Support configurable "rank types" #283
Labels
enhancement
New feature or request
external
issues/bugs with other libraries, frameworks, etc.; might include reproducing an issue minimally
interoperability
Making Qurro work well with other bioinformatics tools
progress
problem explanation
So here's the problem: if you perform Aitchison PCA yourself (for example, in the soon-to-be-merged-in color composition tutorial -- thanks @cameronmartino!!!), you already have the sample and feature loadings conveniently in a DataFrame. It's totally possible to just output the feature loadings to a TSV file, and then use that in standalone Qurro as the
--ranks
. (This is easier than building up a skbio OrdinationResults object yourself.) edit: the tutorial currently does that to avoid this problem.However, a problem with that is that Qurro's code sees that you passed in a TSV file and assumes that it was a file of differentials -- so the Qurro interface will be all like "yeah check out all of these differentials that just happen to be named PC1, PC2, PC3, ..." for the ranking selector and for the rank plot y-axis, which is obviously misleading since these aren't differentials.
One solution to this problem is adding a
--rank-type
command-line parameter for standalone Qurro that'd let you adjust the text shown in the interface, but I feel like no one will use that. An easier solution (and one that would also knock out a lot of the problems associated with #281) would just be renaming the ranking selector back fromDifferential
/Feature Loading
to justRanking
, and renaming the y-axis prefix fromDifferential
/Feature Loading
toMagnitude
orValue
or something.The text was updated successfully, but these errors were encountered: