muon.atac.pp.tfidf#

muon.atac.pp.tfidf(data: Union[anndata._core.anndata.AnnData, mudata._core.mudata.MuData], log_tf=True, log_idf=True, log_tfidf=False, scale_factor=10000.0)#

Transform peak counts with TF-IDF (Term Frequency - Inverse Document Frequency).

TF: peak counts are normalised by total number of counts per cell DF: total number of counts for each peak IDF: number of cells divided by DF

By default, log(TF) * log(IDF) is returned.

Parameters
  • data – AnnData object with peak counts or multimodal MuData object with ‘atac’ modality.

  • log_idf – Log-transform IDF term (True by default)

  • log_tf – Log-transform TF term (True by default)

  • log_tfidf – Log-transform TF*IDF term (False by default) Can only be used when log_tf and log_idf are False

  • scale_factor – Scale factor to multiply the TF-IDF matrix by (1e4 by default)