ingest

Integrates embeddings and annotations of an adata with a reference dataset adata_ref through projecting on a PCA (or alternate model) that has been fitted on the reference data. The function uses a knn classifier for mapping labels and the UMAP package [McInnes18]_ for mapping the embeddings.

Parameters

obs: List[str] List of obs keys in adata_ref.obs which need to be mapped to adata.obs.

Web view

ingest_screenshot

Python equivalent

import scanpy as sc

sc.pp.neighbors(adata_ref.adata)
sc.tl.umap(adata_ref.adata)
sc.tl.ingest(adata=adata_target, adata_ref=adata_ref.adata, obs='umap')
  