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 ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.