PLS-DA Formatting a Graph in R

Question

Here is code from an example I was viewing from a mix0mics package about PLS-DA.

library(mixOmics)
data(srbct)

X <- srbct$gene
Y <- srbct$class 


final.plsda.srbct <- plsda(X,Y, ncomp = 3)

plotIndiv(final.plsda.srbct, ind.names = FALSE, legend=TRUE,
          comp=c(1,2), ellipse = TRUE, 
          title = 'PLS-DA on SRBCT comp 1-2',
          X.label = 'PLS-DA comp 1', Y.label = 'PLS-DA comp 2')

The code generates a figure like this from the PlotIndiv() code line. I want to clean up the graph a bit and remove the gridlines, and only have dashed lines over the X=0 line and Y=0, and to remove the awkward gray box at the top of the figure.

I tried to do title=NULL, but that wouldn't remove that portion. And I though doing something like theme_classic() may change how the figure would look, but still having difficulty to adjust this after looking online sources.

Any feedback on how to change the aesthetics of a plot would be appreciated please.

Thank you.

score 1 · Accepted Answer · answered Jul 05 '23 at 00:07

You can use the base graphics style:

plotIndiv(final.plsda.srbct, ind.names = FALSE, legend=TRUE,
          comp=c(1,2), ellipse = TRUE, 
          title = 'PLS-DA on SRBCT comp 1-2',
          X.label = 'PLS-DA comp 1', Y.label = 'PLS-DA comp 2',
          size.title = 1,
          style="graphics" )
          
          abline(h=0, lty="dotted", col="grey")
          abline(v=0, lty="dotted", col="grey")

PLS-DA Formatting a Graph in R

1 Answers1