[BioC] Limma: 2 venn diagrams on single page

Daren Tan darentan76 at gmail.com
Fri Mar 20 02:58:26 CET 2009

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.

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),

> sessionInfo()
R version 2.8.1 (2008-12-22)

LC_COLLATE=English_United States.1252;LC_CTYPE=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
 [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>

More information about the Bioconductor mailing list