Question: Gviz: Flip tracks so 5 prime end always on left hand side.
0
gravatar for stephen.williams
12 months ago by
stephen.williams10 wrote:

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 • 235 views
ADD COMMENTlink modified 12 months ago by Robert Ivanek590 • written 12 months ago by stephen.williams10

You want to plot all the genes on the reverse strand as if they are on the forward strand?

ADD REPLYlink written 12 months ago by James W. MacDonald50k
Answer: Gviz: Flip tracks so 5 prime end always on left hand side.
2
gravatar for Robert Ivanek
12 months ago by
Robert Ivanek590
Switzerland
Robert Ivanek590 wrote:
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.
ADD COMMENTlink written 12 months ago by Robert Ivanek590

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

ADD REPLYlink written 12 months ago by stephen.williams10
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