umap for one gene split by condition
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Area - Plotting 🌺
- Dominant language
- Python
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Description
- Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - New plotting function: A kind of plot you would like to seein
sc.pl? - External tools: Do you know an existing package that should go into
sc.external.*? - Other?
...
How to generate two umaps for one gene split by a condition[one variable in obs] ?
so you can compare where gene expressed in cell types and how they differ in the two conditions.
could we add option split by to umap scanpy function?
https://github.com/theislab/scanpy/issues/759
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 the linked issue 759 and the sc.pl UMAP plotting entry point. Clarify how a condition column in obs should split the plots and how gene expression across cell types should remain comparable. Done means the UMAP function supports the requested split-by behavior with documented, comparable outputs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 25/100