dynamo.tl.scc(adata, min_cells=100, spatial_key='spatial', e_neigh=30, s_neigh=6, resolution=None, copy=False)[source]

Spatially constrained clustering (scc) to identify continuous tissue domains.

  • adata (AnnData) – an Anndata object, after normalization.

  • min_cells (int) – minimal number of cells the gene expressed.

  • spatial_key (str) – the key in .obsm that corresponds to the spatial coordinate of each bucket.

  • e_neigh (int) – the number of nearest neighbor in gene expression space.

  • s_neigh (int) – the number of nearest neighbor in physical space.

  • resolution (Optional[float]) – the resolution parameter of the leiden clustering algorithm.

  • copy (bool) – Whether to return a new deep copy of adata instead of updating adata object passed in arguments. Defaults to False.

Return type



Depends on the argument copy return either an ~anndata.AnnData object with cluster info in “scc_e_{a}_s{b}” or None.