[BioC] vennDiagram in Limma

[Francois Pepin]

Hi James,

Unfortunately, there is nothing in the code to prevent that 0 from 
appearing.

The two main solutions I would offer would be:
1- edit the image externally to remove the offending digit.
2- edit the source code using "fix(vennDiagram)" and comment out the 
lines containing this code:
   text(2.3, -2.1, counts[1], cex = cex, col = col,
        adj = adj)

Note that there are 3 such calls for vennDiagrams with 1,2 and 3 
categories. You can either comment out the 2nd one (for 2 categories) or 
all 3.

I do not think it would be a good idea to add an option in the code to 
hide this, as it is almost always crucial information for this plot.

Francois

James Perkins wrote:
> 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
> 
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