have not followed the thread completely, but:
have you tried `bitmap' with `type = pdfwrite' (or psgrb)
for comparison? at least with `pdf' there are some issues which
can be avoided by using ghostscript via `bitmap'.
joerg
On Mon, Mar 31, 2008 at 04:17:50PM -0400, Francois Pepin wrote:
> Prof Brian Ripley wrote:
> > 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
>
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