Refactor clonotype_imbalance
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breaking-change
good first issue
- Dominant language
- Python
- Stars
- 265
- Forks
- 50
- Avg merge
- 9d 9h
- Merged PRs (30d)
- 4
Description
Analogous to #156, at some point
- make volcano and dotplot a different function
- make clear what is computed by the tool and what on-the-fly
- more compact representation for dotplot, potentially a heatmap could work.
- speed up:
- use implementation of fisher's test that approximates using chi-square when sample size is large enough
- should be trivial to parallelize
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 locating the current clonotype_imbalance implementation and comparing it with analogous issue #156. Define the separation between volcano and dotplot, document which values are computed by the tool versus on the fly, and evaluate the proposed heatmap, Fisher test approximation, and parallelization; done requires agreement on these design decisions and their implementation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data-visualization, performance
- Issue type
- Refactor
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Quiet
- Clarity
- Needs clarification
- Newbie friendliness
- 30/100