[BioC] plotAffyRNAdeg x-axis length of RNA digestion plot

James W. MacDonald jmacdon at med.umich.edu
Wed Jun 14 19:15:39 CEST 2006

Hi Sue,

Sue Jones wrote:
> I am using the plotAffyRNAdeg function from affy to create a RNA digestion 
> plot. I use the following code
> Data <- ReadAffy()
> deg<-AffyRNAdeg(Data[,c(1,2,3,4)])
> jpeg(file="RNA_digestion_plot.jpeg")
> plotAffyRNAdeg(deg,col=c(1,2,3,4))
> labels<-c("E2h rep 1", "E2h rep 2", "E2h rep 3", "E2h rep 4")
> legend(5,6,labels,lty=1,col=c(1,2,3,4))
> dev.off()
> The problem I have is that the x-axis is too short (only extends 0-10) 
> and the lines extend over the end. How do I extend the x-axis up to 15 as 
> I have 13 probes?

The xlim argument is automatically set in the plotAffyRNAdeg() function, 
so you won't be able to extend it without doing some hacking. You can 
either copy and paste the function into an editor, change it to your 
liking and then source() it back in, or if you can install source 
packages, you can change the source .R file and then re-build the package.

Of course this is a bit of work to just make this slight change.

You might also want to add width = 700, height =  700 (or something 
similar) to your call to jpeg(), which will make the resulting plot a 
reasonable size.



> Thanks
> Sue Jones
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109

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