Gviz - Plot genes and data from - strand (3'-5') in 5'-3' direction
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Janet Young ▴ 740
@janet-young-2360
Last seen 5.0 years ago
Fred Hutchinson Cancer Research Center,…
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 -------------------------------------------------------------------
Cancer Cancer • 899 views
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Malcolm Cook ★ 1.6k
@malcolm-cook-6293
Last seen 3 months ago
United States
+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
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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
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