As far as I can see, the recommended way of using pdf() plot dev.off()
works precisely, just zoom in far enough so that your screen is able to display the gaps, e.g. by zooming in by 6400%
Uwe Ligges On 17.04.2012 15:53, Unger, Kristian, Dr. wrote:
Thanks Uwe. Please use the following below to reproduce the problem. Also, find the plots as I get them in my Dropbox: http://dl.dropbox.com/u/42940015/Rplot.pdf (plot as I get it when I use the "save as..." function from the Mac GUI menu. http://dl.dropbox.com/u/42940015/test.pdf (plot using the pdf() function. There should be red and blue boxes alternating with small white spaces in between. Actually neither the pdf from the screen plot nor the pdf() plot show exactly what I would expect. pdf("test.pdf",useDingbats=FALSE) ytp<- c(-89325387,-89216522,-60796604,-58334752,-57765318,-55659470,-55054287,-53883354,-50215659,-50118524,-50072127,-50045267,-49883861,-48749073,-48689425,-48304344,-48232108,-48200930,-47389665,-47334632,-47006453,-46801749,-46779857,-46500741,-34202088,-106271) ybp<- c(-90163070,-89315653,-89212325,-60737864,-58320017,-57748589,-55640346,-54993254,-53873394,-50204330,-50104099,-50064400,-50006459,-49870854,-48727216,-48665687,-48296706,-48221116,-48190704,-47378997,-47321850,-46998634,-46789748,-46765297,-35147449,-33961185) col<- rep(c("blue","red"),13) plot(c(0, 200), c(0, -90163070), type= "n", xlab="", ylab="",axes=F) rect( 35+((p-1)*20), ytp,50+((p-1)*20),ybp,col=col,border=NA,main="hhh") dev.off() ________________________________ Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 Am 17.04.2012 um 14:47 schrieb Uwe Ligges: On 17.04.2012 14:35, Unger, Kristian, Dr. wrote: Thanks Petr. Unfortunately this does not help. In that case, we need a reproducible example. Uwe Ligges Kristian Am 17.04.2012 um 14:18 schrieb Petr PIKAL: Hi Hi there is it possible that pdfs generated using the pdf() function with default settings leads to loss of information? I was plotting copy number changes from Agilent 180k data in form of rectangles (rect()) while each rectangle represents one region of copy number change. When plotting into a pdf I noticed that some very small rectangles do not appear (even after extensive zooming) in the pdf using the pdf() function. But they do when writing the screen output into a pdf using the GUI. Does anyone have some advice on this how I can plot pdfs without losing information? I am not sure if it has something to do with dingbats but you could try it. Set useDingbats=FALSE in you pdf call. Regards Petr Best wishes Kristian R version 2.14.0 (2011-10-31) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] de_DE.UTF-8/de_DE.UTF-8/de_DE.UTF-8/C/de_DE.UTF-8/de_DE.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] CGHregions_1.12.0 CGHcall_2.14.0 CGHbase_1.12.0 marray_1.32.0 [5] limma_3.10.3 Biobase_2.14.0 DNAcopy_1.28.0 impute_1.28.0 loaded via a namespace (and not attached): [1] tools_2.14.0 ________________________________ Arbeitsgruppenleiter Integrative Biologie / Head of Integrative Biology Group Abteilung für Strahlenzytogenetik / Research Unit of Radiation Cytogenetics Tel.: +49-89-3187-3515 ________________________________ Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de<http://www.helmholtz-muenchen.de> Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671 [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org<mailto: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. Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de<http://www.helmholtz-muenchen.de> Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671 ______________________________________________ R-help@r-project.org<mailto: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. ________________________________ Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH) Ingolstädter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir´in Bärbel Brumme-Bothe Geschäftsführer: Prof. Dr. Günther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht München HRB 6466 USt-IdNr: DE 129521671
______________________________________________ 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.
