[Bioc-sig-seq] overlaying coverage plots

[LU Zen]

Hi Martin,

Thanks for your help again. 

While I can zoom in the plot by limiting the range of the x-coordinates, I can't get the ylim to work. The presence of a some exceptionally high coverage values just distords the plot. When I included ylim, this is what I got:

> plotLongVector(cvg, ylim = range(0,100))
Error in plot.default(NULL, xlab = xlab, ylab = ylab, xlim = offset +  :
  formal argument "ylim" matched by multiple actual arguments

Is there any trick that I'm missing here?

Thanks,
Zen

> -----Original Message-----
> From: Martin Morgan [mailto:mtmorgan at fhcrc.org]
> Sent: 12 August 2010 20:04
> To: LU Zen
> Cc: 'bioc-sig-sequencing at r-project.org'
> Subject: Re: [Bioc-sig-seq] overlaying coverage plots
> 
> On 08/12/2010 11:47 AM, LU Zen wrote:
> > 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)
> 
> I guess here x is now a data.frame. Suppose the position is in the first
> column, the coverage at that position in the second column; I'm assuming
> that position is 1-based, i.e., that the first nucleotide on the
> chromosome is nucleotide number 1, and not nucleotide number 0. You
> could create a vector cvg that is as long as the maximum position.
> 
>   cvg = numeric(max(x[[1]]))
> 
> cvg is initially all 0, and you could set the non-zero values to the
> correct coverage with
> 
>   cvg[x[[1]]] = x[[2]]
> 
> and then
> 
>   plotLongVector(cvg)
> 
> Your use of quotes below isn't correct; try working through 'An
> Introduction to R', available in a browser after typing
> 
>   help.start()
> 
> Martin
> 
> >> 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
> >
> 
> 
> --
> 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.