Hi @ari_sh70,
It sounds like you just want to make PCoA plots in R using data arrived from QIIME 2.
If you had access to a beta diversity matrix in QIIME 2, I would recommend following this tutorial.
The data table you show is basically a normal site x species table (if you subtract column 2:3, and assuming column 1 is your sample-ids) that you can use to make PCoA plots in R. There are no shortage of tutorials on this topic around the web. For example first one I saw was here. I did notice however that your table appears to be in relative abundances, which is not how I would recommend making your PCoA plots. So hopefully you can retrieve the original table...
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