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

Janet Young jayoung at fhcrc.org
Wed Dec 4 20:34:13 CET 2013

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....




Dr. Janet Young 

Malik lab

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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