Biplot for (s)PLSDA

Dear mixOmics devs,

Thank you for the package, I enjoy using it.

I am trying to obtain biplot for PLDA sparse or not.

I think the answer here is outdated:
(section : * Can I produce a biplot representation where individuals and variables are superimposed?)
I was not able to use the code, some parameters seems outdated and after few attempts, I can’t reach a plot with both variables and individuals.

Then I read this:

And I was able to reproduce it
Then I tried to apply it to the example from the FAQ but the result seems quite surprising to me.

X <- liver.toxicity$gene
Y <- as.factor(liver.toxicity$treatment[, 4])
res = splsda(X, Y, ncomp = 2, keepX = c(20, 20))

I expected variables to be projected on both component. here they seem to belong to only 1 or 2, never both.

MixOmics : 6.18.0
R 4.1.0


hi @AlbanOtt ,

This output is expected in the case where you perform variable selection, as the variables selected on Comp 1 will be orthogonal to the variables selected on Comp 2.
If you output a biplot with no variable selection, you will see a big cloud of variables :slight_smile: but some will contribute to both Comp 1 and Comp 2.