library("mixOmics")
gtex.plsda <- plsda(X, Y, ncomp = 2)
background = background.predict(gtex.plsda, comp.predicted = 2, dist = "max.dist")
plotIndiv(gtex.plsda , comp = 1:2, group = Y, ind.names = FALSE, ellipse = TRUE,
          legend = TRUE, title = 'PLSDA on GTEX Skeletal Muscles', background = background)
plotLoadings(gtex.plsda, comp = 1, title = 'Loadings on comp 1', contrib = 'max',
             method = 'median', ndisplay = 10, size.name = 0.6)
plotLoadings(gtex.plsda, comp = 2, title = 'Loadings on comp 2', contrib = 'max',
             method = 'median', ndisplay = 10, size.name = 0.6)