SpaRCL.aucell#

SpaRCL.aucell(adata, auc_threshold=0.05, noweights=False, normalize=False, random_state=0, num_workers=1, regulon_key=None, key_added=None, copy=False)[source]#

Compute the regulon activity AUCell matrix [Aibar17].

Parameters:

adata : AnnData: Annotated data matrix.
auc_threshold : float (default: 0.05): The fraction of the ranked genome to take into account for the calculation of the Area Under the recovery Curve.
noweights : bool (default: False): Should the weights of the genes part of a signature be used in calculation of enrichment?
normalize : bool (default: False): Normalize the AUC values to a maximum of 1.0 per regulon.
random_state : int (default: 0): Change to use different initial states for the optimization.
num_workers : int (default: 1): The number of cores to use.
regulon_key : str | NoneOptional[str] (default: None): The key of regulon inference.
key_added : str | NoneOptional[str] (default: None): If not specified, the AUCell data is stored in adata.uns[‘aucell’] and the AUCell matrix is stored in adata.obsm[‘aucell’]. If specified, the AUCell data is added to adata.uns[key_added] and the AUCell matrix is stored in adata.obsp[key_added].
copy : bool (default: False): Return a copy instead of writing to adata.

Return type:

AnnData | NoneOptional[AnnData]

Returns:

Depending on copy, returns or updates adata with the following fields.

See key_added parameter description for the storage path of the AUCell matrix.

.obsm[‘aucell’]DataFrame: The regulon activity AUCell matrix.