Improve gene expression visualisatio non UMAP
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- Python
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Description
- [ x] Additional function parameters / changed functionality / changed defaults?
- New analysis tool: A simple analysis tool you have been using and are missing in
sc.tools? - [x ] 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?
...
It would be nice to have something like https://github.com/powellgenomicslab/Nebulosa to plot sparse genes.
On one hand, ordering with highest value on top (top plot) does not always work as what is below top layer is hidden and decreasing point size to combat this is not always good if different regions of UMAP are differently dense, thus creating white patches. On the other hand, random ordering (middle plot) can be hard to look at for sparse genes.
The gene on the plot is highly correlated with pattern from the bottom plot, but this is not so clear when plotting the gene alone.
Sort order=True

Random cell ordering

Strongly correlated with

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First steps
- Read the whole issue, then the project's contributing guide.
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Research direction
Start by reviewing the existing plotting functions under sc.pl and the linked Nebulosa approach for sparse-gene visualization. Determine the intended plotting behavior and API changes needed to address occlusion and uneven UMAP density; done should mean sparse genes can be visualized more clearly than with the current ordering options.
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
- Needs clarification
- Newbie friendliness
- 30/100