Hi,
I am using ran rank_genes_groups specifying pts as true as I want the percentage of cells in the cluster that have the gene I am calling. This is what I am using:
sc.tl.rank_genes_groups(adata, 'cell type', pts = True)
markers = sc.get.rank_genes_groups_df(adata, None)
markers = markers[(markers.pvals_adj < 0.05) & (markers.logfoldchanges > .5)]
markers
But I notice that markers also has two columns pct_nz_group and pct_nz_reference. Does anyone know what these are? I cannot find information on that in the documentation…
Also, do people know how to get violin plots of the differentially expressed genes across the clusters in scanpy?