[Bioc-devel] Bugfix for Gviz::AlignedReadTrack

[Steve Lianoglou]

Hi Florain, and the Gvizerati al,

I know that the AlignedReadTrack is still experimental, but I think
there is a bug way its drawAxis and drawGrid methods are implemented.

They `ylim` for these is set to be from 0 to the max value of the
coverage over the "*" strand

Its drawGD assumes the ylim to the the max of the coverage from either
the negative or positive (which I believe to be is correct), so the
coverage is drawn higher up on the y-scale than it really is (if one
assumes the vals on the y-tick marks are correct).

You can no doubt easily fix yourself, but you're free to pinch my two
fixes from here:

https://github.com/lianos/Gviz/commit/a977ec5b3f315b53e8f4e8cbcfdbea2816b7fb6f

Starting from about half way down into that diff you'll see the
drawGrid and drawAxis fixes.

HTH,
-steve

-- 
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