[BioC] vennDiagram in Limma

James Perkins jperkins at biochem.ucl.ac.uk
Fri Jul 25 13:06:26 CEST 2008

Im using vennDiagram and vennCounts with 2 lists of characters (set1 and 
set2), to show how they compare.

However I notice that vennDiagram by defaults puts an 0 outside the 
circles, to show there was nothing in the universe which wasnt in the 
union of the two sets. I don't want this 0 appearing!


example here.. notice the 0 at the bottom left of the image.

Can I get rid of this? Have I missed something obvious in the limma user 
guide or the help page? I appreciate I am not using vennDiagram for its 
original purpose and as such this might not be possible, if not is there 
another way around it?



set1 = scan("set1.txt",what='character',sep="\n")

set2 = scan("set2.txt",what='character',sep="\n")

set1 = set1[1:10]

set2 = set2[1:10]

universe = sort(union(set1,set2))

Counts <- matrix(0, nrow=length(universe), ncol=2)

colnames(Counts) <- c("label perm", "gene perm")

for (i in 1:length(universe)) {

        Counts[i,1] <- universe[i] %in% set1

        Counts[i,2] <- universe[i] %in% set2





Kindest regards,

Jim Perkins
PhD student,

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