[BioC] Displaying very deep coverage in Gviz

[Lance Parsons]

I have been using Gviz to display coverage plots quite nicely using the 
new AlignmentsTrack, however, I've now run into a bit of an issue.  
There are some regions where we have very deep coverage (>20000 reads).  
This is causing Gviz to use excessive amounts of memory and thus makes 
plotting these regions unfeasible.

Since I only need to plot coverage, I thought a solution might be to use 
bedgraph or bigwig files and the DataTrack class to plot these.  
However, it appears that the AlignmentsTrack object does some nice 
smoothing of the data when plotting.  When I plot the coverage using a 
"polygon" type in the DataTrack class, the plot does not look comparable 
to my other plots and indeed doesn't look very nice.

Any suggestions on how to either get the AlignmentsTrack class to handle 
very deep data for coverage plots only or to replicate the smoothing in 
the DataTracks class? Thanks.

-- 
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University