Nice page Thomas, really a must see! Thanks, H. Thomas Girke wrote: > 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.h tml#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 No?l 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.callminter.int, args[-1])) >> } >> munion.int <- function(...) >> { >> unique(unlist(list(...))) >> } >> lm <- mkAllLogicalVect(length(sets)) >> parts <- apply(lm, MARGIN=1, >> function(ii) >> { >> s1 <- do.callminter.int, sets[ii]) >> s2 <- do.callmunion.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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > -- 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

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.htm l#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 No?l 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.callminter.int, args[-1])) > > } > > munion.int <- function(...) > > { > > unique(unlist(list(...))) > > } > > lm <- mkAllLogicalVect(length(sets)) > > parts <- apply(lm, MARGIN=1, > > function(ii) > > { > > s1 <- do.callminter.int, sets[ii]) > > s2 <- do.callmunion.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. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC

4 isn't 5 but is beter than 3. I need to go for now for the weekend but I will take a look at it monday. Thank's you. Selon Thomas Hampton <thomas.h.hampton at="" dartmouth.edu="">, 02.07.2009: > I used Thomas Girke's package vennDia.R > > I know he just made a few changes, so you may want to grab the latest > from him. > > T > > > On Jul 2, 2009, at 5:05 PM, Simon No?l wrote: > > > 4 way is beter than 3. How do you procede? > > > > Selon Thomas Hampton <thomas.h.hampton at="" dartmouth.edu="">, 30.06.2009: > > > >> A ten way Venn diagram, if that is what you envision, would be > >> extremely difficult to > >> grasp. I have recently created a 4 way diagram, and it is possible, > >> but not easy to read. > >> > >> T > >> > >> On Jun 30, 2009, at 2:52 PM, Simon No?l 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? > >>> > >>> Simon No?l > >>> VP Externe CADEUL > >>> Association des ?tudiants et ?tudiantes en Biochimie, Bio- > >>> informatique et Microbiologie de l'Universit? Laval > >>> CdeC > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor at stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >> > >> > >> > > > > > > Simon No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC

Thank you. The gplots fonction for a 5 way venn diagram isn't really perfect but it's beter than nothing. Selon Thomas Girke <thomas.girke at="" ucr.edu="">, 02.07.2009: > There are plenty of options for this: > > gplots does 2-5 way venn diagrams > http://cran.at.r-project.org/web/packages/gplots/index.html > > vennerable has functions for proportional venn diagrams > http://doapstore.org/view.php?uri=nodeID%3A%2F%2F1000056780 > > My personal hack does 2-4 way diagrams: > http://faculty.ucr.edu/~tgirke/Documents/R_BioCond/R_BioCondManual.htm l#R_graphics_venn > > In addition, there are also many online tools: > http://www.pangloss.com/seidel/Protocols/venn4.cgi > http://bioinfogp.cnb.csic.es/tools/venny/index.html > > Thomas > > On Thu, Jul 02, 2009 at 05:14:53PM -0400, Simon No?l wrote: > > 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 No?l 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 No?l > > > > VP Externe CADEUL > > > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > > > informatique et Microbiologie de l'Universit? Laval > > > > CdeC > > > > > > > > _______________________________________________ > > > > Bioconductor mailing list > > > > Bioconductor at stat.math.ethz.ch > > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > Search the archives: > > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > > > 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 No?l > > VP Externe CADEUL > > Association des ?tudiants et ?tudiantes en Biochimie, Bio- > > informatique et Microbiologie de l'Universit? Laval > > CdeC > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > Simon No?l VP Externe CADEUL Association des ?tudiants et ?tudiantes en Biochimie, Bio- informatique et Microbiologie de l'Universit? Laval CdeC