n_bins not respected in highly_variable_genes(..., flavour='cell_ranger')
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 2.6k
- Forks
- 779
- Avg merge
- 1d 4h
- Merged PRs (30d)
- 27
Description
This code creates the range [10, 15, …, 100], which is 19 values. Taking those percentiles together with -inf and +inf creates 20 bins (from 21 bin borders), understood.
But 1. why start at 10% and 2. why is n_bins ignored and there are always 20 bins created?
@Koncopd @falexwolf you introduced this in #330, is this what cellranger does?
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 in scanpy/preprocessing/_highly_variable_genes.py at the linked line and inspect the cell_ranger flavour's bin construction. Review issue #330 and determine whether the 10% starting point and fixed 20-bin behavior match Cell Ranger. Done means the intended n_bins behavior and percentile range are established and the implementation or documentation reflects that decision.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100