Use deres plotting methods
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- Python
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Description
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
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by reviewing issues #317 and #348, then inspect the plotting functions provided by deres referenced in this request. Identify the PyDESeq2 entry points for differential-expression results and determine which wrappers and tests are needed. Done means the requested volcano, fold-change, and other deres plots are callable from PyDESeq2.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 30/100