plot xy data
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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