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

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Steffen Moeller ▴ 90

@steffen-moeller-2412

Last seen 22 months ago

Germany

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

GO limma GO limma • 1.2k views

ADD COMMENT • link updated 17.2 years ago by James W. MacDonald 67k • written 17.2 years ago by Steffen Moeller ▴ 90

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 4 hours ago

United States

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

ADD COMMENT • link 17.2 years ago James W. MacDonald 67k

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Here is a script that does something similar: http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.htm l#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 > -- 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

ADD REPLY • link 17.2 years ago Thomas Girke ★ 1.7k

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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.h tml#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

ADD REPLY • link 17.2 years ago James W. MacDonald 67k

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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

ADD REPLY • link 17.2 years ago Thomas Girke ★ 1.7k

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