Hi Steffan, I'd be interesting in using your 295 lines of code right away if you'd be willing to send me a copy. Thanks much, Dick ********************************************************************** ********* Richard P. Beyer, Ph.D. University of Washington Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 Seattle, WA 98105-6099 http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html http://staff.washington.edu/~dbeyer ********************************************************************** ********* ------------------------------ Message: 23 Date: Fri, 5 Oct 2007 10:50:23 +0200 From: Steffen Moeller <steffen_moeller@gmx.de> Subject: [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more) To: bioconductor at stat.math.ethz.ch Message-ID: <200710051050.23983.steffen_moeller at gmx.de> Content-Type: text/plain; charset="iso-8859-1" Dear all, I needed Venn Diagrams to accomodate 4 sets rather than the 3 that I got via the limma package and I could not find it elsewhere. # Some test data A<- 1:20 B<- 1:20 C<- 2:20 D<- 3:21 # input gathered into a list, the names # appear in the diagram input<-list(a=A,b=B,c=C,d=D) # calculation of values that should # go into all the fields vc <- getVennCounts(input) # drawing of diagram drawVennDiagram(vc) The diagrams look like the ones from limma, i.e., no variation of circle shape and to reflect the size of the sets. The only novelty is that is also works on 4 sets and it is avoiding the use of classes. What should I do with these 295 lines of code now? It does not seem enough for a package on its own. Is anybody interested? Gordon? Cheers, Steffen

I would be glad to add the code to the gplots package, which already serves as a 'grab bag' of graphical tools. -G On Oct 5, 2007, at 10:23AM , Dick Beyer wrote: > Hi Steffan, > > I'd be interesting in using your 295 lines of code right away if > you'd be willing to send me a copy. > > Thanks much, > Dick > ********************************************************************** > ********* > Richard P. Beyer, Ph.D. University of Washington > Tel.:(206) 616 7378 Env. & Occ. Health Sci. , Box 354695 > Fax: (206) 685 4696 4225 Roosevelt Way NE, # 100 > Seattle, WA 98105-6099 > http://depts.washington.edu/ceeh/ServiceCores/FC5/FC5.html > http://staff.washington.edu/~dbeyer > ********************************************************************** > ********* > > > ------------------------------ > > Message: 23 > Date: Fri, 5 Oct 2007 10:50:23 +0200 > From: Steffen Moeller <steffen_moeller at="" gmx.de=""> > Subject: [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for > more) > To: bioconductor at stat.math.ethz.ch > Message-ID: <200710051050.23983.steffen_moeller at gmx.de> > Content-Type: text/plain; charset="iso-8859-1" > > Dear all, > > I needed Venn Diagrams to accomodate 4 sets rather than the 3 that > I got via > the limma package and I could not find it elsewhere. # Some test data > A<- 1:20 > B<- 1:20 > C<- 2:20 > D<- 3:21 > > # input gathered into a list, the names > # appear in the diagram > input<-list(a=A,b=B,c=C,d=D) > > # calculation of values that should > # go into all the fields > vc <- getVennCounts(input) > > # drawing of diagram > drawVennDiagram(vc) > > The diagrams look like the ones from limma, i.e., no variation of > circle shape > and to reflect the size of the sets. The only novelty is that is > also works on > 4 sets and it is avoiding the use of classes. > > What should I do with these 295 lines of code now? It does not seem > enough for > a package on its own. Is anybody interested? Gordon? > > Cheers, > > Steffen > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor

Deal List, I had this problem a while back, so I had extended the limma vennDiagram function to work with 4 (not more) using the ellipse method some have eluded to. An example can be found http://bioinfo-mite.crb.wsu.edu/Rcode/pmaVenns.pdf and the code can be found http://bioinfo-mite.crb.wsu.edu/Rcode/Venn.R Feel free to use and modify Matt Settles >Dear Steffen, > >In principle I'd be very happy to extend the vennDiagram() function >in limma to more than 3 groups. So please send me your code. Your >email seems too good to be true though, because it's geometrically >impossible to draw Venn diagrams for 4 groups with circles. Venn >diagrams can be done with 4 groups by going to elllipses. With more >than 5 groups, Venn diagrams seem to me to be so complicated as to be >perhaps no longer useful. The geometric theory of Venn diagrams has >been worked out by the statistician AWF Edwards, see eg his book >"Cogwheels of the Mind". >Best wishes >Gordon >Date: Fri, 5 Oct 2007 10:50:23 +0200 >From: Steffen Moeller <steffen_moeller at="" gmx.de=""> >Subject: [BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for > more) >To: bioconductor at stat.math.ethz.ch > >Dear all, > >I needed Venn Diagrams to accomodate 4 sets rather than the 3 that I got via >the limma package and I could not find it elsewhere. > ># Some test data >A<- 1:20 >B<- 1:20 >C<- 2:20 >D<- 3:21 > ># input gathered into a list, the names ># appear in the diagram >input<-list(a=A,b=B,c=C,d=D) > ># calculation of values that should ># go into all the fields >vc <- getVennCounts(input) > ># drawing of diagram >drawVennDiagram(vc) > >The diagrams look like the ones from limma, i.e., no variation of >circle shape >and to reflect the size of the sets. The only novelty is that is also works >on 4 sets and it is avoiding the use of classes. > >What should I do with these 295 lines of code now? It does not seem >enough for >a package on its own. Is anybody interested? Gordon? > >Cheers, > >Steffen