Dear all, The following is a function to plot Venn diagram for 5 sets, which I promised two weeks ago. You can input 5 lists to the function and get the Venn diagram. Hope it?s useful for some of you. Best wishes, Liqun He Karolinska Institute, Stockholm ###An example of how to use the function list1=letters[1:6]; list2=letters[6:10]; list3=letters[6:15]; list4=letters[6:21]; list5=letters[6:26]; plot_venn5(list1, list2, list3, list4, list5); ### ================================================= ### here is code for the function plot_venn5=function(listA, listB, listC, listD, listE){ all_ids=unique(c(listA, listB, listC, listD, listE)); all_n=length(all_ids); #create counting matrix all_matrix=cbind(affy=rep(0,all_n),est=rep(0,all_n),glomchip=rep(0,all _n),sage=rep(0,all_n),stanford=rep(0,all_n)); rownames(all_matrix)=all_ids; colnames(all_matrix)=c(substitute(listA), substitute(listB), substitute(listC), substitute(listD), substitute(listE)); all_matrix[all_ids %in% listA, 1]=1; all_matrix[all_ids %in% listB, 2]=1; all_matrix[all_ids %in% listC, 3]=1; all_matrix[all_ids %in% listD, 4]=1; all_matrix[all_ids %in% listE, 5]=1; #elements only in one data set. only1= apply(all_matrix,1,sum) == 1; nA=sum(all_matrix[only1, 1]); nB=sum(all_matrix[only1, 2]); nC=sum(all_matrix[only1, 3]); nD=sum(all_matrix[only1, 4]); nE=sum(all_matrix[only1, 5]); #elements overlapped in two data set. only2= apply(all_matrix,1,sum) == 2; nAB=sum(only2 & all_matrix[,1] & all_matrix[,2]); nAC=sum(only2 & all_matrix[,1] & all_matrix[,3]); nAD=sum(only2 & all_matrix[,1] & all_matrix[,4]); nAE=sum(only2 & all_matrix[,1] & all_matrix[,5]); nBC=sum(only2 & all_matrix[,2] & all_matrix[,3]); nBD=sum(only2 & all_matrix[,2] & all_matrix[,4]); nBE=sum(only2 & all_matrix[,2] & all_matrix[,5]); nCD=sum(only2 & all_matrix[,3] & all_matrix[,4]); nCE=sum(only2 & all_matrix[,3] & all_matrix[,5]); nDE=sum(only2 & all_matrix[,4] & all_matrix[,5]); #elements overlapped in three data set. only3= apply(all_matrix,1,sum) == 3; nABC=sum(only3 & all_matrix[,1] & all_matrix[,2] & all_matrix[,3]); nABD=sum(only3 & all_matrix[,1] & all_matrix[,2] & all_matrix[,4]); nABE=sum(only3 & all_matrix[,1] & all_matrix[,2] & all_matrix[,5]); nACD=sum(only3 & all_matrix[,1] & all_matrix[,3] & all_matrix[,4]); nACE=sum(only3 & all_matrix[,1] & all_matrix[,3] & all_matrix[,5]); nADE=sum(only3 & all_matrix[,1] & all_matrix[,4] & all_matrix[,5]); nBCD=sum(only3 & all_matrix[,2] & all_matrix[,3] & all_matrix[,4]); nBCE=sum(only3 & all_matrix[,2] & all_matrix[,3] & all_matrix[,5]); nBDE=sum(only3 & all_matrix[,2] & all_matrix[,4] & all_matrix[,5]); nCDE=sum(only3 & all_matrix[,3] & all_matrix[,4] & all_matrix[,5]); #elements overlapped in four data set. only4= apply(all_matrix,1,sum) == 4; nABCD=sum(only4 & all_matrix[,1] & all_matrix[,2] & all_matrix[,3] & all_matrix[,4]); nABCE=sum(only4 & all_matrix[,1] & all_matrix[,2] & all_matrix[,3] & all_matrix[,5]); nABDE=sum(only4 & all_matrix[,1] & all_matrix[,2] & all_matrix[,4] & all_matrix[,5]); nACDE=sum(only4 & all_matrix[,1] & all_matrix[,3] & all_matrix[,4] & all_matrix[,5]); nBCDE=sum(only4 & all_matrix[,2] & all_matrix[,3] & all_matrix[,4] & all_matrix[,5]); #elements overlapped in five data set. all5= apply(all_matrix,1,sum) == 5; nABCDE=sum(all5); #make the plot. elps=cbind(150*cos(seq(0,2*pi,len=1000)), 60*sin(seq(0,2*pi,len=1000))); relocate_elp=function(e, alpha, x, y){ phi=(alpha/180)*pi; xr=e[,1]*cos(phi)+e[,2]*sin(phi); yr=-e[,1]*sin(phi)+e[,2]*cos(phi); xr=x+xr; yr=y+yr; return(cbind(xr, yr)); } par(mar=c(1,1,1,1)); plot(c(0, 400), c(0, 400), type="n", axes=F, ylab="", xlab=""); polygon(relocate_elp(elps, 90,200, 250)); polygon(relocate_elp(elps, 162,250, 220)); polygon(relocate_elp(elps, 234,250, 150)); polygon(relocate_elp(elps, 306,180, 125)); polygon(relocate_elp(elps, 378,145, 200)); #label the data set name. text(50, 280, colnames(all_matrix)[1]); text(170,400, colnames(all_matrix)[2]); text(350,300, colnames(all_matrix)[3]); text(350,20, colnames(all_matrix)[4]); text(55,10, colnames(all_matrix)[5]); #label the numbers text(61, 228, nA); text(194, 329, nB); text(321, 245, nC); text(290, 81, nD); text(132, 69, nE); text(146, 250, nAB, cex=0.7); text(123, 188, nAC, cex=0.7); text(275, 152, nAD, cex=0.7); text(137, 146, nAE, cex=0.7); text(243, 268, nBC, cex=0.7); text(175, 267, nBD, cex=0.7); text(187, 117, nBE, cex=0.7); text(286, 188, nCD, cex=0.7); text(267, 235, nCE, cex=0.7); text(228, 105, nDE, cex=0.7); text(148, 210, nABC,cex=0.7); text(159, 253, nABD,cex=0.7); text(171, 141, nABE,cex=0.7); text(281, 175, nACD,cex=0.7); text(143, 163, nACE,cex=0.7); text(252, 145, nADE,cex=0.7); text(205, 255, nBCD,cex=0.7); text(254, 243, nBCE,cex=0.7); text(211, 118, nBDE,cex=0.7); text(267, 211, nCDE,cex=0.7); text(170, 231,nABCD,cex=0.7); text(158, 169,nABCE,cex=0.7); text(212, 139,nABDE,cex=0.7); text(263, 180,nACDE,cex=0.7); text(239, 232,nBCDE,cex=0.7); text(204,190,nABCDE); } ###end