Shaun Adkins

https://github.com/scverse/scanpy/blob/2e98705347ea484c36caa9ba10de1987b09081bf/scanpy/plotting/_tools/__init__.py#L1151-L1156 For reference, `sc.pl.rank_genes_groups` assigns "_gene_names" as such https://github.com/scverse/scanpy/blob/2e98705347ea484c36caa9ba10de1987b09081bf/scanpy/plotting/_tools/__init__.py#L402-L406 This is causing a situation where I can pass identical parameters to both functions but `rank_genes_groups_violin` fails where `rank_genes_groups` succeeds. Basically...

- [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on the latest version of scanpy. - [X] (optional)...

Possible to set reference condition for two_sample tests?

6

I was originally trying to use the `rank_genes_groups()` function in scanpy to get p-values and logfoldchanges between a single condition and a reference condition. My end-goal was to take the...

Clustergram - Request to cluster based on a selected aggregated "groupby" column

2

Currently the Dash clustergram is restricted to clustering based on all row or column values. There are cases where I would like to sort my data based on a chosen...

- [ ] Additional function parameters / changed functionality / changed defaults? - [x] New analysis tool: A simple analysis tool you have been using and are missing in `sc.tools`?...

### Please make sure these conditions are met - [X] I have checked that this issue has not already been reported. - [X] I have confirmed this bug exists on...