Question: Gviz (GenomicInteractions) arc height and boundaries
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gravatar for Nik dAK
10 weeks ago by
Nik dAK10
Nik dAK10 wrote:

Hi everybody,

I am currently start working with Gviz (thanks for the amazing package), but have a small issue with the interaction track: I use makeGenomicInteractionsFromFile() and InteractionTrack() on a bedpe file. Everything works fine, but the arcs are squeezed against the top border (see image https://imgur.com/sut9uHn ).

I tried to cheat my way around by modifying the counts columns to a lower number or changing different display parameters (e.g. for title rotation hic.track@dp@pars$rotation.title <- 0).

Is there another way to either change the arc height or somehow prevent them to be cut at the back of the bow?

Thank you very much!

gviz genomicinteractions • 89 views
ADD COMMENTlink modified 10 weeks ago by liz.ingsimmons140 • written 10 weeks ago by Nik dAK10

Hi Nik,

If you provide me with a reproducible example I can have a look what could be implemented in Gviz to improve your visualisation.

Best, Robert

ADD REPLYlink written 5 weeks ago by Robert Ivanek610
Answer: Gviz (GenomicInteractions) arc height and boundaries
0
gravatar for liz.ingsimmons
10 weeks ago by
Germany
liz.ingsimmons140 wrote:

Hi Nik, glad you are finding the GenomicInteractions package useful.

The top of the arc doesn't appear to be cut off in your image, rather the arcs take up the full height of the panel. This is by design, and is similar to other Gviz track types where the y axis limits are set based on the values in the data.

I'm not sure if there is an option in Gviz to add padding between tracks, but that seems like what you'd want here.

ADD COMMENTlink written 10 weeks ago by liz.ingsimmons140

Hi Liz, thank you for the answer. Unfortunately I can't modify the track parameters in any way. stackHeight and other parameters can not be predefined in InteractionTrack() and if I add them manually they are ignored: hic.track@dp@pars$stackHeight <- 0.5

Any suggestions? Thanks

ADD REPLYlink written 6 weeks ago by Nik dAK10
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