Source code for stlearn.adds.add_deconvolution

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