[Bioc-devel] "patches" for Gviz: utr plotting support and direct BamFile plotting

Steve Lianoglou mailinglist.honeypot at gmail.com
Wed Aug 22 08:12:57 CEST 2012

Hi Florian (and other interested Gviz'ers),

I thought I'd use Gviz to whip up pretty plots for my thesis (yay!)
where I need to plot lots of NGS data over 3'UTRs.

I wanted to tackle the "more standard" drawing of UTRs (thin exons
(vs. thick coding)) in gene regions as well as making repeated
plotting of the same data over different regions easier -- there is
also an unplanned for increase in plotting speed of ~ 5-8x
(unscientific benchmark) when plotting gene regions using my TxDbTrack
vs. GeneRegionTrack.

I have a more thorough summary of what I did here:

With the relevant pics at the bottom. It's still a work in progress
but I thought I'd put it out there now to see if you think it'd be
useful for patching back into Gviz -- I'd be happy to groom things
further to make it easier to add back into Gviz, or change things to
make the approach more "inline" with the coding style/philosophy of
the package (which I tried to stick to).

Thanks (again) for this package -- it's really great.


Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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