plotIndiv with MINT and swapping pch and default colors

[Kim-Anh Le Cao]

Hello! I would like to swap the pch batch info with the colors in MINT to visualise more easily the batch effect. It works with the graphics style option, but not our beloved ggplot2:

data(stemcells)


res = mint.splsda(X = stemcells$gene, Y = stemcells$celltype,
                  study = stemcells$study)

plotIndiv(res, legend = TRUE)

# that works
plotIndiv(res, legend = TRUE, pch = as.numeric(stemcells$celltype) +1,
          group = stemcells$study,  legend.title = 'batch', legend.title.pch = 'Cell line',  
          style = 'graphics')

# this does not
plotIndiv(res, legend = TRUE, pch = as.numeric(stemcells$celltype) +1,
          group = stemcells$study,  legend.title = 'batch', legend.title.pch = 'Cell line')