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Use deres plotting methods

Open BorisMuzellec opened this issue 8 months ago • 1 comments

Is your feature request related to a problem? Please describe. Even though some have already been implemented, PyDESeq2 currently lacks plotting functions (volcano plots, fold change plots, etc.)

Describe the solution you'd like @grst's deres implements many DE-related plotting functions. We should import it and add wrapper methods to call them from pydeseq2.

Describe alternatives you've considered anndata-plot could be an alternative if it gains momentum

Additional context cf #317 and #348

BorisMuzellec avatar Mar 27 '25 10:03 BorisMuzellec

I made an initial release of deres to be played around with. It still lacks proper test cases and some other things should be improved (see issues). But the basic functionality is there (see example.

I'm not sure if anndata-plot would be an appropriate location for e.g. volcano plots (their data source is typically not in anndata). But maybe its scope is more general and should it should be renamed into something like scverse-plot? But that's a separate discussion...

grst avatar Apr 18 '25 13:04 grst