can't open pdf plot r

Question

For some reason, in this loop the PDFs that it produces end up corrupt. However, when I plot each individually it is saved and I can open them. Please advise, going mad!

for (l in 1:length(which_genes)) {
        gene_name <- which_genes[[l]]
        cases_values <- cases[cases$HGNC == genes[gene_name],]
        controls_values <- controls[controls$HGNC == genes[gene_name],]
        t <- t.test(cases_values[c(2:ncol(cases_values))], controls_values[c(2:ncol(controls_values))])
        case <- cbind(t(cases_values[c(2:ncol(cases_values))]), "cases")
        cont <- cbind(t(controls_values[c(2:ncol(controls_values))]), "controls")
        dat <- as.data.frame(rbind(case, cont))
        names(dat) <- c("expression", "type")
        dat$expression <- as.numeric(dat$expression)
        #plot significant genes
        pdf(file = paste(genes[gene_name], "_different.pdf", sep=""))
        ggplot(dat, aes(type, expression, fill=type)) + 
        geom_boxplot() +
        ggtitle(paste(genes[gene_name], "pvalue", t$p.value)) + 
        xlab("cases vs controls")
        dev.off()
}

Can you add a sample of your data? http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example — Travis, Mar 09 '17 at 18:54
Try using Sys.sleep to give ggplot2/grid more time to finish the plot. — Roland, Mar 09 '17 at 19:00
@Roland I tried Sys.sleep(5) before and after the pdf, now I can see the size of the plot being saved from 163bytes to 4KB - still corrupt. When I plot without the loop the PDF saved that opens is 5KB. Do you have any other suggestions? — user3324491, Mar 09 '17 at 19:16
Have you put it before dev.off? Make sure that you have closed all open devices before testing the code. — Roland, Mar 09 '17 at 19:18
@Roland, yes! before dev.off, I tried 5, 10, and now 20... It's the tinniest boxplot, how much time do you think it needs? — user3324491, Mar 09 '17 at 19:20

score 2 · Accepted Answer · answered Mar 09 '17 at 19:38

Yet another instance of the failure-to-print error (as described in the R-FAQ). Use this instead inside the loop:

pdf(file = paste(genes[gene_name], "_different.pdf", sep=""))
    print( ggplot(dat, aes(type, expression, fill=type)) + 
    geom_boxplot() +
    ggtitle(paste(genes[gene_name], "pvalue", t$p.value)) + 
    xlab("cases vs controls")
          )
dev.off()

If the goal was to have a multi-page output then you should have opened the PDF-device outside the loop, print-ed within the loop, and then closed the device outside.

can't open pdf plot r

1 Answers1