Legend in plotIndiv does not respect pch levels order

[Kim-Anh Le Cao]

See email from André Luis Neves, June 24.

Here it is the code that didn't change the correct order of time (in days).

time = factor(map$TimeOld, levels = c("0", "80", "100", "180"))

plotIndiv(splsda.res, comp = c(1,2),
          ind.names = FALSE, 
          ellipse = TRUE, 
          legend = TRUE,
          group=Y,
          id.names=time,
          pch= time,
          pch.levels=time,
          legend.title="Breeds",
          legend.title.pch ="Time (in days)",
          title = 'Gene Families, sPLSDA comp 1 - 2') 

[Kim-Anh Le Cao]

This is an issue inherent to ggplot2 that assigns letters to factors (here the pch) inside the function. Best option is to use the

style = 'graphics' or 'lattice'

in plotIndiv.