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YuLab-SMU / MicrobiotaProcess

:microbe: A comprehensive R package for deep mining microbiome
https://www.sciencedirect.com/science/article/pii/S2666675823000164
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How to display only a taxonomic level in the ggdiffbox #23

Open rsiani opened 3 years ago

rsiani commented 3 years ago

Gratitude for developing this package.

I was wondering whether there was a way to not display the full taxonomy in the diff_analysis plot as my figures look a bit overcrowded (e.g. only genus level). Is there a workaround for that? ggdiffbox

xiangpin commented 3 years ago

This is because there are many unclassified, ambiguous, and unknown taxa names. I think you should first check the taxonomy annotation. If there are too many unclassified taxa names, I suggest you can perform the different analysis with all OTU or ASV, but all the taxa. you can set the alltax=FALSE in diff_analysis, which will do the different analysis in OTU level or ASV or the features of your input.

If you want to perform all the levels of taxa, you can reinstall the MicrobiotaProcess by remotes::install_github("YuLab-SMU/MicrobiotaProcess"), then do it.