[BioC] Displaying very deep coverage in Gviz

[Hahne, Florian]

Hi Lance,
If you want to go down the DataTrack road you may want to take a look at
the window parameter to introduce a bit of smoothing. However I suspect
that your problem is already in the calculation of the coverage vector for
your bigwig files, because the AlignmentsTrack does not do much to that
vector but rather tries to plot it as is, in a similar fashion as the
DataTrack(type="histogram²) method would do.
There seems to be a more general issue here with these kinds of ultra-deep
coverage tracks, and I am wondering whether a reasonable resampling
strategy wouldn¹t be a better way to go forward. I will have to check the
Rsamtools functions that I am using for computing the coverage vectors
from BAM file, but I am pretty sure that resampling is already in place.
Will let you know.
Florian

On 15/05/14 18:36, "Lance Parsons" <lparsons at princeton.edu> wrote:

>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
>