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 normalized AnnData object.min_cells (
int) – minimal number of cells the gene expressed. Defaults to 100.spatial_key (
str) – the key in .obsm corresponding to the spatial coordinate of each bucket. Defaults to “spatial”.e_neigh (
int) – the number of nearest neighbor in gene expression space. Defaults to 30.s_neigh (
int) – the number of nearest neighbor in physical space. Defaults to 6.resolution (
Optional[float]) – the resolution parameter of the leiden clustering algorithm. Defaults to None.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:
An updated AnnData object with cluster info stored in .obs[scc_e_{a}_s{b}] if copy is set to be true.