neighbourhood graph
Compute neighbourhood graph with color mapping for selected genes.
Parameters
genes: List[str] Genes to supply as color argument in PCA.
Web view
Python equivalent
import scanpy as sc
genes = ['brca1', 'brca2']
sc.pp.neighbors(adata, n_neighbors=10, n_pcs=40)
sc.tl.leiden(adata)
sc.tl.paga(adata)
sc.pl.paga(adata, use_raw=use_raw, plot=False)
sc.tl.umap(adata, init_pos='paga')
sc.pl.umap(adata)