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.

Returns

• Modify adata.obsm[‘X_emb’].

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