sccoda.util.cell_composition_data.from_scanpy_list

sccoda.util.cell_composition_data.from_scanpy_list(samples, cell_type_identifier, covariate_key=None, covariate_df=None)

Creates a compositional analysis data set from a list of scanpy data sets.

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_list([adata1, adata2, adata3], cell_type_identifier="Louvain", covariate_df="covariates")

Parameters

samples : List[AnnData]List[AnnData]

list of scanpy data sets

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