How to download the axis values of weighted/unweighted unifrac analysis graph generated by qiime in qiime2view?
I want to go for further analysis and drawing plots with this (using R) as performed in Kang et. al (Anaerobe 2018) Redirecting
Hi, do you want to recreate it outside?
Hi @Mashuk,
The PC distances that can be used in these boxplots are calculated on the fly in QIIME 2 and so are not available for download (at least not that I can remember! Perhaps someone will correct me). But since you are going to be using R anyways, you can calculate these easily using the vegan package’s ‘vegdist’ command. Just make sure you rarefy or normalize your data prior to doing this (the same way you would in Qiime2)
Also, check out qiime2R for super convenient way of importing your QIIME2 files into R.
Hope this helps!
Hi @Mehrbod_Estaki and @Mashuk,
There are so many ways to do this! I think it can be a super useful visualization.
The pcoa artifact (from qiime diveristy pcoa) is the way the coordinates get generated for Emperor (or any other way you want to plot your PCoA). So, you could use qiime2R to get that into R. Coordinates should be in the sample property… although I will admit I work primarily in python. You could also export the data to a file and work with it in your plotting platform of choice.
Best,
Justine
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