I used scanpy to do DE analysis for 2 conditions within a cluster. I set it up like shown here:
sc.tl.rank_genes_groups(adata, 'type', method='wilcoxon', groups=["A"], reference='B')
I want to confirm the directionality of the log fold change of the results so I would like to plot the average expression of a specific gene for group A and B within a specific cluster. How can I do that?
I think that the way I set up the rank_genes_groups means that a positive log fold change for a gene indicates that A has higher expression of that gene compared to B.