I was wondering, I understand that if you do plotVar on a pca, you’ll be plotting cor(mypca$X, mypca$x, use = “pairwise”). However, that object does not exist as such under myacp$whatever. Wouldn’t it be nice to easily getting it? How about under $loadings instead of loadings = rotation? That could be handy if one chooses not to use plotVar and plot the data otherwise.
Long time no see! What you want is already stored in plotVar but the output names are not very explicit, I am afraid, hence the confusion. Here is an example using rcc (but applies to any method)
X <- nutrimouse$lipid
Y <- nutrimouse$gene
nutri.res <- rcc(X, Y, ncomp = 3, lambda1 = 0.064, lambda2 = 0.008)
result <- plotVar(nutri.res, comp = c(1,3), cutoff = 0.5) # here to simplify I put a cutoff on the variables
The x and y coordinates of this plot give you those correlations, and you can extract them as:
And because we have not made this very user-friendly, the matching names of the variables are in:
We will take your suggestion on board and make this output more explicit and more beautiful. Thanks!
Thanks a lot, Kim-Anh!