netmap.downstream.clustering.process

netmap.downstream.clustering.process(grn_adata, n_clu=2, key_added='spectral', **kwargs)[source]

Prepare GRN AnnData and run the full clustering pipeline.

Fills NaN values in grn_adata.X with 0, calls downstream_recipe(), then adds spectral clustering via spectral_clustering().

Parameters:

  • grn_adata (anndata.AnnData) – GRN AnnData to cluster.

  • n_clu (int) – Number of spectral clusters. Defaults to 2.

  • key_added (str) – Column name for spectral labels in .obs. Defaults to 'spectral'.

  • **kwargs – Forwarded to downstream_recipe().

Returns:

Clustered GRN AnnData.

Return type:

anndata.AnnData