spamosaic.utils.mclust_R

spamosaic.utils.mclust_R(adata, num_cluster, modelNames='EEE', used_obsm='emb', random_seed=2020)[source]

Run R’s Mclust (via rpy2) on an embedding to obtain soft clustering.

Parameters:

  • adata (AnnData) – AnnData with embedding stored in .obsm.

  • num_cluster (int) – Desired number of clusters.

  • modelNames (str, default='EEE') – Covariance structure model in Mclust.

  • used_obsm (str, default='emb') – Key in .obsm to use for clustering.

  • random_seed (int, default=2020) – Random seed for both NumPy and R.

Returns:

Annotated object with a categorical column obs['mclust'].

Return type:

AnnData