past.Evaluation.default_leiden¶
- past.Evaluation.default_leiden(adata, refine=False, num_nbs=6, use_rep='embedding')¶
Default leiden clustering algorithm applied in scanpy package with default resolution 1.0
- Parameters:
adata – target dataset of anndata format with latent feature stored in adata.obsm[use_rep] or with result of pp.neighbors
refine – whether or not refine clustering results, if True, spatial coordinate should be stored in adata.obsm[“spatial”]
num_nbs – number of neighbors to consider when refining clustering labels, valid only if refine is True
use_rep – key of adata.obsm implying latent features
- Returns:
target dataset of anndata format with default leiden clustering result stored in adata.obs[“Dleiden”] and refined clustering result stored in adata.obs[“Dleiden_refined”] if refined is True
- Return type:
scanpy.anndata