[BioC] Venn Diagram
Simon Noël
simon.noel.2 at ulaval.ca
Thu Jul 2 23:27:56 CEST 2009
I speak to some collegue and it's possible to split my data in 2 group of 5 list
so a 5 set diagram can be possible... But now how to create that? I need to do
it with a pensil or there is a way to do it in R or with a program?
Selon Thomas Girke <thomas.girke at ucr.edu>, 02.07.2009:
> To get an impression how "pretty and confusingly complex" venn diagrams
> with more than 5 sets would look like, one can take a look at this page
> from combinatorics.org:
> http://www.combinatorics.org/Surveys/ds5/VennSymmEJC.html.
>
> Also, here is a small collection of methods/ideas for analyzing intersect
> relationships among large numbers of sample sets:
>
http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.html#R_graphics_overlapper
> These approaches are much more scalable than venn comparisons, but lack
> their logical 'not in' relations. The function for computing 'All
> Possible Intersects' is utility wise the closest alternative to venn
> diagrams.
>
> Thomas
>
>
> On Wed, Jul 01, 2009 at 09:41:25PM -0700, hpages at fhcrc.org wrote:
> > Oops, this is wrong, sorry! See a modified version of
> > makeVennTable() below that hopefully does the right thing.
> >
> > Quoting Hervé Pagès <hpages at fhcrc.org>:
> >
> > >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
> >
> > The above table is clearly not the expected thing because the subsets
> > in the last column are not a partition of the initial set of genes
> > (some ids appear in several rows).
> > Try this instead:
> >
> > 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)
> > }
> > minter.int <- function(...)
> > {
> > args <- list(...)
> > if (length(args) == 0)
> > return(integer(0))
> > if (length(args) == 1)
> > return(args[[1]])
> > intersect(args[[1]], do.call(minter.int, args[-1]))
> > }
> > munion.int <- function(...)
> > {
> > unique(unlist(list(...)))
> > }
> > lm <- mkAllLogicalVect(length(sets))
> > parts <- apply(lm, MARGIN=1,
> > function(ii)
> > {
> > s1 <- do.call(minter.int, sets[ii])
> > s2 <- do.call(munion.int, sets[!ii])
> > part <- setdiff(s1, s2)
> > if (length(part) == 0)
> > return("")
> > paste(sort(part), collapse=",")
> > })
> > data.frame(lm, parts)
> > }
> >
> > Then:
> >
> > >makeVennTable(mysets)
> > X1 X2 X3 X4 X5 parts
> > 1 TRUE TRUE TRUE TRUE TRUE 4
> > 2 TRUE TRUE TRUE TRUE FALSE
> > 3 TRUE TRUE TRUE FALSE TRUE
> > 4 TRUE TRUE TRUE FALSE FALSE
> > 5 TRUE TRUE FALSE TRUE TRUE
> > 6 TRUE TRUE FALSE TRUE FALSE
> > 7 TRUE TRUE FALSE FALSE TRUE
> > 8 TRUE TRUE FALSE FALSE FALSE
> > 9 TRUE FALSE TRUE TRUE TRUE
> > 10 TRUE FALSE TRUE TRUE FALSE 12
> > 11 TRUE FALSE TRUE FALSE TRUE
> > 12 TRUE FALSE TRUE FALSE FALSE
> > 13 TRUE FALSE FALSE TRUE TRUE
> > 14 TRUE FALSE FALSE TRUE FALSE 5
> > 15 TRUE FALSE FALSE FALSE TRUE
> > 16 TRUE FALSE FALSE FALSE FALSE 1,9,29
> > 17 FALSE TRUE TRUE TRUE TRUE
> > 18 FALSE TRUE TRUE TRUE FALSE
> > 19 FALSE TRUE TRUE FALSE TRUE
> > 20 FALSE TRUE TRUE FALSE FALSE
> > 21 FALSE TRUE FALSE TRUE TRUE
> > 22 FALSE TRUE FALSE TRUE FALSE 3
> > 23 FALSE TRUE FALSE FALSE TRUE
> > 24 FALSE TRUE FALSE FALSE FALSE 11,18
> > 25 FALSE FALSE TRUE TRUE TRUE
> > 26 FALSE FALSE TRUE TRUE FALSE
> > 27 FALSE FALSE TRUE FALSE TRUE
> > 28 FALSE FALSE TRUE FALSE FALSE 8,19,22
> > 29 FALSE FALSE FALSE TRUE TRUE
> > 30 FALSE FALSE FALSE TRUE FALSE 7
> > 31 FALSE FALSE FALSE FALSE TRUE 2,24,25
> > 32 FALSE FALSE FALSE FALSE FALSE
> >
> > H.
> >
> > _______________________________________________
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> >
>
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>
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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