Plotting in R

[aevgup]

Hi Everyone,

I am trying to plot a histogram in R using this command which is serving my purpose

x <- read.table(file="cov.txt",header =FALSE)
When you look at the graph(see attached) then from 715 to 777 is my CODING REGION. I want to make a rectangular bar from position 715-777 and place it on the top of the graph. How can I do it

I wrote this and try to add lines or points but was not able to do it
firstCodonCdr1 = 239
lastCodonCdr1 = 259
cdr1NTs = ((firstCodonCdr1-1)*3+1)3*lastCodonCdr1)
cdrPositions = cdr1NTs

Any help !!

Thanks

[blakeoft]

I think you want to use the polygon function. See ?polygon to look at the help info. Basically:

polygon(x,y,col)

where x is the vector containing x coordinates of the vertices, y is y vertices and col is the color of the polygon. I think you'll plot your histogram, and then polygon() right after it. So it'll look like:

> hist(data)
> polygon(x,y,col)

[aevgup]

plotting in R

Hi I used this code
x <- read.table(file="cov.txt",header =FALSE)

firstCodonCdr1 = 239
lastCodonCdr1 = 259
cdr1NTs = ((firstCodonCdr1-1)*3+1)3*lastCodonCdr1)
cdrPositions = cdr1NTs

plot(x$V2,x$V3,type="h",col="blue")
r = rep(50,63) # to make 63 times 50 to occur so that it matches length of x
par(new=TRUE)

polygon(cdrPositions,r,col="red")

No change happens in the graph.

I am attaching the cov.txt file too

I have been trying points and lines too but no luck!!

THanks

[blakeoft]

This looks terrible, but I just did

> x <- read.table(file="cov.txt",header =FALSE)
> plot(x$V2,x$V3,type="h",col="blue")
> polygon(c(715,777,777,715),c(40,40,45,45), col="blue")

and got this picture. You can change the coordinates of the box if you want so that it doesn't look as bad, and also, the color might need some work. I think you can do it like col = rgb(a,b,c) where a b and c are the red blue and green color values.

[aevgup]

Thanks for the reply. Your answer gave me another way to do it. How about this

x <- read.table(file="cov.txt",header =FALSE)
plot(x$V2,x$V3,type="h",col="blue")
lines(c(715,777),c(45,45),col="red",lwd=8)

Regards

[Thias]

Seems your problem is already solved, but in case you have 5o plot similar data in future again, I recommend the Gviz package on Bioconductor, which can be used to output beautiful plots for NGS-data.

[aevgup]

Hi,
Thanks for letting me know about the package. I am trying this package now