scmorph.pp.umap

scmorph.pp.umap(adata, **kwargs)

Embed the neighborhood graph using UMAP [McInnes et al., 2018].

This function wraps the higher-level function umap() ([Wolf et al., 2018].)

Parameters:

adata AnnData

AnnData object

kwargs

Additional arguments passed to umap().

Return type:

AnnData | None

Returns:

Returns None if copy=False, else returns an AnnData object. Sets the following fields:

adata.obsm['X_umap' | key_added]numpy.ndarray (dtype float)

UMAP coordinates of data.

adata.uns['umap' | key_added]dict

UMAP parameters.