[BioC] CGH DNAcopy plot multiple samples on one plot

[Sean Davis]

On Nov 13, 2007 7:56 AM, Gavin Kelly <gavin.kelly at cancer.org.uk> wrote:
> Daniel Brewer wrote:
> > Hi, Is there anyway to plot the results of DNAcopy
> > for all or some samples on one plot? Just the segments
> > not the underlying data points. This is to allow visual
> > comparison of samples. Many thanks Dan
>
> In the snapCGH you can have their version of DNAcopy (runDNAcopy), and
> you can overplot as many segmented genomes as you want with the
> plotSegmentedGenome command.  It's a bit of a roundabout way, you may
> have to make multiple copies of your segmentations, and then permute the
> array indices in one copy to make sure the arrays you want to plot are
> all at the same index, but it should do it.
>
> What I do nowadays, though, is export the values out as a text file, and
> then load them into affymetrix' Integrated Genome Browser, where you can
> load and superimpose as many tracks as you want.  I'll try to get around
> to making available my code for doing this.

Along the same lines, one can make pretty nice plots using the UCSC
genome browser, also.  One can use the "data" to make a wiggle track,
or one can simply color-code the regions of gain/loss and make bed
tracks.  The latter option keeps the filesize down and allows one to
quickly view the results of segmentation for dozens of samples.  The
file formats for the UCSC genome broswer pretty simple.  Descriptions
are available here:

http://genome.ucsc.edu/goldenPath/help/customTrack.html

Sean