mmc.get_data()

mmochi.utils.get_data(adata, parameter, preferred_data_key=None, return_source=False, force_preferred=False)

Searches an AnnData object along its .var, .var[MODALITY_COLUMN], .obs, .layers, and .obsm[preferred_data_key] for a specified parameter.

Parameters:

• adata (AnnData) – Object to search through

• parameter (str) –

  string to search the AnnData object for. Append: “_gex” to limit checking to the .var, “_obs” to limit checking to the .obs or where .var[MODALITY_COLUMN] == ‘obs’, “_mod_” followed by an var name in .var[MODALITY_COLUMN] or an obs key.

  Note, these symbols overwrite preferred data key, and it is assumed that these symbols are not used elsewhere for variable names

• preferred_data_key (Union[str, List, None] (default: None)) – Used to point to key(s) in .layers, .var[MODALITY_COLUMN], or in .obsm to check in

• return_source (bool (default: False)) – Whether to return where the parameter was found in addition to the list of matches

• force_preferred (bool (default: False)) – Whether to raise an error if the parameter is not found in the preferred_data_key

Returns:

Array of data in the AnnData object whose label matches parameter

Return type:

data