PCA analysis using R

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1

Hello all,

I have some questions related to analyzing my data at the level of phylum (L5).
I would like to do a PCA using R on my dataset which I clean them manually. The dataset stored in csv format. How can I do that without using phyloseq function? Because I do not have access to the previous output of qiime analysis that has been done by someone else.
I brought a small part of the data. The data format is like the following:

phylum
phylum819×460 14.7 KB

Thanks for your time!

2

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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3

Hi Mehrbod,
Thanks so very much for helping me out.
Yes, the table is in relative abundances.
Although, I made some PCA plot this afternoon but I need to digging into the links you've provided here and I hope I can find out more.

Thanks again,

Armin

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