Hi, I have a multi-omics dataset where I would like to plot the AUROCs for each dataset run by itself and for the combination of the datasets in one figure just like the one attached here. How can I do this in mixomics?
Thank you for such a great tool!
Best wishes,
Stef
If using a supervised model, multiple lines will be plotted corresponding to each class in the response variable:
suppressMessages(library(mixOmics))
data(breast.TCGA)
X.train <- breast.TCGA$data.train$mirna
Y.train <- as.vector(breast.TCGA$data.train$subtype)
X.test <- breast.TCGA$data.train$mirna
Y.test <- as.vector(breast.TCGA$data.train$subtype)
MyResult.splsda.final <- splsda(X.train, Y.train)
auroc(MyResult.splsda.final)
Created on 2022-09-20 with reprex v2.0.2
There isn’t currently a way to plot multiple models on the auroc() plot. I’ll have a look today to see if this can be easily and quickly implemented for you
Hej Max,
Yes, I have been able to make a plot similar to the one you posted. But I typically have only 2 groups, thus one graph and it would be fantastic to be able to plot und thus be able to compare visually several models.
Thank you very much! 
/Stef
G’day Stepra.
Yesterday arvo and this morning I’ve put together a build for you which allows for the combination of AUROC plots. You can see the functionality below:
suppressMessages(devtools::load_all("D:/My Files/Work/mixOmics/mixOmics"))
data(breast.TCGA)
X <- list(miRNA = breast.TCGA$data.train$mirna,
mRNA = breast.TCGA$data.train$mrna,
proteomics = breast.TCGA$data.train$protein)
Y <- breast.TCGA$data.train$subtype
model1 <- splsda(X$miRNA, Y, ncomp=3)
model2 <- splsda(X$mRNA, Y, ncomp=3)
model3 <- splsda(X$proteomics, Y, ncomp=3)
models <- list(miRNA.Model=model1,
mRNA.Model=model2,
proteomics.Model=model3)
auroc.out <- auroc(models, print = F, plot=T, roc.comp = 1)
auroc.out <- auroc(models, print = F, plot=T, roc.comp = 3)
Created on 2022-09-23 with reprex v2.0.2
Session info
sessioninfo::session_info()
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As this is not yet deployed, feel free to install this branch from the Github using the following steps:
- Navigate to the R directory on your computer. Ensure the folder is titled like “R-X.X.X” (in my case,
R-4.2.1). This can be found using the following command in RStudio:
> file.path(R.home())
[1] "D:/Programs/Work Programs/R-4.2.1"
-
Go into this folder, then to
libraryand look formixOmics. Select themixOmicsfolder and delete it. -
Load the devtools package (ensure you have it installed):
install.packages("devtools")
library(devtools)
- Download the package on the “issue-242” branch or via the specific pull request:
install_github("mixOmicsTeam/mixOmics",
ref = github_pull("243"))
# OR
install_github("mixOmicsTeam/mixOmics",
branch = "issue-242")
- Load the mixOmics library, and voilà!
library(mixOmics)
Hej @MaxBladen. The code works very well! I have 4 models I want to compare and overlay all with one outcome and several curves are similar. Please, see figure below. How can I draw the curves in different colors instead?
Thanks a lot for your help!
/Stef
hi @stepra
Glad to know it is working. @MaxBladen has left the team now.
Looking at the auroc() function, we have ‘…’ arguments stating external optional arguments for plotting - line.col for custom colors and legend.title for custom legend title which means that you could either try ‘col=’ or any ggplot2 argument for color. It may work, it may not!
Kim-Anh
Thank you for the advice! Unfortunately, I could not get it to work.
/Stef
hi @stepra,
Ah that is a shame, I will be in the process of training a new maintainer, but it may take up to end of October to actually give you a code. If you have any R specialist around you, they will be able to help.
Kim-Anh
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