[BioC] Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction

[Steve Lianoglou]

Hi,

On Fri, Sep 13, 2013 at 12:39 AM, Hahne, Florian
<florian.hahne at novartis.com> wrote:
> Since Gviz track objects are essentially GRanges, one could use the
> reflect method to archive this.

Indeed -- I felt like a few judicially placed reflect calls would do the trick.

> Not quite sure why one would like to do this, because the resulting
> coordinates are no longer genomic coordinates, but you guys may have a
> convincing use case I am sure.

Imagine you want to show several examples of binding of <whatever> to
some landmark within the gene -- for instance, something binding close
to the transcript start site.

If I want to single out a few examples to show during a presentation
on a slide and I have a mix of (+) and (-) strand genes, not only do I
have to explain the main idea of the slide -- that there is some
spatial preference for XXX -- but I also have to remind the audience
that these genes are on the (+) and these are on the (-) "so filp the
coords for examples 2, 5, and 7 in your head and imagine you see the
spatial bias I am explaining because once flipped, the peaks will end
up (pretty much) on top of each other ... trust me."

There are times when the strand is irrelevant and what I really want
to show is something as a function of the direction of transcription.

Know what I mean?

-steve

-- 
Steve Lianoglou
Computational Biologist
Bioinformatics and Computational Biology
Genentech