  • key_added (str (default: 'leiden')) – The key to store the cluster assignments in the adata object, by default “leiden”.

  • flavor (str (default: 'igraph')) – The flavor of the Leiden algorithm to use, by default “igraph”.

  • n_iterations (int (default: 2)) – The number of iterations for the Leiden algorithm, by default 2.

  • **kwargs (dict) – Additional keyword arguments to be passed to sc.tl.leiden.

Returns:

None

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