I am using a function in R (specifically limma::plotMDS) that produces a plot and also returns a useful value. I want to get the returned value without producing the plot. Is there an easy way to call the function but suppress the plot that it creates?
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Ryan C. Thompson
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4You might try putting `pdf("NULL")` and `dev.off` around your plot function/object. – Jota Dec 03 '13 at 22:53
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Won't that create a PDF file called "NULL"? – Ryan C. Thompson Dec 04 '13 at 08:06
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1It will. Sorry about that. Try calling `suppressWarnings(windows("NULL"))` before your call to your plot function/object. But note that this solution is Windows-specific. – Jota Dec 04 '13 at 15:23
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@Jota `pdf(file = NULL)` should work, without the quotes. – Dec 22 '20 at 15:17
1 Answers
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You can wrap the function call like this :
plotMDS.invisible <- function(...){
ff <- tempfile()
png(filename=ff)
res <- plotMDS(...)
dev.off()
unlink(ff)
res
}
An example of call :
x <- matrix(rnorm(1000*6,sd=0.5),1000,6)
rownames(x) <- paste("Gene",1:1000)
x[1:50,4:6] <- x[1:50,4:6] + 2
# without labels, indexes of samples are plotted.
mds <- plotMDS.invisible(x, col=c(rep("black",3), rep("red",3)) )
agstudy
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3It seems unnecessary to create a temp file. Could I use /dev/null instead? – Ryan C. Thompson Dec 04 '13 at 08:30