[BioC] Creating a Venn Diagram with 4 sets

Fri Apr 13 23:59:07 CEST 2012

Please have a look at some prior art in the gplots library. It is used the same way, so you can save that code, and plots elliptic Venn diagrams for up to 5 sets - no variation in the sizes of the ellipses, though.

Steffen

-------- Original-Nachricht --------
> Datum: Fri, 13 Apr 2012 12:24:54 -0500
> Von: Nitish Kumar Mishra <nitishimtech at gmail.com>
> An: "James W. MacDonald" <jmacdon at uw.edu>
> CC: bioconductor at r-project.org
> Betreff: Re: [BioC] Creating a Venn Diagram with 4 sets

> Hi,
> vennDiagram can use up to 3 sets, it can't use for 4 sets. You can use
> online tool Venny (use up to 4 set, also produce good quality image) :
> http://bioinfogp.cnb.csic.es/tools/venny/index.html for Venn diagram plot.
> Hope that Venny can help you.
> 
> Thanks
> Nitish
> On Fri, Apr 13, 2012 at 8:25 AM, James W. MacDonald <jmacdon at uw.edu>
> wrote:
> 
> > Hi Whomever,
> >
> > Three things.
> >
> > First, VennDiagram isn't a BioC package, so this isn't the correct list
> > for this question. You would be better off on R-help, or directly
> > contacting the author of that package.
> >
> > Second, anonymous posts tend to bring out the less civilized nature of
> > man. If you choose not to identify yourself, it is less likely you will
> get
> > a response, and if you do get a response it will likely be more terse
> and
> > possibly rude than if you had identified yourself.
> >
> >
> > Third, the data you show in your matrix are not the same as what you get
> > from the list (x) you use in your call to venn.diagram(). How did you
> > decide to construct the list (x), and why did you think it would give
> you
> > the same results as in your data structure? When you re-post on R-help,
> you
> > should at least show how you arrived at your data matrix, and explain
> why
> > you think the list you pass to venn.diagram() should give identical
> results.
> >
> > Best,
> >
> > Jim
> >
> >
> >
> > On 4/13/2012 4:02 AM, lcarvalh at btk.fi wrote:
> >
> >> I am trying to create a Venn diagram for this data, and the Venn
> diagram
> >> needs
> >> to show the number of occurring cases of each different intersection,
> for
> >> example in the diagram section were c1,c2 intersect each other should
> be
> >> the
> >> value 13.
> >>
> >> Data:
> >>
> >>       c1 c2 c3 c4 Counts
> >>  [1,]  0  0  0  0     26
> >>  [2,]  0  0  0  1     27
> >>  [3,]  0  0  1  0      4
> >>  [4,]  0  0  1  1      6
> >>  [5,]  0  1  0  0      5
> >>  [6,]  0  1  0  1     12
> >>  [7,]  0  1  1  0     42
> >>  [8,]  0  1  1  1     78
> >>  [9,]  1  0  0  0     18
> >> [10,]  1  0  0  1     52
> >> [11,]  1  0  1  0      4
> >> [12,]  1  0  1  1     63
> >> [13,]  1  1  0  0     13
> >> [14,]  1  1  0  1     47
> >> [15,]  1  1  1  0     88
> >> [16,]  1  1  1  1    182
> >>
> >> I have been trying to use the package VennDiagram, with the function
> >> venn.diagram. But I am only able to get some of the values correct in
> the
> >> diagram. Can anyone give me some help? maybe some other way of making a
> >> nice
> >> looking venn diagram? or help me correcting this code so that I can
> >> produce the
> >> correct venn diagram?
> >>
> >> Code:
> >>
> >>
> >> library (VennDiagram)
> >> library(grid)
> >>
> >> venn.diagram(
> >>        x = list(
> >>               comp1=c(1:18, 19:31, 32:119, 120:123, 124:186, 187:238,
> >> 239:420,
> >> 421:467),
> >>
> >>                comp4=c(692:695,561:603,472:**560,120:123, 187:238,
> >> 239:420, 603:681,682:688),
> >>                comp2=c(468:472,19:31, 32:119, 239:420, 421:467,
> 561:602,
> >> 603:680, 681:6918),
> >>                comp3=c(780:807,716:779,603:**680,681:691, 239:420,
> >> 421:467, 124:186,
> >> 187:238)                ),
> >>        filename = "quadruple_Venn.tiff",
> >>        col = "black",
> >>        lty = "dotted",
> >>        lwd = 4,
> >>        fill = c("cornflowerblue", "green", "yellow", "darkorchid1"),
> >>        alpha = 0.50,
> >>        label.col = c("orange", "white", "darkorchid4", "white",
> "white",
> >> "white",
> >> "white", "white", "darkblue", "white", "white", "white", "white",
> >> "darkgreen",
> >> "white"),
> >>        cex = 2.5,
> >>        fontfamily = "serif",
> >>        fontface = "bold",
> >>        cat.col = c("darkblue", "darkgreen", "orange", "darkorchid4"),
> >>        cat.cex = 2.5,
> >>        cat.fontfamily = "serif"
> >>        );
> >>
> >> ______________________________**_________________
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> >>
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> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
> >>
> >
> > --
> > James W. MacDonald, M.S.
> > Biostatistician
> > University of Washington
> > Environmental and Occupational Health Sciences
> > 4225 Roosevelt Way NE, # 100
> > Seattle WA 98105-6099
> >
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> >
> 
> 
> 
> -- 
> Nitish Kumar Mishra
> Office: 580-224-6163
> 
> Mob  : 240-898-7311
> 
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