ps or pdf

Please see the footer of this message.  

Sorry, here is an example. For some reason, I cannot reproduce it 
without using actual gene names.

set.seed(1)
##The row names were originally obtained using the hgug4112a library 
##from bioconductor. I set it manually for people who don't have it 
##installed.
##library(hgug4112a);row<-sample(na.omit(unlist(as.list(hgug4112aSYMBOL))),50)
row<-c("BDNF", "EMX2", "ZNF207", "HELLS", "PWP1", "PDXDC1",  "BTD", 
"NETO1", "SLCO4C1", "FZD7", "NICN1", "TMSB4Y", "PSMB7",  "CADM2", 
"SIRT3", "ADH6", "TM6SF1", "AARS", "TMEM88", "CP110",  "ADORA2A", 
"ATAD3A", "VAPA", "NXPH3", "IL27RA", "NEBL", "FANCF",  "PTPRG", 
"HSU79275", "CCDC34", "EPDR1", "FBLN1", "PCAF", "AP1B1",  "TXNRD2", 
"MUC20", "MBNL1", "STAU2", "STK32C", "PPIAL4", "TGFBR2",  "DPY19L2P3", 
"TMEM50B", "ENY2", "MAN2A2", "ZFYVE26", "TECTA",  "CD55", "LOC400794", 
"SLC19A3")
postscript('/tmp/heatmap.ps',paper='letter',horizontal=F)
heatmap(matrix(rnorm(2500),50),labRow=row)
dev.off()

Neither postscript() nor pdf() 
graphics devices split up strings they are passed (by e.g. text()), so 
this is being done either by the code used to create the plot (and we 
have no idea what that is) or by the viewer.  I suspect the problem is 
rather in the viewer, but without the example we asked for it is 
impossible to know.

Example of row names that are truncated in Illustrator (* denoting 
truncation):
CCDC3*4 (2nd row)
MUC2*0 (3rd row)
MBNL*1 (8th row)
...

It is likely that Illustrator (CS 3, OS X version) is at fault.  I do 
not see any truncation if I look at the ps file by hand (lines 4801 and 
4802):

540.22 545.88 (MUC20) 0 0 0 t
540.22 553.90 (CCDC34) 0 0 0 t

There also seems to be somewhat arbitrary grouping of the last column
cells in heatmaps in ps files.

Again, we need an example.

The top right cell (26, TXNRD2) is grouped with the cell just below it 
(26, CCDC34). It's more of a curiosity than anything else.

I used to prefer the ps because they embed more easily in latex
documents (although pdf are not difficult and conversions are trivial
anyhow), but I'm curious if there are other reasons why one format might
be preferred over the other in this context.

The graphics devices are very similar (they share a lot of code).  One 
small difference is that PostScript has an arc primitive, and PDF does not.

This is what I thought at first, which is why I found these differences 
surprising. I think your idea of blaming the viewer is correct. I 
thought that Adobe of all people could deal with Postscript files 
properly, but I guess I was overly trusting.

Thanks for the help,

Francois