from typing import Optional, Union
from anndata import AnnData
import pandas as pd
import numpy as np
from pathlib import Path
[docs]def add_deconvolution(
adata: AnnData,
annotation_path: Union[Path, str],
copy: bool = False,
) -> Optional[AnnData]:
"""\
Adding label transfered from Seurat
Parameters
----------
adata
Annotated data matrix.
annotation_path
Path of the output of label transfer result by Seurat
copy
Return a copy instead of writing to adata.
Returns
-------
Depending on `copy`, returns or updates `adata` with the following fields.
**[cluster method name]_anno** : `adata.obs` field
The annotation of cluster results.
"""
label = pd.read_csv(annotation_path, index_col=0)
label = label[adata.obs_names]
adata.obsm["deconvolution"] = label[adata.obs.index].T