[BioC] Limma: 2 venn diagrams on single page

[James W. MacDonald]

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
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826