Source code for stlearn.adds.add_loupe_clusters

from pathlib import Path

import numpy as np
import pandas as pd
from anndata import AnnData
from natsort import natsorted




def add_loupe_clusters(
    adata: AnnData,
    loupe_path: Path | str,
    key_add: str = "multiplex",
    copy: bool = False,
) -> AnnData | None:
    """\
    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.

    """
    adata = adata.copy() if copy else adata

    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")),
    )

    return adata if copy else None