Implement SWNE embedding
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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?
For gEAR (Gene Expression Analysis Resource), we have had a few users request Similarity Weighted Nonnegative Embedding (SWNE) plots instead of tSNE or UMAP plots. Having this embedding option (scanpy.tl and scanpy.pl) would allow use to expand functionality in several of our tools without having to leave the scanpy environment in order to provide them.
Repo: https://github.com/yanwu2014/swne
Paper: https://www.sciencedirect.com/science/article/pii/S240547121830440X?via%3Dihub
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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 existing scanpy.tl and scanpy.pl embedding APIs, then read the linked SWNE repository and paper to understand the method and expected plots. Define how SWNE should integrate with Scanpy and what inputs, outputs, and plotting behavior are required; the work is done when the analysis and plotting functionality are implemented with appropriate coverage.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization, machine-learning
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100