[BioC] vennDiagram in Limma

[James Perkins]

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!

http://i327.photobucket.com/albums/k454/jimineep/venn1.jpg

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?

Code:

library(limma)

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

}

jpeg("venn1.jpg")

vennDiagram(vennCounts(Counts))

dev.off()

Kindest regards,

Jim Perkins
PhD student,
UCL