omicverse.space.create_communication_anndata¶

omicverse.space.create_communication_anndata(adata, clustering_column, n_permutations=100)[source]¶

Build a CellChat-style communication AnnData from commot outputs.

Parameters:

adata (anndata.AnnData) – Input spatial AnnData containing commot communication matrices in adata.obsp and optional commot database metadata in adata.uns.
clustering_column (str) – Column name for cell type clustering
n_permutations (int) – Number of permutations for p-value calculation

Returns:

comm_adata – Communication results with structure: - obs: cell type pairs (‘celltype1|celltype2’) - var: ligand-receptor pairs with metadata - layers: ‘pvalues’ and ‘means’

Return type:

anndata.AnnData