Source code for stlearn.adds.add_lr

import pandas as pd
from anndata import AnnData




def lr(
    adata: AnnData,
    db_filepath: str,
    sep: str = "\t",
    source: str = "connectomedb",
    copy: bool = False,
) -> AnnData | None:
    """Add significant Ligand-Receptor pairs into AnnData object

    Parameters
    ----------
    adata: AnnData
        The data object to add L-R info into
    db_filepath: str
        The path to the CPDB results file
    sep: str
        Separator of the CPDB results file
    source: str
        Source of LR database (default: connectomedb, can also support 'cellphonedb')
    copy: bool
        Copy flag indicating copy or direct edit

    Returns
    -------
    adata: AnnData          The data object that L-R added into

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

    if source == "cellphonedb":
        cpdb = pd.read_csv(db_filepath, sep=sep)
        adata.uns["cpdb"] = cpdb
        lr = cpdb["interacting_pair"].to_list()
        lr2 = [i for i in lr if "complex" not in i]
        lr3 = [i for i in lr2 if " " not in i]
        lr4 = [i for i in lr3 if i.count("_") == 1]
        adata.uns["lr"] = lr4
        print("cpdb results added to adata.uns['cpdb']")
        print("Added ligand receptor pairs to adata.uns['lr'].")

    elif source == "connectomedb":
        ctdb = pd.read_csv(db_filepath, sep=sep, quotechar='"', encoding="latin1")
        adata.uns["lr"] = (
            ctdb["Ligand gene symbol"] + "_" + ctdb["Receptor gene symbol"]
        ).values.tolist()
        print("connectomedb results added to adata.uns['ctdb']")
        print("Added ligand receptor pairs to adata.uns['lr'].")

    return adata if copy else None