I need to extract the x,y coordinates of a PCA plot (generated in R) to plot into excel (my boss prefers excel)
The code to generate the PCA:
pca <- prcomp(data, scale=T, center=T) autoplot(pca, label=T)
If we take a look at
pca$x, the first two PC scores are as follows for an example point is:
29. 3.969599e+01 6.311406e+01
So for sample 29, the PC scores are
However if you look at the output plot in R, the coordinates are not
63.11406 but ~0.09 ~0.2.
Obviously some simple algebra can estimate how the PC scores are converted into the plotted coordinates but I can't do this for ~80 samples.
Can someone please shed some light on how R gets these coordinates and maybe a location to a mystery coordinate file or a simple command to generate a plotted data matrix?
NOTE: pca$x does not give me what I want