cospar.pp.get_state_info

cospar.pp.get_state_info(adata, n_neighbors=20, resolution=0.5)

Update state_info using scanpy.tl.leiden()

We assume that adata.obsm[‘X_pca’] exists. It first runs KNN graph construction.

Parameters
adata : AnnData object

n_neighbors : int, optional (default: 20)

Neighber number for constructing the KNN graph, using the UMAP method.

resolution : float, optional (default: 0.5)

A parameter value controlling the coarseness of the clustering. Higher values lead to more clusters.

Returns

  • Modify adata.obs[‘state_info’].

  • If ‘state_info’ existed before, save a copy at adata.obs[‘state_info_old’]