embedFonts is changing the bounding box of my R plot

Question

I have made a beautiful plot in R to be used in a scientific journal. According to the journal's specifications, I need an eps file format with embedded fonts. Since R does not export eps files with embedded fonts, I am using the base graphics call embedFonts() to convert it. However, this call is changing the bounding box of my figure. In this simple example below, the white space is cropped. In my OCD-adjusted publication-quality plot, white space is added because I've already adjusted it perfectly to the edges.

I want the fonts to be embedded, but everything else to stay the same!

Here is an example:

setEPS()
postscript(file = "~/Desktop/test.eps", family = "Helvetica", colormodel = "srgb", width = 5, height = 3)
plot(x = 1:10, y = 1:10, col = "red", main = "Keep everything the same but embed my fonts!")
dev.off()
embedFonts(file = "/Users/athena/Desktop/test.eps", format = "eps2write", outfile = "/Users/athena/Desktop/stupid.eps")

So far I have:
- installed ghostscript using homebrew: $ brew install ghostscript
- learned that embedFonts needs FULL paths, no tilda's allowed
- specified the format as "eps2write" because the default "ps2write" changes it to a postscript

I spent so much effort on "reproducible research" with open data, open code, open journal, bla bla bla... I really don't want to have to make my final figures using illustrator conversion or something :(

Answer 1

The reason this happens is because embedFonts internally calls Ghostscript which in turn tries to act smart by fitting an "optimal" bounding box by trimming out some of the surrounding white space.

We can prevent that by drawing an invisible box around the perimeter of our 5inx3in drawing area in R. Just add one more line to your code snippet:

setEPS()
postscript(file = "~/Desktop/test.eps", family = "Helvetica", colormodel = "srgb", width = 5, height = 3)
plot(x = 1:10, y = 1:10, col = "red", main = "Keep everything the same but embed my fonts!")
box(which="outer", col="white")
dev.off()
embedFonts(file = "/Users/athena/Desktop/test.eps", format = "eps2write", outfile = "/Users/athena/Desktop/stupid.eps")

Another way to go about this is Jonathan's answer here which basically uses sed to read in Bounding Box info from the input file and writes it to the output file: http://r.789695.n4.nabble.com/eps-file-with-embedded-font-td903387.html as pointed out by @neilfws in a comment above.