[BioC] edgeR: plotSmear for multiple detags

[Mark Robinson]

Hi Steve,

The standard plot parameters are passed through.  But, to do want you want, you'll have to construct it by hand.  Here is a worked example:

# concocted example
y <- matrix(rnbinom(10000,mu=5,size=2),ncol=4)
y[1:10,1:2] <- round(y[1:10,1:2]*4)
d <- DGEList(counts=y, group=rep(1:2,each=2), lib.size=colSums(y))
d <- estimateCommonDisp(d)
de <- exactTest(d)

# construct colors, expansion and plot character manually
cols <- rep("grey",nrow(d))
conc <- d$conc$conc.group
k <- conc[,1]==min(conc[,1]) | conc[,2]==min(conc[,2])
cols[k] <- "orange"
cols[de$table$p.value<.05 & de$table$logFC < 0] <- "blue"
cols[de$table$p.value<.05 & de$table$logFC > 0] <- "red"
cexs <- rep(.2, nrow(d))
cexs[k] <- .8
cexs[1:10] <- 2

plotSmear(de, col=cols, cex=cexs)

Of course, don't take my example as a reasonable way to find DE genes (it's not, no mult. test correction), or as a reasonable way to simulate DE (also not!).

Hope that helps,
Mark


On 20.10.2011, at 19:08, steve Shen wrote:

> Hi,
> 
> Is there anyway to plot multiple detags in one figure with plotSmear labeled
> with either different color or shape? Thanks,
> 
> Steve
> 
> 	[[alternative HTML version deleted]]
> 
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