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? 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 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]]
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 numberchanges> from Agilent 180k data in form of rectangles (rect()) while eachrectangle> 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 havesome> 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 BiologyGroup> Abteilung f?r Strahlenzytogenetik / Research Unit of RadiationCytogenetics> > Tel.: +49-89-3187-3515 > > > ________________________________ > Helmholtz Zentrum M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht M?nchen HRB 6466 > USt-IdNr: DE 129521671 > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html> and provide commented, minimal, self-contained, reproducible code.
Thanks Petr. Unfortunately this does not help. 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 f?r Strahlenzytogenetik / Research Unit of Radiation > Cytogenetics >> >> Tel.: +49-89-3187-3515 >> >> >> ________________________________ >> Helmholtz Zentrum M?nchen >> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >> Ingolst?dter Landstr. 1 >> 85764 Neuherberg >> www.helmholtz-muenchen.de >> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum >> Registergericht: Amtsgericht M?nchen HRB 6466 >> USt-IdNr: DE 129521671 >> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-help at 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 M?nchen Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) Ingolst?dter Landstr. 1 85764 Neuherberg www.helmholtz-muenchen.de Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum Registergericht: Amtsgericht M?nchen HRB 6466 USt-IdNr: DE 129521671
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 f?r Strahlenzytogenetik / Research Unit of Radiation >> Cytogenetics >>> >>> Tel.: +49-89-3187-3515 >>> >>> >>> ________________________________ >>> Helmholtz Zentrum M?nchen >>> Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) >>> Ingolst?dter Landstr. 1 >>> 85764 Neuherberg >>> www.helmholtz-muenchen.de >>> Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe >>> Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum >>> Registergericht: Amtsgericht M?nchen HRB 6466 >>> USt-IdNr: DE 129521671 >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________________________ >>> R-help at 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 M?nchen > Deutsches Forschungszentrum f?r Gesundheit und Umwelt (GmbH) > Ingolst?dter Landstr. 1 > 85764 Neuherberg > www.helmholtz-muenchen.de > Aufsichtsratsvorsitzende: MinDir?in B?rbel Brumme-Bothe > Gesch?ftsf?hrer: Prof. Dr. G?nther Wess und Dr. Nikolaus Blum > Registergericht: Amtsgericht M?nchen HRB 6466 > USt-IdNr: DE 129521671 > > ______________________________________________ > R-help at 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.
On Apr 17, 2012, at 7:08 AM, Unger, Kristian, Dr. wrote:> 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? > > 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_2.14.0If you can provide some reproducible code (small example that yields the problem), that would help. However, you may be experiencing a problem in your PDF viewer (Preview?) due to anti-aliasing, which is noted here: http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-are-there-unwanted-borders Regards, Marc Schwartz
There must be loss of accuracy: coordinates in PDF are recorded to finite accuracy (for pdf(), something like 0.01" as I recall). In addition, the R plot engine assumes finite accuracy, a minimum width for lines .... And as people are pointing out, so do PDF viewers. Do not expect to zoom into a plot (PDF or otherwise): if you want a large plot, plot it large in the first place. On 17/04/2012 13:58, Marc Schwartz wrote:> On Apr 17, 2012, at 7:08 AM, Unger, Kristian, Dr. wrote: > >> 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? >> >> Best wishes >> >> Kristian >> >> R version 2.14.0 (2011-10-31) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)Which is already 3 versions old: see what the posting guide has to say about that ....>> >> 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 > > > > If you can provide some reproducible code (small example that yields the problem), that would help. However, you may be experiencing a problem in your PDF viewer (Preview?) due to anti-aliasing, which is noted here: > > http://cran.r-project.org/doc/FAQ/R-FAQ.html#Why-are-there-unwanted-borders > > Regards, > > Marc Schwartz > > ______________________________________________ > R-help at 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.-- Brian D. Ripley, ripley at stats.ox.ac.uk Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595