Ellipses colour do not match plot points colour

[qutkat]

Hello - I am trying to run an sPLSDA showing beta diversity data for 3 different weeks. When the plot is produced the ellipses are correct for all 3 weeks, but the colour of the data points for 2 of the weeks does not match the colour of the ellipses - they are switched around. I tried restarting Rstudio and reloading mixOmics from github but it is still happening.

betaplot$Week <- factor(betaplot$Week, levels = c("1", "5", "11"), labels = c("Week 1", "Week 5", "Week 11"))
taxon = taxa %>% rownames_to_column('Sample ID') %>% semi_join(betaplot, taxa, by = 'Sample ID') %>% column_to_rownames('Sample ID')

result = splsda(taxon, betaplot$Week, ncomp = 2, keepX = c(466,466))
plot = plotIndiv(result,centroid = FALSE, ellipse = TRUE,ind.names = FALSE, title = "sPLSDA - Beta diversity by Week", legend=TRUE)

I have tried to upload the resulting image here:

[qutkat]

Hello - please note that I also tried running your Case Study of sPLS-DA with SRBCT dataset using the exact code provided and I encountered the same issue. The blue and orange data points were switched around and did not match the image provided in the tutorial, but the ellipses were correct.

[samuelmontgomery]

I am having the same issue (and have for a few versions now but it seems to have not been fixed) when using plotIndiv - I much prefer using mixOmics for my work, but I am having to find alternative for plotting results at the moment as it makes it hard to interpret

[evaham1]

Also mentioned by post in mixOmics discussion forum:
https://mixomics-users.discourse.group/t/data-points-and-ellipses-colour-do-not-match/1576

[samuelmontgomery]

Is there a way to install the pre-release version with this fix?
Installing via GitHub installs a version older than the Bioconductor release (6.30)
I am trying to produce some plots for a manuscript but now all the colours are still off

[evaham1]

Hi @samuelmontgomery yes the github version needed a version bump because of the new Bioconductor release, thanks for pointing that out have just done that!

If you run the following command this will install the Github version of mixOmics which is ahead of the Bioconductor version (currently at 6.30.3) and should have the fix incorporated. Please let me know if you have any issues!
devtools::install_github("mixOmicsTeam/mixOmics")