commot.tl.cluster_position

commot.tl.cluster_position(adata, clustering=None, method='geometric_mean', copy=False)

Assign spatial positions to clusters.

Parameters

• adata (AnnData) – The data matrix of shape n_obs × n_var. Rows correspond to cells or positions and columns to genes.

• clustering (Optional[str]) – Name of clustering with the labels stored in .obs[clustering].

• method (str) – ‘geometric_mean’ geometric mean of the positions. ‘representative_point’ the position in the cluster with minimum total distance to other points.

• copy (bool) – Whether to return a copy of the anndata.AnnData.

Returns

adata – Add cluster positions to .uns['cluster_pos-clustering_name'] for the clustering named ‘clustering_name’. If copy=True, return the AnnData object and return None otherwise.

Return type

anndata.AnnData