[BioC] Venn Diagram

[Hervé Pagès]

Hi Simon,

Simon Noël wrote:
> Hello every one.
> 
> I have ten list of between 4 to 3000 genes and I woudlike to put them all
> together in a venn diagram.
> 
> I have try to load the library ABarray and to use doVennDiagram but it can only
> une 3 list.
> 
> Does any one know a way to put all of my ten list in the same venn diagram?

A venn diagramm is a 2-D drawing of all the possible intersections
between 2 or 3 sets where each set is represented by a simple 2-D
shape (typically a circle). In the case of 3 sets, the resulting
diagram defines a partitioning of the 2-D plane in 8 regions.
Some people have tried (with more or less success) to put 4 sets on
the diagram but then they need to use more complicated shapes and
the resulting diagram is not as easy to read anymore. With 10 sets,
you would end up with 1024 (2^10) regions in your drawing and you
would need to use extremely complicated shapes for each region
making it really hard to read! Maybe in that case it's easier
to generate the table below.

## Let's say your genes are in 'set1', 'set2', etc... Put all the
## sets in a big list:

mysets <- list(set1, set2, ..., set10)

makeVennTable <- function(sets)
{
   mkAllLogicalVect <- function(length)
   {
     if (length == 0L)
       return(logical(0))
     ans0 <- mkAllLogicalVect(length - 1L)
     ans1 <- cbind(TRUE, ans0)
     ans2 <- cbind(FALSE, ans0)
     rbind(ans1, ans2)
   }
   lm <- mkAllLogicalVect(length(sets))
   subsets <- apply(lm, MARGIN=1,
                function(ii)
                {
                  s <- sets[ii]
                  if (length(s) == 0)
                    return("")
                  paste(sort(unique(unlist(s))), collapse=",")
                })
   data.frame(lm, subsets)
}

Then call makeVennTable() on 'mysets'. For example, with 5 small sets:

   > mysets <- list(c(1,5,12,4,9,29),
                   c(4,11,3,18),
                   c(22,4,12,19,8),
                   c(7,12,4,5,3),
                   c(25,24,4,2))

   > makeVennTable(mysets)
         X1    X2    X3    X4    X5                                 subsets
   1   TRUE  TRUE  TRUE  TRUE  TRUE 1,2,3,4,5,7,8,9,11,12,18,19,22,24,25,29
   2   TRUE  TRUE  TRUE  TRUE FALSE         1,3,4,5,7,8,9,11,12,18,19,22,29
   3   TRUE  TRUE  TRUE FALSE  TRUE   1,2,3,4,5,8,9,11,12,18,19,22,24,25,29
   4   TRUE  TRUE  TRUE FALSE FALSE           1,3,4,5,8,9,11,12,18,19,22,29
   5   TRUE  TRUE FALSE  TRUE  TRUE         1,2,3,4,5,7,9,11,12,18,24,25,29
   6   TRUE  TRUE FALSE  TRUE FALSE                 1,3,4,5,7,9,11,12,18,29
   7   TRUE  TRUE FALSE FALSE  TRUE           1,2,3,4,5,9,11,12,18,24,25,29
   8   TRUE  TRUE FALSE FALSE FALSE                   1,3,4,5,9,11,12,18,29
   9   TRUE FALSE  TRUE  TRUE  TRUE       1,2,3,4,5,7,8,9,12,19,22,24,25,29
   10  TRUE FALSE  TRUE  TRUE FALSE               1,3,4,5,7,8,9,12,19,22,29
   11  TRUE FALSE  TRUE FALSE  TRUE           1,2,4,5,8,9,12,19,22,24,25,29
   12  TRUE FALSE  TRUE FALSE FALSE                   1,4,5,8,9,12,19,22,29
   13  TRUE FALSE FALSE  TRUE  TRUE               1,2,3,4,5,7,9,12,24,25,29
   14  TRUE FALSE FALSE  TRUE FALSE                       1,3,4,5,7,9,12,29
   15  TRUE FALSE FALSE FALSE  TRUE                   1,2,4,5,9,12,24,25,29
   16  TRUE FALSE FALSE FALSE FALSE                           1,4,5,9,12,29
   17 FALSE  TRUE  TRUE  TRUE  TRUE        2,3,4,5,7,8,11,12,18,19,22,24,25
   18 FALSE  TRUE  TRUE  TRUE FALSE                3,4,5,7,8,11,12,18,19,22
   19 FALSE  TRUE  TRUE FALSE  TRUE            2,3,4,8,11,12,18,19,22,24,25
   20 FALSE  TRUE  TRUE FALSE FALSE                    3,4,8,11,12,18,19,22
   21 FALSE  TRUE FALSE  TRUE  TRUE                2,3,4,5,7,11,12,18,24,25
   22 FALSE  TRUE FALSE  TRUE FALSE                        3,4,5,7,11,12,18
   23 FALSE  TRUE FALSE FALSE  TRUE                       2,3,4,11,18,24,25
   24 FALSE  TRUE FALSE FALSE FALSE                               3,4,11,18
   25 FALSE FALSE  TRUE  TRUE  TRUE              2,3,4,5,7,8,12,19,22,24,25
   26 FALSE FALSE  TRUE  TRUE FALSE                      3,4,5,7,8,12,19,22
   27 FALSE FALSE  TRUE FALSE  TRUE                    2,4,8,12,19,22,24,25
   28 FALSE FALSE  TRUE FALSE FALSE                            4,8,12,19,22
   29 FALSE FALSE FALSE  TRUE  TRUE                      2,3,4,5,7,12,24,25
   30 FALSE FALSE FALSE  TRUE FALSE                              3,4,5,7,12
   31 FALSE FALSE FALSE FALSE  TRUE                               2,4,24,25
   32 FALSE FALSE FALSE FALSE FALSE

Cheers,
H.

> 
> Simon Noël
> VP Externe CADEUL
> Association des étudiants et étudiantes en Biochimie, Bio-
> informatique et Microbiologie de l'Université Laval
> CdeC
> 
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-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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