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 > > > >------------------------------------------------------------------- > > > >_______________________________________________ > >Bioconductor mailing list > >Bioconductor at r-project.org > >https://stat.ethz.ch/mailman/listinfo/bioconductor > >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor > >_______________________________________________ >Bioconductor mailing list >Bioconductor at r-project.org >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor