bedapub / bedapub/besca

percent_mito in reality reflects the fraction not the pct

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enhancement invalid
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Python
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Description

Hi @kohleman and @swalpe, in besca sw there is a param called percent_mito with scale 0-1, and thus what is plotted is the fraction of mitochondria and not the percentage.
I would prefer to really have the % (scale 0-100%) and be reflected in the QC plots. I find the fraction less visual specially when we have very low cutoffs as for nuclei (e.g 0.01 cutoff)

What do you think? Could this be updated?
Thanks a lot,
Llucia

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by locating the percent_mito parameter and the QC plotting entry points in the Python code. Trace how values on the 0–1 scale are calculated and displayed, then check existing tests or plot-related checks if present. Done means percent_mito and the QC plots consistently represent percentages on a 0–100 scale, including low cutoffs such as 0.01.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Feature
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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