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

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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor