Frank E Harrell Jr
2009-Mar-14 18:51 UTC
[R] Problem with figure size when embedding fonts
Dear Colleagues:
I need to make a graphic that uses the Nimbus rather than Helvetica font
family so that the font can be embedded in the encapsulated postscript
file. This is to satisfy a requirement from a journal for electronic
submission of figures. I do the following:
postscript('lowess.eps', onefile=FALSE, pointsize=18, horizontal=FALSE,
family='NimbusSan')
spar(mfrow=c(3,2))
. . .
dev.off()
At this point lowess.eps looks fine. When I run:
embedFonts('lowess.eps') or
embedFonts('lowess.eps', options='-sPAPERSIZE=letter')
the figures are wider and the right panel of the 3x2 matrix of plots
expands past the paper edge. Advice welcomed.
Thanks
Frank
platform i486-pc-linux-gnu
arch i486
os linux-gnu
system i486, linux-gnu
status
major 2
minor 8.1
year 2008
month 12
day 22
svn rev 47281
language R
version.string R version 2.8.1 (2008-12-22)
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
On Sat, Mar 14, 2009 at 1:51 PM, Frank E Harrell Jr <f.harrell at vanderbilt.edu> wrote:> Dear Colleagues: > > I need to make a graphic that uses the Nimbus rather than Helvetica font > family so that the font can be embedded in the encapsulated postscript file. > ?This is to satisfy a requirement from a journal for electronic submission > of figures. ?I do the following: > > postscript('lowess.eps', onefile=FALSE, pointsize=18, horizontal=FALSE, > ? ? ? ? ? family='NimbusSan') > spar(mfrow=c(3,2)) > . . . > dev.off() > > At this point lowess.eps looks fine. ?When I run: > embedFonts('lowess.eps') or > embedFonts('lowess.eps', options='-sPAPERSIZE=letter') > > the figures are wider and the right panel of the 3x2 matrix of plots expands > past the paper edge. ?Advice welcomed. >Hello Frank: This is an interesting post. I've not played with this until you brought it to my attention. I made a little progress. It appears to me either that there is something wrong with embedFonts as applied to postscript files or you and I need to learn a lot of ghostscript options. I created a small test and I see the same problem you do--the margins bump if you embed the fonts. I think the problem may be worse than that, it looks like the embedFonts wrecks the bounding box of the eps file. Do this: x <- rnorm(100) y <- rnorm(100) ml <- loess(y~x) plot(x,y) lines(ml) postscript('lowess.eps', onefile=FALSE, pointsize=18, horizontal=FALSE, family="NimbusSan") plot(x,y) lines(ml) text (-1,1,"Really big writing") dev.off() Copy "lowess.eps" to a safe place, then run embedFonts("lowess.eps") when you compare the two eps files, the margins are quite different. I see the difference more sharply when I add the features I usually have in postscript: postscript('lowess.eps', onefile=FALSE, pointsize=18, horizontal=FALSE, family="NimbusSan", height=6,width=6,paper="special") plot(x,y) lines(ml) text(-1,1, "Really big writing" dev.off() If you run that, save a copy of lowess.eps, then run embedFonts, you see the new lowess.eps no longer has the proper bounding box. Here's the top of lowess-orig.eps %!PS-Adobe-3.0 EPSF-3.0 %%DocumentNeededResources: font NimbusSanL-Regu %%+ font NimbusSanL-Bold %%+ font NimbusSanL-ReguItal %%+ font NimbusSanL-BoldItal %%+ font StandardSymL %%Title: R Graphics Output %%Creator: R Software %%Pages: (atend) %%BoundingBox: 0 0 432 432 %%EndComments %%BeginProlog On the other hand, the one that results from the embedFonts is not EPS anymore, and the bounding box is, well, confusing. %!PS-Adobe-3.0 %%Pages: (atend) %%BoundingBox: 0 0 0 0 %%HiResBoundingBox: 0.000000 0.000000 0.000000 0.000000 %................................................. %%Creator: GPL Ghostscript 863 (pswrite) %%CreationDate: 2009/03/15 20:00:36 %%DocumentData: Clean7Bit %%LanguageLevel: 2 %%EndComments %%BeginProlog It appears to me that running the eps output file through ps2epsi will re-create a tight bounding box, perhaps it is sufficient for your need. Rather than wrestle with the postscript & ghostscript, I re-did this on a pdf output device. It appears to me that the margin placement is not affected by embedFonts. pdf('lowess.pdf', onefile=FALSE, pointsize=18, family="NimbusSan",height=6,width=6,paper="special") plot(x,y) lines(ml) text (-1,1,"Really big writing") dev.off() I believe it is important to specify paper="special" here. I wondered about your experience with par(mfcol---). Lately, I've had more luck printing out the smaller separate components and putting them on the same LaTeX figure. That way, I have a little more control, and the fonts in the figure captions are identical to my text, which I like. PJ -- Paul E. Johnson Professor, Political Science 1541 Lilac Lane, Room 504 University of Kansas