[R] How to draw a histogram for some intervals in R

[Jim Lemon]

On 04/22/2014 06:32 AM, VG wrote:
> Hello Everyone,
> I have a text file which has data in this format.
>
> gene    start    end    freq
> Slc19a1    81    144    1
> Slc19a1    192    255    6
> Slc19a1    273    336    7
> Slc19a1    363    426    4
> Slc19a1    465    528    3
> Slc19a1    540    603    5
> Slc19a1    813    876    5
> Slc19a1    912    975    6
> Slc19a1    987    1050    8
> Slc19a1    1062    1125    6
> Slc19a1    1170    1233    8
> Slc19a1    1278    1341    6
>
> I want to draw a histogram between start and end of the above files on the
> x axis and freq associated with each interval on the y axis. How can I do
> this. I am just beginning to plot graphs in R.
>
Hi VG,
Here is a very basic way to do this:

vgdf<-read.table(text="gene    start    end    freq
Slc19a1    81    144    1
Slc19a1    192    255    6
Slc19a1    273    336    7
Slc19a1    363    426    4
Slc19a1    465    528    3
Slc19a1    540    603    5
Slc19a1    813    876    5
Slc19a1    912    975    6
Slc19a1    987    1050    8
Slc19a1    1062    1125    6
Slc19a1    1170    1233    8
Slc19a1    1278    1341    6",header=TRUE)

fbePlot<-function(ext,freq) {
  plot(range(ext),range(freq),type="n",xlab="Extent",ylab="Frequency")
  dimext<-dim(ext)
  for(extent in 1:dimext[1])
   rect(ext[extent,1],0,ext[extent,2],freq[extent])
}

fbePlot(vgdf[,c("start","end")],vgdf[,"freq"])

Jim