[BioC] Plot Venn diagram for 5 sets

[Liqun He]

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