[Bioc-sig-seq] overlaying coverage plots

[LU Zen]

Hi Martin,

Thanks for your help. This may sound really silly. My understanding of vector in R is that this is a row of numbers. In my case, I have a table consisting of 2 columns, position vs coverage. So I went tried:

> x<-read.table(file="B6_CAST_s1_cov1.txt", sep="\t", header=F)
> r<-Rle('x')
> plotLongVector('r')
Error in plot.window(...) : invalid 'ylim' value

Do I need to transpose my data first?

Thank you.

Cheers,
Zen



> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: 12 August 2010 18:00
> To: LU Zen
> Cc: 'bioc-sig-sequencing at r-project.org'
> Subject: Re: [Bioc-sig-seq] overlaying coverage plots
> 
> On 08/12/2010 09:20 AM, LU Zen wrote:
> > I'm trying to overlay coverage plots of individual chromosomes from
> > different experiments to get a quick overview of probable CNVs. I've
> > tried using simple plot, ggplot and plotrix packages of R (and I'm a
> > real novice in R) but it seems that my linux machine with 64GB of
> > memory is unable to handle the task. I've also reduced my file size
> > by putting only the coordinates and the coverages derived from
> > samtools pileup into a single file.
> >
> > My understanding is that I should be able to plot the coverage of a
> > single chromosome with the bioconductor package but is it possible to
> > overlay multiple plots using the package? I'll be really grateful if
> > someone can advice on the way to do this.
> 
> One easy possibility is to use HilbertVis' plotLongVector function with
> standard R graphics commands. So here's some long data (simulated with
> another function in HlibertVis)
> 
>   library(HilbertVis)
>   x <- makeRandomTestData() # 1e7 entries
> 
> Then we set up a device so that we'll plot into 4 'rows' and 1 'column',
> with margins on each plot fairly tight (see ?par)
> 
>   par(mfcol=c(4, 1), mar=c(1, 4, 2, 2))
> 
> And then we'll create four plots, showing progressively more extreme peaks
> 
>   par(mfcol=c(4, 1), mar=c(1, 4, 2, 2))
>   plotLongVector(x)
>   plotLongVector(x * (abs(x) > 50))
>   plotLongVector(x * (abs(x) > 100))
>   plotLongVector(x * (abs(x) > 200))
> 
> This would also work with IRanges' Rle objects
> 
>   library(IRanges)
>   r <-	Rle(x)
>   plotLongVector(r)
>   plotLongVector(r * (abs(r) > 50))
>   plotLongVector(r * (abs(r) > 100))
>   plotLongVector(r * (abs(r) > 200))
> 
> One could also easily 'zoom in'
> 
>   len = length(r)
>   plotLongVector(r)
>   plotLongVector(seqselect(r, len/10, 9 * len / 10))
>   plotLongVector(seqselect(r, len/100, 9 * len / 100))
>   plotLongVector(seqselect(r, len/1000, 9 * len / 1000))
> 
> (though here the x-coordinates are not correct).
> 
> Also of course one might explore the raison d'etre of the package, and
> its companion HilbertVisGUI
> 
>   showHilbertImage(hilbertImage(x))
> 
> Martin
> 
> >
> > Thank you.
> >
> > Zen
> >
> >
> >
> >
> >
> > The University of Edinburgh is a charitable body, registered in
> > Scotland, with registration number SC005336.
> >
> >
> >
> > _______________________________________________ Bioc-sig-sequencing
> > mailing list Bioc-sig-sequencing at r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
> 
> 
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
> 
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793

-- 
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.