Source code for stlearn.adds.add_loupe_clusters

from typing import Optional, Union
from anndata import AnnData
import pandas as pd
import numpy as np
import stlearn
from pathlib import Path
from natsort import natsorted

[docs]def add_loupe_clusters( adata: AnnData, loupe_path: Union[Path, str], key_add: str = "multiplex", 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 use_label Choosing cluster type. threshold Quantile threshold of label 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(loupe_path) adata.obs[key_add] = pd.Categorical( values=np.array(label[key_add]).astype("U"), categories=natsorted(label[key_add].unique().astype("U")), )