liana.method.cellphonedb.__call__

cellphonedb.__call__(adata: AnnData | MuData, groupby: str, resource_name: str = 'consensus', expr_prop: float = 0.1, min_cells: int = 5, groupby_pairs: DataFrame | None = None, base: float = np.float64(2.718281828459045), supp_columns: list | None = None, return_all_lrs: bool = False, key_added: str = 'liana_res', use_raw: bool | None = True, layer: str | None = None, de_method: str = 't-test', n_perms: int = 1000, seed: int = 1337, n_jobs: int = 1, resource: DataFrame | None = None, interactions: list | None = None, mdata_kwargs: dict = {}, inplace: bool = True, verbose: bool | None = False)

Run a ligand-receptor method.

Parameters:

adata

Annotated data object.

groupby

Key to be used for grouping.

resource_name

Name of the resource to be used for ligand-receptor inference. See li.rs.show_resources() for available resources.

expr_prop

Minimum expression proportion for the ligands and receptors (+ their subunits) in the corresponding cell identities. Set to 0 to return unfiltered results.

min_cells

Minimum cells (per cell identity if grouped by groupby) to be considered for downstream analysis.

groupby_pairs

A DataFrame with columns source and target to be used to subset the possible combinations of interacting cell types. If None, all possible combinations are used.

base

Exponent base used to reverse the log-transformation of the matrix. Relevant only for the logfc method.

supp_columns

Additional columns to be added from any of the methods implemented in liana, or any of the columns returned by scanpy.tl.rank_genes_groups, each starting with ligand_* or receptor_*. For example, [‘ligand_pvals’, ‘receptor_pvals’]. None by default.

return_all_lrs

Bool whether to return all ligand-receptor pairs, or only those that surpass the expr_prop threshold. Ligand-receptor pairs that do not pass the expr_prop threshold will be assigned to the worst score of the ones that do. False by default.

key_added

Key under which the results will be stored in adata.uns if inplace is True.

use_raw

Use raw attribute of adata if present.

layer

Layer in anndata.AnnData.layers to use. If None, use anndata.AnnData.X.

de_method

Differential expression method. scanpy.tl.rank_genes_groups is used to rank genes according to 1vsRest. The default method is ‘t-test’.

verbose

Verbosity flag.

n_perms

Number of permutations for the permutation test. Relevant only for permutation-based methods (e.g., CellPhoneDB). If None is passed, no permutation testing is performed.

seed

Random seed for reproducibility.

n_jobs

Number of jobs to run in parallel.

resource

A pandas dataframe with [ligand, receptor] columns. If provided will overrule the resource requested via resource_name

interactions

List of tuples with ligand-receptor pairs [(ligand, receptor), …] to be used for the analysis. If passed, it will overrule the resource requested via resource and resource_name.

mdata_kwargs

Keyword arguments to be passed to li.fun.mdata_to_anndata if adata is an instance of MuData. If an AnnData object is passed, these arguments are ignored.

inplace

Whether to store results in place, or else to return them.

Returns:

If inplace = False, returns a DataFrame with ligand-receptor results

Otherwise, modifies the adata object with the following key:

• anndata.AnnData.uns [`key_added`] with the aforementioned DataFrame