spamosaic.utils.clustering

spamosaic.utils.clustering(adata, n_cluster, used_obsm, algo='kmeans', key='tmp_clust')

Cluster cells using k-means or Mclust and store labels in .obs.

Parameters:

• adata (AnnData) – Input data with an embedding in .obsm[used_obsm].

• n_cluster (int) – Number of clusters.

• used_obsm (str) – Key in .obsm to cluster on.

• algo ({'kmeans', 'mclust'}, default='kmeans') – Clustering algorithm to use.

• key (str, default='tmp_clust') – Column name in .obs to store cluster labels.

Returns:

Annotated object with cluster assignments in .obs[key].

Return type:

AnnData