venn diagrams
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@stefanie-gerstberger-4507
Last seen 7.4 years ago
Hi list, I'm looking for a scalable way to draw venn diagrams. I previously used vennerable, but this doesn't seem to be supported any more in R version 2.13. is there any other way to draw scaled venn diagrams? Thanks, Stefanie > sessionInfo() R version 2.13.0 (2011-04-13) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats     graphics  grDevices utils     datasets  methods  base     other attached packages: [1] limma_3.8.3 loaded via a namespace (and not attached): [1] tools_2.13.0 > install.packages("Vennerable", repos="http://R-Forge.R-project.org") Warning: unable to access index for repository http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.13 Warning message: In getDependencies(pkgs, dependencies, available, lib) :   package ‘Vennerable’ is not available (for R version 2.13.0) [[alternative HTML version deleted]]
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@steve-lianoglou-2771
Last seen 13 hours ago
United States
Forgot to CC list: Hi Stefi, On Sat, Apr 21, 2012 at 2:30 PM, Stefanie Gerstberger <stefanie.gerstberger at="" ymail.com=""> wrote: > > > Hi list, > I'm looking for a scalable way to draw venn diagrams. I previously used vennerable, but this doesn't seem to be supported any more in R version 2.13. > is there any other way to draw scaled venn diagrams? Not sure, but this thread seems to suggest gplots has some venn diagram capability and also mentions another package called venneuler: http://cran.r-project.org/web/packages/venneuler/index.html But still, assuming you have Vennerable's dependencies installed, I suspect you can get Vennerable to install if you specify type="source". Instead of this: > install.packages("Vennerable", repos="http://R-Forge.R-project.org") > Warning: unable to access index for repository http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.13 Try: install.packages("Vennerable", repos="http://r-forge.r-project.org", type="source") (or you can also svn checkout the package and `R CMD INSTALL` from the command line) HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
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there is vennDiagram, vennCounts in limma package. But only for 3 groups. It can not deal with more then 3 groups. On Sun, Apr 22, 2012 at 11:02 AM, Steve Lianoglou < mailinglist.honeypot@gmail.com> wrote: > Forgot to CC list: > > Hi Stefi, > > On Sat, Apr 21, 2012 at 2:30 PM, Stefanie Gerstberger > <stefanie.gerstberger@ymail.com> wrote: > > > > > > Hi list, > > I'm looking for a scalable way to draw venn diagrams. I previously used > vennerable, but this doesn't seem to be supported any more in R version > 2.13. > > is there any other way to draw scaled venn diagrams? > > Not sure, but this thread seems to suggest gplots has some venn > diagram capability and also mentions another package called venneuler: > > http://cran.r-project.org/web/packages/venneuler/index.html > > But still, assuming you have Vennerable's dependencies installed, I > suspect you can get Vennerable to install if you specify > type="source". Instead of this: > > > install.packages("Vennerable", repos="http://R-Forge.R-project.org") > > Warning: unable to access index for repository > http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.13 > > Try: > > install.packages("Vennerable", repos="http://r-forge.r-project.org", > type="source") > > (or you can also svn checkout the package and `R CMD INSTALL` from the > command line) > > HTH, > -steve > > -- > Steve Lianoglou > Graduate Student: Computational Systems Biology > | Memorial Sloan-Kettering Cancer Center > | Weill Medical College of Cornell University > Contact Info: http://cbio.mskcc.org/~lianos/contact > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Wenhuo Hu Park lab Memorial Sloan Kettering Cancer Center Zuckerman Research Building 408 East 69th Street Room ZRC-527 New York, NY 10065 Phone 646-888-3220 huw@mskcc.org [[alternative HTML version deleted]]
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Hi Stefi, Perhaps the venn.diagram function in the VennDiagram package might be useful. HTH, Natasha -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of Steve Lianoglou Sent: 22 April 2012 16:02 To: bioconductor at r-project.org list Subject: Re: [BioC] venn diagrams Forgot to CC list: Hi Stefi, On Sat, Apr 21, 2012 at 2:30 PM, Stefanie Gerstberger <stefanie.gerstberger at="" ymail.com=""> wrote: > > > Hi list, > I'm looking for a scalable way to draw venn diagrams. I previously used vennerable, but this doesn't seem to be supported any more in R version 2.13. > is there any other way to draw scaled venn diagrams? Not sure, but this thread seems to suggest gplots has some venn diagram capability and also mentions another package called venneuler: http://cran.r-project.org/web/packages/venneuler/index.html But still, assuming you have Vennerable's dependencies installed, I suspect you can get Vennerable to install if you specify type="source". Instead of this: > install.packages("Vennerable", repos="http://R-Forge.R-project.org") > Warning: unable to access index for repository > http://R-Forge.R-project.org/bin/macosx/leopard/contrib/2.13 Try: install.packages("Vennerable", repos="http://r-forge.r-project.org", type="source") (or you can also svn checkout the package and `R CMD INSTALL` from the command line) HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact _______________________________________________ Bioconductor mailing list Bioconductor at r-project.org https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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