[R] pdf() device uses fonts to represent points - data alteration?

[Paul Murrell]

Hi


jiho wrote:
> Hello all,
> 
> I discovered that the pdf device uses fonts to represent "points"  
> symbols (as in plot(...,type="p",...) ). Namely it uses ZapfDingbats  
> with symbol U+25cf. This can lead to problems when the font is not  
> available, or available in another version (such as points being  
> replaced by other symbols, or worst: slightly displaced).  
> Furthermore, it also causes problems when opening the pdf files for  
> editing in other programs. I know that for reproducibility one should  
> avoid doing this but there are cases where R is simply not suited to  
> produce the end result graphic directly using code (Ex: replace some  
> colors by CMYK versions for color consistency in print). In addition,  
> publishers also often like being able to retouch graphics to ensure  
> fonts consistency or such, and this will be destructive in the case  
> of these pdfs. For example, Inkscape interprets points as squares  
> (more like U+2751 in ZapfDingbats) and Adobe Illustrator does not  
> even recognize the font (substituting AdobePiStd).
> I tried to embed fonts with embedFonts() but his does not solves the  
> issue with editing (Inkscape produces a kind of star and AI still  
> chokes on the font) and worst, it modifies how the original graphic  
> renders in pdf viewers: the circles are now filled (I believe this is  
> because this is the default state of the ZapfDingbats character).
> 
> So my questions are:
> - does anyone have a work around this?
> - why can't the pdf device use shapes instead of fonts to represent  
> data point? It would appear as a much more robust approach and would  
> ensure that the points are rendered the same everywhere. Font  
> substitution in axes labels is not as bad since it does not modify  
> the data itself (at worst the labels are offset a little bit) but  
> font substitution on the data points can really harm the graphic.


If I recall correctly, the PDF device uses a character for small circles 
because that looks better.  There is no PDF circle primitive, so circles 
have to be drawn using bezier curves.  The original author may be able 
to elaborate on that.

Two suggestions for workarounds:
(i)  produce PostScript and then convert to PDF using something like 
ghostscript (e.g., ps2pdf)
(ii)  use an almost-but-not-quite opaque colour, e.g., rgb(0, 0, 0, .99) 
for the points.  If the points are not fully opaque, the character is 
not used.

Paul


> Examples of code:
> 	pdf("test.pdf")
> 	plot(0,0,xlab="",ylab="",bty="n",xaxt="n",yaxt="n"); grid(lty=1);
> 	dev.off()
> 	embedFonts("test.pdf","pdfwrite","test_embed.pdf")
> 
> visualize the fonts:
> 	pdffonts test.pdf
> 
> and a package with the two pdf files and bitmaps of how they render  
> or are interpreted in various programs:
> 	http://jo.irisson.free.fr/dropbox/test_R_pdf_fonts.zip
> 
> Thank you in advance for your attention and help.
> 
> JiHO
> ---
> http://jo.irisson.free.fr/
> 
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-- 
Dr Paul Murrell
Department of Statistics
The University of Auckland
Private Bag 92019
Auckland
New Zealand
64 9 3737599 x85392
paul at stat.auckland.ac.nz
http://www.stat.auckland.ac.nz/~paul/