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