33

I want to append a plot to an existing pdf long after dev.off() has been called*. After reading the pdf() help file and after reading the Q & A here and here, I'm pretty sure it can't be done in R. But, maybe some of you smarter people have a solution that I wasn't able to find.

pdf("Append to me.%03d.pdf",onefile=T)
plot(1:10,10:1) #First plot (page 1)
dev.off()
pdf("Append to me.%03d.pdf",onefile=T)
plot(1:10,rep(5,10)) #Want this one on page 2
dev.off()

*This not a duplicate of the questions linked above because I want to append to a pdf file after the pdf device has been closed.

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D. Woods
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    Maybe this [Tyler Rinker's video](http://www.youtube.com/watch?feature=player_embedded&v=Eqi4-tuvKkI) is helpful to you. It's not an R answer, but it is interesting. – Jilber Urbina Nov 07 '12 at 16:14
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    What OS are you on? You could pipe the output through a command to merge the pdf stream with the existing PDF. – Gavin Simpson Nov 07 '12 at 16:16
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    +1 An `append.pdf` function would be handy. – Roland Nov 07 '12 at 16:22
  • @Jilber. This is an excellent question, I should've tried to address it in my original question. I'm calibrating a simulation where the runs take ~1 hour and the entire calibration process can take a week or more. At the end of each run, I want to save a historical plot that I can compare to past runs. I don't think it is feasible to keep the device open for a week+ if I have other plots that I want to produce during the simulation runs. Eventually, I would like to do some of the runs in parallel and consolidate the outputs into one pdf file. – D. Woods Nov 07 '12 at 16:23
  • @Gavin-Simpson I am conducting my runs on a RedHat box which I access either via the terminal or via RStudio server. But, there are others on my "team" who use OS X and Windows and I would like a solution that would work on those OS's as well. Until then, I'd be interested in seeing the pipe command you proppose. – D. Woods Nov 07 '12 at 16:25
  • @Jilber Just took a look at Tyler Rinker's video. Thanks for that useful Windows solution. My client machine is a Mac, and OS X provides parallel functionality with the "Preview" application. But, as I indicate above, I'd prefer to do this directly in R in a platform independent way. – D. Woods Nov 07 '12 at 16:35
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    See [here](http://trinkerrstuff.wordpress.com/2012/10/08/splitting-and-combining-r-pdf-visuals/) Anandas' Second comment where he provides an R solution for several OS. – Jilber Urbina Nov 07 '12 at 16:50

4 Answers4

23

You could use recordPlot to store each plot in a list, then write them all to a pdf file at the end with replayPlot. Here's an example:

num.plots <- 5
my.plots <- vector(num.plots, mode='list')

for (i in 1:num.plots) {
    plot(i)
    my.plots[[i]] <- recordPlot()
}
graphics.off()

pdf('myplots.pdf', onefile=TRUE)
for (my.plot in my.plots) {
    replayPlot(my.plot)
}
graphics.off()
Matthew Plourde
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  • Excellent suggestion, I wasn't aware of `recordPlot`. Just did some quick testing and it looks like it will do nicely. THANKS! – D. Woods Nov 07 '12 at 16:56
19

If you are willing to install the small, free, platform-independent pdftk utililty, you could use a system call from R to have it stitch all of your figures together:

## A couple of example pdf docs
pdf("Append to me.1.pdf")
plot(1:10,10:1)
dev.off()

pdf("Append to me.2.pdf")
plot(1:10,rep(5,10)) 
dev.off()

## Collect the names of the figures to be glued together
ff <- dir(pattern="Append to me")
## The name of the pdf doc that will contain all the figures
outFileName <- "AllFigs.pdf"

## Make a system call to pdftk
system2(command = "pdftk",
        args = c(shQuote(ff), "cat output", shQuote(outFileName)))

## The command above is equiv. to typing the following at the system command line
## pdftk "Append to me.1.pdf" "Append to me.2.pdf" cat output "AllFigs.pdf"
Josh O'Brien
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6

This is horribly hacky and probably belies my limited UNIX shell fu, but it works for me on a Fedora 17 box with the pdfjam package installed (not an R package, but from the YUM repos)

pdf("pdf1.pdf")
plot(1:10)
dev.off()

pdf("| pdfjoin --outfile \"pdf2.pdf\" && pdfjoin pdf1.pdf pdf2.pdf --outfile pdf1.pdf && rm pdf2.pdf")
plot(10:1)
dev.off()

The output in R is:

> pdf("| pdfjoin --outfile \"pdf2.pdf\" && pdfjoin pdf1.pdf pdf2.pdf --outfile pdf1.pdf && rm pdf2.pdf")## && pdfunite joined.pdf tmp.pdf joined.pdf && rm tmp.pdf")
> plot(10:1)
> dev.off()
          ----
  pdfjam: This is pdfjam version 2.08.
  pdfjam: Reading any site-wide or user-specific defaults...
          (none found)
  pdfjam: No PDF/JPG/PNG source specified: input is from stdin.
  pdfjam: Effective call for this run of pdfjam:
          /usr/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --outfile pdf2.pdf -- /dev/stdin - 
  pdfjam: Calling pdflatex...
  pdfjam: Finished.  Output was to 'pdf2.pdf'.
          ----
  pdfjam: This is pdfjam version 2.08.
  pdfjam: Reading any site-wide or user-specific defaults...
          (none found)
  pdfjam: Effective call for this run of pdfjam:
          /usr/bin/pdfjam --fitpaper 'true' --rotateoversize 'true' --suffix joined --outfile pdf1.pdf -- pdf1.pdf - pdf2.pdf - 
  pdfjam: Calling pdflatex...
  pdfjam: Finished.  Output was to 'pdf1.pdf'.
null device 
          1

Basically, pdfjoin will take input from stdin if it is the only input file so I pipe the output from pdf() to the pdfjoin program and specify the output file using the --outfile argument. Then using && is join the original pdf1.pdf with the pdf2.pdf just created, specifying that the output PDF is pdf1.pdf, the name of the original PDF.

Gavin Simpson
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  • I'll add that it would probably be easier to write a temporary pdf file, then call `pdfjoin` directly using `system()` to merge the PDFs and then delete the temporary one, but the above does work. – Gavin Simpson Nov 07 '12 at 16:54
  • Woah! Your UNIX shell fu is much stronger than mine. I'm going to tuck this away for the future. Until then, I think mplourde's solution will meet immediate my needs. – D. Woods Nov 07 '12 at 17:01
3

I found this excellent work recently (not attempting to claim it as my own)

https://jonkimanalyze.wordpress.com/2014/07/24/r-compile-png-files-into-pdf/

It's not quite what the OP was asking for, but the reason I like it is that I often have quite dense scatterplots and other plots that don't respond particularly well to window resizing etc. within a pdf. However I need to produce multi page output. So if the plots are data-dense I render them as .pngs and then use the above function to recombine at the end.

merge.png.pdf <- function(pdfFile, pngFiles, deletePngFiles=FALSE) {

  pdf(pdfFile)

  n <- length(pngFiles)

  for( i in 1:n) {


    pngFile <- pngFiles[i]

    pngRaster <- readPNG(pngFile)

    grid.raster(pngRaster, width=unit(0.8, "npc"), height= unit(0.8, "npc"))

    if (i < n) plot.new()

  }

  dev.off()

  if (deletePngFiles) {

    unlink(pngFiles)
  }

}
user1438038
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Pascoe
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