plotIndiv annotate sample by two or more grouping

[Former user]

I wonder to class my data based on A+B. but when plotting the figure, I want to legend A and B separately. Like, A by color, B by pch. Is that possible? Thanks.

[Florian Rohart]

Hi there,

I'm not sure what you want to do, but you can have two legends using plotIndiv, one for the color and one for the pch:

library(mixOmics)
data(breast.tumors)
X <- breast.tumors$gene.exp
Y <- breast.tumors$sample$treatment
splsda.breast <- splsda(X, Y,keepX=c(10,10),ncomp=2)
plotIndiv(splsda.breast, ind.names = FALSE, pch = c(3,4,2), legend=T)

or

data(liver.toxicity)
X <- liver.toxicity$gene
Y <- liver.toxicity$clinic
toxicity.spls <- spls(X, Y, ncomp = 3, keepX = c(50, 50, 50),
keepY = c(10, 10, 10))

plotIndiv(toxicity.spls, rep.space= 'X-variate',
group = liver.toxicity$treatment[, 'Time.Group'],
ind.names = FALSE,
legend = TRUE,pch=c(1,2,3))