Plotting genomic interactions in Gviz
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enricoferrero ▴ 660
@enricoferrero-6037
Last seen 2.5 years ago
Switzerland

Hello,

What's the best/easiest way to plot genomic interactions (e.g.: ChIA-PET, Hi-C, promoter - enhancer correlations) data with GViz?

You can think of genomic interaction data as a paired `GRanges` object or BED file where each row represents an interaction between two sets of coordinates, e.g.:

chr1:100-1000 -- chr1:2000-2200
chr2:200-250  -- chr2:300-350

I can see that a sashimi visualisation type is implemented for the `AlignmentTracks` class but I don't understand how to shape my genomic interaction data in the correct format.

  1. Is there a way to force genomic interaction data in an  `AlignmentTrack` container? How?
  2. Does Gviz support the `GenomicInteractions` class from the `GenomicsInteractions` package?

Thanks!

 

gviz genomicinteractions • 2.6k views
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Similar but old question with some references: plotting interactions in gviz (Chia-Pet, HiC, 5C). New feature?

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@lizingsimmons-6935
Last seen 3.5 years ago
Germany

Hi Enrico,

The GenomicInteractions package includes a function to create an 'InteractionTrack' object for plotting with Gviz. You can see an example at the end of the vignette here. There are some further examples in the paper, and R scripts to generate those figures are provided as additional files with the paper - these should give you an idea of the ways you can customise the display of interactions. Currently the options for mapping interaction properties to visualisation properties are limited, and we're hoping to develop this further in the future. If you have any questions or suggestions please let us know!

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That's fantastic, thank you!

Does this work also in Bioconductor 3.2 or only in the development version?

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This functionality is also in the current release version, we just added the example in the vignette in the development version.

I should also let you know we're switching over to using the new InteractionSet package as a backend in the next version of Bioconductor (released at the start of May), so there will be some small changes to how some things work (more complex types of overlaps! etc), but the InteractionTrack function should be unaffected.

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