sccoda.util.cell_composition_data.from_scanpy_dir

sccoda.util.cell_composition_data.from_scanpy_dir(path, cell_type_identifier, covariate_key=None, covariate_df=None)

Creates a compositional analysis data set from all scanpy data sets in a directory.

To use this function, all data sets need to have one identically named column in adata.obs that contains the cell type assignment. Covariates can either be specified via a key in adata.uns, or as a separate DataFrame

Usage: data = from_scanpy_dir("./path/to/directory", cell_type_identifier="Louvain", covariate_key="covariates")

Parameters

path : strstr

path to directory

cell_type_identifier : strstr

column name in adata.obs that specifies the cell types

covariate_key : str, NoneOptional[str] (default: None)

key for adata.uns, where covariate values are stored

covariate_df : DataFrame, NoneOptional[DataFrame] (default: None)

DataFrame with covariates

Return type

AnnDataAnnData

Returns

• A compositional analysis data set

• data – A compositional analysis data set