Lu,
if you type "plotLongVector" into the R interpreter, you will see its
(simple) implementation, and also, see why you currently cannot specify
your own argument for "ylim". I suppose that the implementation will
soon be updated to address this problem, but for the time being, you
could simple define your own copy of that function, and set ylim as you
wish.
Best wishes
Wolfgang.
LU Zen scripsit 13/08/10 13:03:
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:[email protected]]
Sent: 12 August 2010 20:04
To: LU Zen
Cc: '[email protected]'
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:[email protected]]
Sent: 12 August 2010 18:00
To: LU Zen
Cc: '[email protected]'
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
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Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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--
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
--
Wolfgang Huber
EMBL
http://www.embl.de/research/units/genome_biology/huber
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