[BioC] Venn Diagram
Simon Noël
simon.noel.2 at ulaval.ca
Thu Jul 2 23:14:53 CEST 2009
Thank's you for your help but I already have produced a table like that. My
code was really different. Your code run faster than mine... But the result
is the same. What I really need for the next step is a Veen Diagram. To see
how to create a 4 set may help me to see how to create more complicated one.
Selon Hervé Pagès <hpages at fhcrc.org>, 01.07.2009:
> 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
> 1100 Fairview Ave. N, M2-B876
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fhcrc.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
>
>
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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