singleCellHaystack.cluster_genes

singleCellHaystack.cluster_genes(adata, haystack_result, method='kmeans', n_clusters=None, n_genes=100, random_state=None)

Cluster singleCellHaystack results into gene modules.

Parameters:

• adata – AnnData object.

• haystack_result – singleCellHaystack result.

• method – clustering method. Currently only sklearn.cluster.KMeans implemented.

• n_clusters – number of clusters for KMeans.

• n_genes – number of top genes to cluster.

• random_state – number to set random_state in clustering method.