dynamo.tl.scc

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.

Parameters:

  • adata (AnnData) – A normalized AnnData object.

  • min_cells (int (default: 100)) – Minimal number of cells the gene expressed. Defaults to 100.

  • spatial_key (str (default: 'spatial')) – The key in .obsm corresponding to the spatial coordinate of each bucket. Defaults to “spatial”.

  • e_neigh (int (default: 30)) – The number of nearest neighbor in gene expression space. Defaults to 30.

  • s_neigh (int (default: 6)) – The number of nearest neighbor in physical space. Defaults to 6.

  • resolution (Optional[float] (default: None)) – The resolution parameter of the leiden clustering algorithm. Defaults to None.

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

Return type:

Optional[AnnData]

Returns:

An updated AnnData object with cluster info stored in .obs[scc_e_{a}_s{b}] if copy is set to be true.