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

[Hahne, Florian]

Hi Janet, Malcom,
plotting the reverse strand is something that we can do quite easily.
Essentially we just need to reverse the plotting coordinates. I will take
a look at this in the new year, but it should be a trivial code change. It
was more the "force to one strand" option which folks were discussing
before that put me off simply because a negative strand transcript forced
onto the positive strand is not defined well.
Florian


On 12/4/13 8:44 PM, "Cook, Malcolm" <MEC at stowers.org> wrote:

>+2 !
>
> >-----Original Message-----
> >From: bioconductor-bounces at r-project.org
>[mailto:bioconductor-bounces at r-project.org] On Behalf Of Janet Young
> >Sent: Wednesday, December 04, 2013 1:34 PM
> >To: bioconductor at r-project.org
> >Subject: [BioC] Gviz - Plot genes and data from - strand (3'-5') in
>5'-3' direction
> >
> >Hi all,
> >
> >I stumbled across this discussion - I'm looking to do exactly the same
>thing, and wanted to put in a vote that this would be very useful
> >functionality.  When looking at a single gene of interest (or a
>handful), it's so much more intuitive to us biologists to present it
>5'-to-3'.
> >
> >I've often made figures using UCSC's genome browser - if you're looking
>at any region in their browser, the "reverse" button right
> >below the display what we're looking for.  Plots are still shown
>relative to genomic coordinates, it's just that the end coord is plotted
> >on the left, and the start on the right.
> >
> >I could imagine some kind of "reverse=TRUE" option in plotTracks,
>without needing to mess with the underlying GRanges (or
> >whatever data the track is based on).  Not sure how hard that would be
>to code, though....
> >
> >thanks,
> >
> >Janet
> >
> >-------------------------------------------------------------------
> >
> >Dr. Janet Young
> >
> >Malik lab
> >http://research.fhcrc.org/malik/en.html
> >
> >Fred Hutchinson Cancer Research Center
> >1100 Fairview Avenue N., A2-025,
> >P.O. Box 19024, Seattle, WA 98109-1024, USA.
> >
> >tel: (206) 667 4512
> >email: jayoung  ...at...  fhcrc.org
> >
> >-------------------------------------------------------------------
> >
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