Bug in PlotIndiv using subtitle

Bugs
1

Hi,

I am running into a strange error when I use subtitle in plotIndiv.
When I run PlotIndiv without subtitle, all my images scale fine

However, as soon as I add subtitle, the plots are scaled and plotted incorrectly

Suppl-block-plsda
Suppl-block-plsda1920×3840 337 KB

Any ideas?
Code below:

plotIndiv(multi.block.plsda,
ind.names = FALSE,
ellipse = TRUE,
group = groups,
blocks = c(4:10),
pch = c(rep(16,8)),
col.per.group = my.colors,
cex = 1,
subtitle = c(“Biochemical indices in jejunal tissue”,
“mRNA targets in jejunal tissue”,
“Morphology characteristics of jejunal tissue”,
“Cell types in jejunal tissue”,
“Free amino acids in jejunal digesta”,
“Protein bound amino acids in jejunal digesta”,
“Amino metabolites in jejunal digesta”
),
title ="",
X.label =c(expression(paste(“PLS-DA component 1”))),
Y.label =c(expression(paste(“PLS-DA component 2”))),
#legend.title = “”, legend.box = NULL, legend.position = “right”,
#size.title = rel(1.1),
size.xlabel = rel(1), size.ylabel = rel(1),
size.axis = rel(1),
size.legend = rel(1),
style = ‘graphics’,
layout = c(6,2))

2

Sorry for the late reply @qacsciascia,

I have spent some time attempting to reproduce your issue. While the data I’m using will be different, the plotIndiv() call I’ve used is the exact same as yours. I am unable to produce any plots where the ellipses are cut off or the scaling is incorrect.

Could you send a picture of what the plots look like when you don’t include the subtitles? Are the ellipses cut off normally? When the subtitles are included, is every sample found in the plot, or are some cut off too?

If you could try running the below code on the latest version of mixOmics and let me know if the same issue occurs, that would aid in figuring this out.

Cheers,
Max.

library(mixOmics)

data(breast.TCGA) # load in the data

data = list(a = breast.TCGA$data.train$mirna, 
            b = breast.TCGA$data.train$mrna,
            c = breast.TCGA$data.train$protein,
            d = breast.TCGA$data.train$mirna, 
            e = breast.TCGA$data.train$mrna,
            f = breast.TCGA$data.train$protein,
            g = breast.TCGA$data.train$protein, 
            h = breast.TCGA$data.train$mrna,
            i = breast.TCGA$data.train$protein,
            j = breast.TCGA$data.train$protein,
            k = breast.TCGA$data.train$protein)

Y = breast.TCGA$data.train$subtype

design = matrix(0.1, ncol = length(data), nrow = length(data), # for square matrix filled with 0.1s
                dimnames = list(names(data), names(data)))
diag(design) = 0 # set diagonal to 0s

multi.block.plsda = block.splsda(X = data, Y = Y, ncomp = 5, design = design) # form basic DIABLO model
my.colors <- c("blue", "red", "green")
groups <- breast.TCGA$data.train$subtype

# code from user
plotIndiv(multi.block.plsda,
          ind.names = FALSE,
          ellipse = TRUE,
          group = groups,
          col.per.group = my.colors,
          blocks = c(4:10),
          pch = c(rep(16,8)),
          cex = 1,
          X.label =c(expression(paste("PLS-DA component 1"))),
          Y.label =c(expression(paste("PLS-DA component 2"))),
          size.xlabel = rel(1), 
          size.ylabel = rel(1),
          size.axis = rel(1),
          size.legend = rel(1),
          layout = c(6,2),
          #legend.title = "", legend.box = NULL, legend.position = "right",
          
          
          subtitle = c("Biochemical indices in jejunal tissue",
                       "“mRNA targets in jejunal tissue”",
                       "“Morphology characteristics of jejunal tissue”",
                       "“Cell types in jejunal tissue”",
                       "“Free amino acids in jejunal digesta”",
                       "“Protein bound amino acids in jejunal digesta”",
                       "“Amino metabolites in jejunal digesta”"
          ),
          style = "graphics",
          title = "")