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muon.atac.tl.add_genes_peaks_groups

muon.atac.tl.add_genes_peaks_groups#

muon.atac.tl.add_genes_peaks_groups(data: AnnData | MuData, add_peak_type: bool = False, add_distance: bool = False)#

Add gene names to peaks ranked by clustering group

To add gene names to ranked peaks, peaks have to be ranked first. For that, run sc.tl.rank_genes_groups.

Gene names are picked as indices of the peak annotation table. To create annotation table, first run muon.atac.tl.add_peak_annotation. To add gene names instead of gene IDs, consider running muon.atac.tl.add_peak_annotation_gene_names then.

Parameters:

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

  • add_peak_type (bool (False by default)) – If to add peak type to the ranked peaks per group.

  • add_distance (bool (False by default)) – If to add distance to the ranked peaks per group.

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