cospar.pp.get_X_emb¶
-
cospar.pp.
get_X_emb
(adata, n_neighbors=20, umap_min_dist=0.3)¶ Get X_emb using
scanpy.tl.umap()
We assume that X_pca is computed. 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.
- umap_min_dist : float, optional (default: 0.3)
The effective minimum distance between embedded points.
- adata :
- Returns
Modify adata.obsm[‘X_emb’].
If ‘X_emb’ existed before, save a copy at adata.obs[‘X_emb_old’]