Principal Components Analysis

Commands in mothur
1

Hi, I import an mothur OTU table to R and want to do some analysis. One of analyses is Principal Components Analysis. I use the R command is prcomp. If I plot the output of prcomp command in R, it will give me a plot with arrows.

However, most of papers published only show the coordinates of sample sites. I want to export sample site coordinates from R pcoa analysis output. The R pcoa output include 5 items :“sdev” “rotation” “center” “scale” “x” . Should I export “rotation” or “x”.

Which standard for the coordinates of sample sites?

Thank you

2

You’d have to go through the R documentation for that. Our command pcoa likely does what you want and presents the x,y,z, etc coordinates in the axes file