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?

Thank you



Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Browse other questions tagged or ask your own question.