[BioC] edgeR- plotSmear

[Davis McCarthy]

Hi Sridhara

Remember that all of the usual R plotting commands can be passed to plotSmear in the '...' argument (see ?plotSmear). You can just change the pch argument as required (the standard R parameter for plotting symbol).

This code is one way of doing what you want to do (assuming that your DE results are in a DGEExact or DGELRT object called "results"):

de <- as.logical(abs(decideTestsDGE(results)))
plotsymbols <- rep(19, nrow(results))
plotsymbols[de] <- 4
plotSmear(results, cex=0.8, main="MA Plot", pch=plotsymbols)

This will give you closed circles for non-DE genes and 'x's for DE genes. You can play with the choice of symbols as you please.

Cheers
Davis


On Apr 13, 2011, at 11:54 PM, Sridhara Gupta Kunjeti wrote:

> Hello,
> I have used edgeR for DGE analysis and also generated plotSmear. I guess by
> dufault the plotSmear shows red dots for differentially expressed genes.
> But, I want to generate a black and white plot, is there a possbility to
> gene using different shape of the points, may be 'x' for the differentially
> expressed genes.  If any one know how to change this it will be helpful.
> 
> Many thanks in advance!
> Sridhara
> 
> 
> -- 
> Sridhara G Kunjeti
> PhD Candidate
> University of Delaware
> Department of Plant and Soil Science
> email- sridhara at udel.edu
> Ph: 832-566-0011
> 
> 	[[alternative HTML version deleted]]
> 
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------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au


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