Gene expression color legends and gene names
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- Dominant language
- Python
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Description
I have two suggestions/questions about dot/matrix plots:
1- If standard_scale='var' is given, we can write Mean expression\nin group\n(min-max scaled) on the color legend to be more accurate about what is being displayed.
2- People/journals usually expect gene names to be written with italicized characters (don't ask why, see https://en.wikipedia.org/wiki/Gene_nomenclature). So I was wondering if we can simply do that in the plots. One important thing to consider is whether this is organism-dependent. I guess it's not but would be cool to discuss.
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
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- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the dot/matrix plot entry points and the code handling the standard_scale='var' color legend and gene-name labels. Check how scaled expression and labels are currently rendered; done means the legend accurately describes min-max scaling and gene names are italicized appropriately, with organism dependence resolved.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics, data-visualization
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100