I’ve been using sc.pl.violin()
a lot lately, but have not been able to figure out how to make a violin plot with two groups where the first is a specific subset and the second is all cells. An example use case of this is making a violin plot for a specific UMAP cluster against the rest. I am familiar with the groupby
parameter to split based on a metadata factor, but this doesn’t allow selection of one specific metadata factor. Is there a way to do this with scanpy or do we need to build out a custom plotting function? If there is enough demand for this and it is not currently supported, I could look into making a PR on the GitHub repo.