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[Bioc-devel] Help with a Gviz-plot that differs on a Mac and on an Ubuntu machine

3 messages · Dario Strbenac, Stian Lågstad

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Hi,

I hope it is ok that I ask for help here. I have a mac-specific problem
with one of the plot chimeraviz
<https://bioconductor.org/packages/release/bioc/html/chimeraviz.html>
produces. This Github issue
<https://github.com/stianlagstad/chimeraviz/issues/7#issuecomment-337275103>
has code that produces a plot that looks different on a mac and on a Ubuntu
machine. In the plot in question I make use of `Gviz::coords()` to
figure out where in the plot specific exons are drawn. When using
`chimeraviz::plotFusion()` on a mac, the call to `Gviz::coords()` seems to
give the wrong values. Though I haven't been able to create a reproducible
example without using chimeraviz - suggesting that I must be doing
something wrong in chimeraviz.

If anyone has time to take a look I'd be grateful. Or if anyone are aware
of any grid issues/differences between mac and other systems that'd be
helpful as well.
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Good day,

I can't reproduce the problem on Windows, so it seems specific to MacOS.

Is having 5' and 3' labels at the same ends of both DNA strands biologically incorrect? DNA strands are anti-parallel. See http://www.phschool.com/science/biology_place/biocoach/dnarep/strands.html Perhaps making the line corresponding to the strand the gene is encoded on thicker than the other line might also be useful?

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Dario Strbenac
University of Sydney
Camperdown NSW 2050
Australia
1 day later
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Thank you for testing, Dario!

There seems to be something wrong with those 5' and 3' markers. I'll look
into it, thanks!

On Mon, Oct 23, 2017 at 3:00 AM, Dario Strbenac <dstr7320 at uni.sydney.edu.au>
wrote: