[BioC] Venn Diagram for 2, 3 and 4 sets (can be extended for more)

[Thomas Girke]

Well, the values of the remaining intersections are not missed by this function, 
since they are provided below the pseudo 4-way venn diagrams. To plot proper 4-way 
venn diagrams one would need to use ellipses or rectangles, which is possible, but 
a bit harder to print in a nice format with the core plotting utilities in R.

Thomas

On Fri 10/05/07 11:55, James W. MacDonald wrote:
> That is very similar to what Steffen does. However, these are not Venn 
> diagrams, as you are missing two of the intersections. There should be a 
> total of 15 intersections
> 
> choose(4,1) + choose(4,2) + choose(4,3) + choose(4,4)
> 
> And you only have 13.
> 
> Best,
> 
> Jim
> 
> 
> 
> Thomas Girke wrote:
> > Here is a script that does something similar:
> > http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_graphics_venn
> > 
> > Thomas
> > 
> > On Fri 10/05/07 09:29, James W. MacDonald wrote:
> >> Hi Steffen,
> >>
> >> How exactly are you doing this? With more than three sets a true Venn 
> >> diagram cannot be constructed with circles, although I think it can be 
> >> done with ellipses.
> >>
> >> Best,
> >>
> >> Jim
> >>
> >>
> >>
> >> Steffen Moeller wrote:
> >>> 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
> >> -- 
> >> James W. MacDonald, M.S.
> >> Biostatistician
> >> Affymetrix and cDNA Microarray Core
> >> University of Michigan Cancer Center
> >> 1500 E. Medical Center Drive
> >> 7410 CCGC
> >> Ann Arbor MI 48109
> >> 734-647-5623
> >>
> >> _______________________________________________
> >> 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
> >>
> > 
> 
> -- 
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> _______________________________________________
> 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
> 

-- 
Thomas Girke
Assistant Professor of Bioinformatics
Director, IIGB Bioinformatic Facility
Center for Plant Cell Biology (CEPCEB)
Institute for Integrative Genome Biology (IIGB)
Department of Botany and Plant Sciences
1008 Noel T. Keen Hall
University of California
Riverside, CA 92521

E-mail: thomas.girke at ucr.edu
Website: http://faculty.ucr.edu/~tgirke
Ph: 951-827-2469
Fax: 951-827-4437