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iferres / pagoo

A comprehensive and intuitive encapsulated OO class system for analyzing bacterial pangenomes in R.
https://iferres.github.io/pagoo/
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Change Shell and Cloud levels #65

Open alegione opened 10 months ago

alegione commented 10 months ago

Hi there, I'm really enjoying Pagoo, but was wondering if there is a means of adjusting the percentage cut offs for Shell and Cloud genes, much like there is for Core genes? From my rough view, Pagoo is treating all genes that occur in only 1% (or perhaps 1 single?) genome as a cloud gene, whilst tools such as Panaroo treat genes present in fewer than 15% of genomes as Cloud genes. I'd like to get my data to marry up across tools, and therefore set the core, shell, and cloud values in Pagoo to mirror those in Panaroo. Obviously I can change the core, but it would be great to be able to change the rest :) Thanks for any help you can give, even if there is a hacky way I can do it

iferres commented 9 months ago

Hi @alegione , sorry for the delayed answer. I use the "singleton gene" definition, which are those genes present in a single strain, to define "cloud" genes, but maybe is not the same and pagoo should also be able to correct this percentage/definition. I'm not actively working on this anymore, so I have limited bandwidth to approach it these days. I will gladly review and merge a PR if you feel you could make the changes.

I leave this issue open as a self reminder.