umap

Compute UMAP coordinates as part of the integration process.

Parameters

color: List[str] Color of UMAP clusters. If multiple colors are supplied, it will generate separate plots for each color.

Web view

umap_screenshot

Python equivalent

import scanpy as sc

sc.pp.neighbors(adata)
sc.tl.leiden(adata)
sc.tl.umap(adata)
sc.pl.umap(adata, color='BATCH')