Thank you sir..
i analysed denoising and taxonomy and making tree with qiime2!!
and i want more simple PCoA plot so i used DPCoA in phyloseq( Rcode )
but there is something metter....
some dataset x and y were CS1 and 2,
and some dataset x and y were Axis1 and 2...
what mean CS and Axis...
thank you for reading
Hello Seoki,
You can read more about Double PCoA here: From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis - PubMed
The axis numbers (Axis.1, Axis.2) don't mean much. In a PCoA plot, axis 1 and 2 are Principal Coordinates 1 and 2.
But those number in brackets are important!
In your second plot, Axis.1 [42.1%] means that 42.1% of the variation in the distance matrix can be explained by that axis, while only 20.9% can be explained by Axis.2. Because more variance is explained by Axis 1 (about 2x more in this case), the distance between points on this axis should carry more weight in your analysis.
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