Re: [R] ps or pdf

From: Francois Pepin <fpepin_at_cs.mcgill.ca>
Date: Mon, 31 Mar 2008 16:17:50 -0400

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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