Hi,

I think the GenomeGraphs package is very handy to visualize genomics data;
however, I am trying to find a  way to represent sequencing coverage (e.g.
ChipSeq) as polygon, as seen for example in the GBrowse-visualizations.

I have used the makeBaseTrack-function to visualize per-base coverage, and
set the dp=DisplayPars(type="l) to represent coverage as a line. However,
for better visualization (especially for Figures containing several genome
plots), I prefer to have represent the coverage track as polygon...

The possible values that the display parameters for a BaseTrack-object are
not described in the help section, but I figured that there is a "p"
(points) and an "l" (line) option. Maybe there is a "polygon"-option?
Otherwise, are there alternatives, e.g. a different GenomeGraphs-class that
I could use? (besides adding viewports manually into existing plots, which
could be done but is not very userfriendly, I guess)...

Thanks for any help on this issue.

Best wishes, Sam

p.s. I am using GenomeGraphs_1.12.0 on R Version 2.13.0 (Mac version).

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Samuel Wuest
Smurfit Institute of Genetics
Trinity College Dublin
Dublin 2, Ireland
Phone: +353-1-896 2444
Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
Email: wuests@tcd.ie
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