Assistance Required with MixOmics cimDiablo Function Error

1

Hello,

I have been using the MixOmics package in R and encountered some issues,

When I execute the function:

cimDiablo(sgccda.res, size.legend = 0.8, margin = c(5, 15))

I encounter the following errors:

trimming values to [-3, 3] range for cim visualisation. See ‘trim’ arg in ?cimDiablo Error in cim plot: invalid graphics state. See ?cim for help. Error in (function (s, units = “user”, cex = NULL, font = NULL, vfont = NULL, : invalid graphics state

Could this be due to the length of the function name?

I would greatly appreciate it if you could provide any guidance on how to resolve this issue. Sorry to trouble you during your busy schedule, but I look forward to your response.
Best regards,

Anna

2

hi @ana,

Maybe remove the margin argument entirely. It could be due to RStudio and the size of the plot. Try otherwise

X11()
cimDiablo(sgccda.res, size.legend = 0.8)

Or save it as a plot external to RStudio, e.g.

pdf('my plot.pdf')
cimDiablo(sgccda.res, size.legend = 0.8)
dev.off()

Kim-Anh

3

Yes, Kim-Anh,

Thank you for your reply. Following your instructions, I was able to save the figure as a PDF using:

pdf(‘my plot.pdf’)
cimDiablo(sgccda.res, size.legend = 0.8)
dev.off()


Thank you for that! However, the labels for the selected variables are long and get cut off in the PDF. Should I try to shorten the text, or is there a way to adjust the font size using the cim function? I appreciate your guidance on this matter.

Best regards,

Ana
4

Dear Kim-Anh,

I have another question I would like to ask. To draw an ROC curve, I executed the following command: auc.splsda = auroc(sgccda.res, roc.block = "ITS", roc.comp = 2). The data I am using consists of a list that integrates N data from “ITS” and “r16S”. In this case, the ROC curve is generated, but is the result calculated only from the ITS data? Is it possible to calculate the AUC using both ITS and r16S data?