Hi,

I am using the ChIPpeakAnno package for analysis of my ChIPseq data. However, I am having some problems with the makeVennDiagramm function. I have three datasets to overlap. And although I am using the euler and scaled=TRUE I do not succeed in getting a scaled diagram.

makeVennDiagram (RangedDataList(peaksR[[1]], peaksR[[3]], peaksR[[5]]), total=100000, NameOfPeaks=c("A", "B", "C"), cat.cex=1, margin=0.1, cat.dist=0.07, euler.d=TRUE, scaled=TRUE, alpha=c(0.8, 0.8, 0.8), minoverlap=10)

Any suggestions how to do this?

For other analysis I have used the Vennerable package. Would it be possible to export the VennCounts (made by makeVennDiagram) into a data.frame so that I can use it as an input for the other package?

Thanks for your help!
Dagmar

Hi Dagmar,

Thank you for choosing ChIPpeakAnno in your research. This is a bug of VennDiagram package. I think you want to have a try with the package Vennerable. In the vignettes of ChIPpeakAnno, I put codes how to use Vennerable. I also paste a sample here. Hope this will help.

library(ChIPpeakAnno)
peaks1 <- GRanges("chr1", IRanges(seq(1, 100, 5), width=2), "+")
peaks2 <- GRanges("chr1", IRanges(seq(2, 20, 3), width=2), "+")
peaks3 <- GRanges("chr1", IRanges(seq(10, 50, 4), width=2), "+")
res <- makeVennDiagram(Peaks=list(peaks1, peaks2, peaks3), NameOfPeaks=c("TF1", "TF2", "TF3"))
install.packages("Vennerable", repos="http://R-Forge.R-project.org", type="source")
library(Vennerable)
venn_cnt2venn <- function(venn_cnt){
 n <- which(colnames(venn_cnt)=="Counts") - 1
 SetNames=colnames(venn_cnt)[1:n]
 Weight=venn_cnt[,"Counts"]
 names(Weight) <- apply(venn_cnt[,1:n], 1, paste, collapse="")
 Venn(SetNames=SetNames, Weight=Weight)
 }
v <- venn_cnt2venn(res$vennCounts)
plot(v)