Something quite interesting that I learned from the VizBi conference (workshop on visualizing biological data) last month concerns depicting relationships linearly vs by area. Humans can proportionally relate objects of different lengths. That is if A = 10 and B = 5, A looks exactly twice as long, and if A = 10 and B = 9.8, B looks shorter. If A and B are depicted by area, things get difficult to discern because perceived differences in area relate to one another not by the power of 1.0 but by 0.6-0.7. Thus, one loses the degree of difference between objects when using area.

Although Venn diagrams are popular and convenient, this information is something to keep in mind when trying to depict the relationships.

Added 27 Apr 2011: Try Hohli at charts.hohli.com. With Hohli, you can create a Venn diagram and customize its look and feel. One can specify a title, choose data points, and alter the background. Hohli also allows you to create other charts, including scatter plots and other line charts.

The Google Chart API will do this.

Update - the Chart API has now been deprecated (bummer...)

I can recommend Vennerable. It is quite flexible and will allow you to plot proportional Venn/Euler diagrams and define the set names (foo and bar below) and weights directly (bar only has 7 elements, their intersection has 9, and there are 12 unique elements in foo):

Venn(SetNames = c("foo", "bar"), Weight = c('00' = 0, '01' = 7, '11' = 8, '10' = 12))

If you want to stick with Perl, there is Venn::Chart, which I have never used though.

Like others, I have started using The R VennDiagram package. I just presented on this at our local R user's group:

Powerpoint: Venn and Euler Diagrams in R

R code

For 3-way proportional venns, you could also try this Euler Venn Applet or Vennmaster:

Not exactly sure if this is possible but it might be worth checking the following two references taken from Chen and Boutros BMC Bioinformatics 2011, 12:35 VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R:

Hulsen T, de Vlieg J, Alkema W: BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams. BMC Genomics 2008, 9:488.

Kestler HA, Muller A, Kraus JM, Buchholz M, Gress TM, Liu H, Kane DW, Zeeberg BR, Weinstein JN: VennMaster: area-proportional Euler diagrams for functional GO analysis of microarrays. BMC Bioinfo 2008, 9:67.

Andreas

My current favourite (for two sets) is pyvenn (a python script).

I have a version of the script that i altered, which does not display any text. This is good for papers where you want to add your own text.

You may also be interested in this link and the associated comments.

BioVenn is another tool for generating rea-proportional Venn diagrams. It supports only 2 or 3 comparisons, but might be handy anyway.

Have you tried Venny ?

Hi!

I don't know if it's possible to integrate R code into a suite of Perl suite, but to generate proportional and colorful Venn diagrams I use a R package called VennDiagram. You can find it there: VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

I think that the venneuler R package could do the trick.

library("venneuler")
vd <- venneuler(c(A=0.3, B=0.3, C=1.1, "A&B"=0.1, "A&C"=0.2, "B&C"=0.1 ,"A&B&C"=0.1))
plot(vd)

Depending on your needs, you can also have a look at the venn function in gplots package (not proportional but offers venn diagrams with up to 5 sets). You can get colors by slightly modifying the function.

#construct some fake gene names..
oneName <- function() paste(sample(LETTERS,5,replace=TRUE),collapse="")
geneNames <- replicate(1000, oneName())
GroupA <- sample(geneNames, 400, replace=FALSE)
GroupB <- sample(geneNames, 750, replace=FALSE)
GroupC <- sample(geneNames, 250, replace=FALSE)
GroupD <- sample(geneNames, 300, replace=FALSE)
input  <-list(GroupA,GroupB,GroupC,GroupD)
venn(input)

You may also look at the ClueGO cytoscape plugin (which is intended to summarize the results obtained from any functional enrichment analysis). It offers very nice and meaningful outputs.

See also VennMaster.

I've been using this tool. It draws very nice 3-,4- and 5-way Venns. It's very handy, as you give the text or files containing f.e. geneID and it computes the overlap itself:)

No customisation options though...

This vector graphic sw could be helpful

Here’s a Venn diagram that shows the intersection of two opposites. It doesn’t sound logical, but these are human emotions, which are rarely logical. We’ve all held simultaneously happy and sad feelings,

Read the full text here.

--brought to you by mental_floss!

BioVinci can help you with the proportional venn diagrams. It's pretty quick with a drag-and-drop mechanism.

Here's a quick snapshot.

Try this for proportional Venn diagrams https://reneshbedre.github.io/blog/venn.html

This one is sort of new and gives perfectly proportional venn diagrams:

Using nVennR to generate and explore n-dimensional, quasi-proportional Venn diagrams

It can also calculate the common/unique members of different groups from a single list..

Try http://www.deepvenn.com