Ingest Verbose

Source: src/single_cell_python_tools/tools/_ingest_verbose.py

This module contains a modified Scanpy ingest workflow. The package source notes that it supports adding more than one reference observation column to the query object during ingest.

ingest_verbose

ingest_verbose(
    adata,
    adata_ref,
    obs=None,
    embedding_method=("umap", "pca"),
    labeling_method="knn",
    neighbors_key=None,
    inplace=True,
    **kwargs,
)

Map labels and embeddings from a reference AnnData object to a query AnnData object.

Ingest

Ingest(adata, neighbors_key=None)

Class used to map labels and embeddings from existing data to new data. The source docstring notes that scanpy.pp.neighbors should be run on the reference object before initializing Ingest.

Important public methods include:

• fit(adata_new): fit ingest state to a new AnnData object.

• neighbors(k=None, queue_size=5, epsilon=0.1, random_state=0): find neighbors.

• map_embedding(method): map embeddings such as UMAP or PCA.

• map_labels(labels, method): map labels from the reference object.

• to_adata(inplace=False): return or update an AnnData object with mapped results.

• to_adata_joint(...): create a joint object from reference and query data.

Export Note

The current tools/__init__.py comments out _ingest_verbose exports, so import this module directly if needed:

from single_cell_python_tools.tools._ingest_verbose import ingest_verbose, Ingest