Luke Zappia

@LouiseDck I've merged `main` here to fix a bunch of conflicts from my last PR

@LouiseDck Can you please merge `main` here before I check it?

We should check what Python does and match that. Possibly there should also be warnings for other slots (i.e. a matrix in `obsm`). It would make sense to do this...

Just chipping in to say that while I think this would be great, it doesn't really solve https://github.com/scverse/scanpy/issues/1747 as **scanpy** functions will still cause this conversion (unless something has changed)....

This sounds like it might be a dependency issue somewhere. Can you please post the full error message (the output from `traceback()` might also be helpful)?

This looks like it is a problem rendering the plot rather than something inside **{clustree}**. Can you try the default settings without setting any arguments (except `prefix`)? Do you have...

Can you please also post the output of `sessionInfo()`?

It looks like you are both using a development version of **{ggplot2}**. Can you please try with the current release version (v3.3.6)?

Hmmm...ok. I'm running out of obvious ideas for where this might be coming from. I think it will take a bit more investigation to pin down. Unfortunately I won't have...

Ok, thanks for the update! If anyone is able to pin down exactly which package/version combinations are the issue I'm happy to update the dependencies but without that I'm not...