SOAPy_st.tl.domain_from_STAGATE
- SOAPy_st.tl.domain_from_STAGATE(adata: AnnData, cluster_method: Literal['m_clust', 'louvain'] = 'm_clust', cluster_number: int = 10, cluster_key: str = 'domain', rad_cutoff: float | None = None, random_seed: int = 2020, resolution_louvain: float = 0.5, spatial_in_obsm: str = 'spatial', inplace: bool = True, **kwargs) AnnData
Using the STAGATE method generate the spatial domain. Detailed methods for STAGATE are available at https://stagate.readthedocs.io/en/latest/T1_DLPFC.html
Parameters
- adataanndata.AnnData
An AnnData object containing spatial omics data and spatial information.
- cluster_methodLiteral[‘m_clust’, ‘louvain’]
cluster method.
- cluster_numberint
number of clusters (if ‘cluster’ is m_cluster)
- cluster_keystr
Store the new label name for the domain category in adata.
- rad_cutofffloat, optional
radius cutoff of spatial neighborhood.
- random_seedint
Random seed used in m_cluster.
- resolution_louvainfloat
resolution used in louvain cluster.
- spatial_in_obsmstr
The key of spatial coordinates in adata.obsm
- inplacebool
If True, Modify directly in the original adata.
- **kwargsANY
Parameters of STAGATE.train_STAGATE().
Returns
anndata.AnnData.obsdomain- The cluster of spatial domain.