liana.utils.get_variable_loadings

liana.utils.get_variable_loadings#

liana.utils.get_variable_loadings(adata, varm_key=None, view_sep=None, variable_sep=None, pair_sep=None, var_names=None, pair_names=None, drop_columns=True)#

Extract variable loadings from an AnnData object.

Parameters:

  • adata (AnnData | MuData) – Annotated data object.

  • varm_key (str (default: None)) – Key to use when extracting variable loadings from mdata.varm

  • view_sep (str | None (default: None)) – Separator to use when splitting view:variable names into view and variable

  • variable_sep (str | None (default: None)) – Separator to use when splitting variable names into var_names

  • pair_sep (str | None (default: None)) – Separator to use when splitting view names into pair_names

  • var_names (list (default: None)) – Variable names given to the splitted variable (‘ligand_complex’ and ‘receptor_complex’ by default)

  • pair_names (list (default: None)) – Variable names given to the splitted pair (‘source’ and ‘target’ by default)

  • drop_columns (bool (default: True)) – If True, drop the view:variable column

Return type:

DataFrame

Returns:

Returns a pandas DataFrame with the variable loadings for the specified index.

Raises:

ValueError – If varm_key not found in .varm