Plotloadings error (plot = FALSE)

1

apparently, the option plot = FALSE is falling :

mixOmics::plotLoadings(splsda.liver, comp = 2, method = 'median', plot = FALSE,
contrib = "max")
Erreur dans names(contrib.df) <- block : 
  'names' attribute [1] must be the same length as the vector [0]

while this work fine

mixOmics::plotLoadings(splsda.liver, comp = 2, method = 'median', contrib = "max")

Does someone got an idea of what is happening here ?

2

Hello Vincent!

I don’t seem to encounter the same error you are getting, could you please make sure you are running the latest version of mixOmics (6.30.0)? You can install it from Bioconductor using the command:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mixOmics")

Once you’ve installed the latest version, try out this reproducible example code to see if you are still getting the error or if that has solved it.

data(liver.toxicity)
X = as.matrix(liver.toxicity$gene)
Y = as.factor(paste0('treatment_' ,liver.toxicity$treatment[, 4]))
splsda.liver = splsda(X, Y, ncomp = 2, keepX = c(20, 20))
plotLoadings(splsda.liver, comp = 1, method = 'median', contrib = "max") # plot OK
plotLoadings(splsda.liver, comp = 1, method = 'median', contrib = "max", plot = FALSE) # should also work without errors

Please let me know if you are still encountering errors!
Cheers,
Eva

1 Like
3

Apparently a conflict was happening between the current mixOmics version (6.30) and an oldest version still present on my machine (6.28). I resolve the issue by deleting all the previous version, and reinstalling the most recent 6.30.

Thanks.

vincent