I would like to place 2 venn diagrams generated by limma on single page. However they are very squeezy and there are much empty space above and below them. The output is attached to this post. I would like to remove the empty space, so that the venn diagrams are as large as possible while retaining their aspect ratio. I tried reducing oma to 0 but unable to get what I want. library("limma") Y <- matrix(rnorm(100*6),100,6) Y[1:10,3:4] <- Y[1:10,3:4]+3 Y[1:20,5:6] <- Y[1:20,5:6]+3 design <- cbind(1,c(0,0,1,1,0,0),c(0,0,0,0,1,1)) fit <- eBayes(lmFit(Y,design)) results <- decideTests(fit) a <- vennCounts(results) pdf("test.pdf", paper="a4") par(oma=rep(0.5, 4), mfrow=c(2,1), pty="m") vennDiagram(m, include=c("up","down"), counts.col=c("red","green"), mar=rep(1,4), main="test") vennDiagram(m, include=c("both"), counts.col=c("blue"), mar=rep(1,4), main="test") dev.off() > sessionInfo() R version 2.8.1 (2008-12-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] tools stats graphics grDevices utils datasets methods base other attached packages: [1] limma_2.16.4 venn_1.6 pvclust_1.2-1 org.Hs.eg.db_2.2.6 KEGG.db_2.2.5 hgu133a.db_2.2.5 RSQLite_0.7-1 [8] DBI_0.2-4 AnnotationDbi_1.4.3 Biobase_2.2.2 -------------- next part -------------- A non-text attachment was scrubbed... Name: test.pdf Type: application/pdf Size: 37669 bytes Desc: not available URL: <https: stat.ethz.ch="" pipermail="" bioconductor="" attachments="" 20090320="" 6eaf4b59="" attachment.pdf="">

I would use a combination of layout() and the width and height arguments to pdf(). If I run the workable portion of your code, I get pretty reasonable results with this: > pdf("test.pdf", paper="a4", height=11, width=7) > layout(matrix(1:2, ncol=1)) > vennDiagram(a) > vennDiagram(a) > dev.off() Best, Jim Daren Tan wrote: > I would like to place 2 venn diagrams generated by limma on single > page. However they are very squeezy and there are much empty space > above and below them. The output is attached to this post. I would > like to remove the empty space, so that the venn diagrams are as large > as possible while retaining their aspect ratio. I tried reducing oma > to 0 but unable to get what I want. > > library("limma") > Y <- matrix(rnorm(100*6),100,6) > Y[1:10,3:4] <- Y[1:10,3:4]+3 > Y[1:20,5:6] <- Y[1:20,5:6]+3 > design <- cbind(1,c(0,0,1,1,0,0),c(0,0,0,0,1,1)) > fit <- eBayes(lmFit(Y,design)) > results <- decideTests(fit) > a <- vennCounts(results) > pdf("test.pdf", paper="a4") > par(oma=rep(0.5, 4), mfrow=c(2,1), pty="m") > vennDiagram(m, include=c("up","down"), counts.col=c("red","green"), > mar=rep(1,4), main="test") > vennDiagram(m, include=c("both"), counts.col=c("blue"), mar=rep(1,4), > main="test") > dev.off() > >> sessionInfo() > R version 2.8.1 (2008-12-22) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] tools stats graphics grDevices utils datasets > methods base > > other attached packages: > [1] limma_2.16.4 venn_1.6 pvclust_1.2-1 > org.Hs.eg.db_2.2.6 KEGG.db_2.2.5 hgu133a.db_2.2.5 > RSQLite_0.7-1 > [8] DBI_0.2-4 AnnotationDbi_1.4.3 Biobase_2.2.2 > > > -------------------------------------------------------------------- ---- > > _______________________________________________ > 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 -- James W. MacDonald, M.S. Biostatistician Douglas Lab 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826