While making a biplot from Deicode results in R basing on this tuto (How to make pcoa biplot in R using q2-deicode ordination), I noticed that different features where being selected to plot as arrows in the graph in R and Emperor.
In the R code, features to plot are selected with the following cmd,
mutate(a=sqrt(PC1^2+PC2^2)) %>% top_n(8, a) according to the tuto; after some attempts I added the PC3 in the cmd like
mutate(a=sqrt(PC1^2+PC2^2+PC3^2)) %>% top_n(8, a) and the selected features between Emperor and R were the same.
Questions: is it correct to add the PC3 in the R calculation even if that "dimension" isn't going to be plotted? Which way is the best to select the features?.
Also, in the Emperor plot there is a Confidence value related to the arrows, I haven't been able to find it in the ordination file, where does it come from? should be taken into account while plotting in R?.