Documentation for rank_genes_groups
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Description
Hi,
Thanks for the great tools included in scanpy.
I was searching to see what the logfoldchange numbers in the rank_genes_groups are. i.e. is it natural log/log base 10 or log2? The code in https://github.com/theislab/scanpy/blob/master/scanpy/tools/_rank_genes_groups.py shows that it is log2foldchange.
Perhaps this should be made clear in the documentation? Or logfoldchange should be chnaged to log2foldchange.
Cheers,
S
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Research direction
Start with scanpy/tools/_rank_genes_groups.py and the documentation for rank_genes_groups to confirm how logfoldchange is calculated and presented. Update the documentation to state the logarithm base, or clarify the naming if appropriate; done means users can determine the scale unambiguously.
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Assessment
- Tech stack
- python
- Domain
- documentation
- Issue type
- Documentation
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 42/100