Gviz: Flip tracks so 5 prime end always on left hand side.
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@stephenwilliams-15198
Last seen 3.2 years ago

I'm plotting a BiomartGeneRegionTrack() and some DataTrack() using Gviz for a bunch of genes. This is going fine and the plots look great. I it would be really nice to have all the 5' ends of the genes of interest begin on the left hand side of the track. Is there a way to simply "flip" this track (or any track for that matter) when potting using plotTracks()?

Any suggestions would be greatly appreciated so I don't have to spend hours in illustrator doing this.

gviz gviz-package • 444 views
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You want to plot all the genes on the reverse strand as if they are on the forward strand?

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Robert Ivanek ▴ 700
@robert-ivanek-5892
Last seen 5 days ago
Switzerland
Hi, I believe you do not need to spend hours with Illustrator but few minutes with vignette :) plotTracks has argument ‘reverseStrand’, by setting it to TRUE will do what you want. Best Robert > On 22 May 2018, at 20:59, stephen.williams [bioc] <noreply@bioconductor.org> wrote: > > Activity on a post you are following on support.bioconductor.org > User stephen.williams wrote Question: Gviz: Flip tracks so 5 prime end always on left hand side.: > > I'm plotting a BiomartGeneRegionTrack() and some DataTrack() using Gviz for a bunch of genes. This is going fine and the plots look great. I it would be really nice to have all the 5' ends of the genes of interest begin on the left hand side of the track. Is there a way to simply "flip" this track (or any track for that matter) when potting using plotTracks()? > > Any suggestions would be greatly appreciated so I don't have to spend hours in illustrator doing this. > > Post tags: gviz, gviz-package > > You may reply via email or visit Gviz: Flip tracks so 5 prime end always on left hand side.
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Hi Robert,

Thanks for the very helpful, albeit very snarky, response. I have spent hours with this vignette but did not remember this section.

For anyone who is interested these display parameters can be found in the settings {Gviz} section of the R documentation