[R] plot xy data

David Winsemius dwinsemius at comcast.net
Sat Nov 26 17:15:37 CET 2011

On Nov 25, 2011, at 11:27 PM, sutada Mungpakdee wrote:

> Hi,
> Has anyone know about how to get the correct plot?
> I have use this R script (as below), so I expect the plot is based  
> on x axis, but the result was opposite. Any suggestion will be great.

You question doesn't make clear what you expected and what you are  
seeing. I also do not see why you added library(IRanges) because I see  
nothing from that package in the code. We cannot run it because the  
data is not provided and you made not effort to construct a   
data.frame that would match the attributes of the real "data". It  
would be better of course to call your data something other than "dog".

> library(IRanges)
> data <-read.table(file="~/q20snpref/ 
> illusmp454merbed",sep="\t",header=F)
> colnames(data)<-c("Scaffold","sca_position","coverage")
> depth<-mean(data[,"coverage"])
> #depth now has the mean (overall)coverage
> #set the bin-size
> window<-10001
> rangefrom<-0
> rangeto<-length(data[,"sca_position"])
> data.10kb<-runmed(data[,"coverage"],k=window)
> png(file="cov_10k.png",width=1000,height=1000)
> plot(x=data. 
> 10kb 
> [rangefrom 
> :rangeto 
> ],y 
> = 
> data 
> [rangefrom 
> :rangeto 
> ,"sca_position 
> "],pch=".",cex=1,xlab="depth",ylab="bp_position",type="p")

If you want to swap the roles of "data.10kb" (AKA "coverage") and  
"sca_position" then just reverse the x and y assignments.

> dev.off()
> Best regards,
> Sutada
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David Winsemius, MD
West Hartford, CT

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