episcanpy.api.tl.identify_cluster

episcanpy.api.tl.identify_cluster(adata, cell_type, cell_type_markers, peak_promoter_file, gene_name_pos=5, path='', n_peaks_per_cluster=1000)

Use markers of a given cell type to plot peak openness for peaks in promoters of the given markers Input cell type, cell type markers, peak promoter intersections

cell_type: str, cell type that is to be investigated (must be the same as in the dictionary) cell_type_markers: dict, output of load_markers peak_promoter_file: tab-separated file that stores information about peak/promoter intersections and gene names for these promoters gene_name_pose: int, indicates the column in the peak_promoter_file where the gene name is stored path: str, path to the peak_promoter_file n_peaks_per_cluster: int, number of peaks per louvain cluster that should be searched for matches with the markers

Returns

umap depicting peak openness for promoters of marker genes for a given cell type