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suhrig / arriba

Fast and accurate gene fusion detection from RNA-Seq data
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Dynamic view of results with Shiny R #134

Closed lavauxt closed 3 years ago

lavauxt commented 3 years ago

Just a suggestion for improvement, do you think it can be possible to integrate a dynamic view of the results with a Shiny R application ? Like for exemple, with some interactions : choose a sample results from a list, download graphs in svg format, make annotation interactive, you name it...

suhrig commented 3 years ago

Can you elaborate a little on the use case, so I can get a better understanding of what would need to be done? There are many many possibilities.

Some thoughts:

  1. The current plots are generated in PDF format, which contains vector graphics. Many tools are readily available to convert them to SVG, PNG, etc.
  2. Generating the plots interactively is not feasible in my opinion (if you are asking about the draw_fusions.R script). It takes several seconds to generate a plot and up to a minute of overhead to fire up the script. You could cache the overhead in memory, but there would still be a noticeable delay in generating the plots dynamically, which would be annoying to users. So I don't think there is a way around pre-rendering the plots.
  3. There are already some platforms available for interactive exploration of variants of a sample, such as the one you linked. Rather than developing a new one from scratch, it makes more sense to tap into existing resources. This shifts the effort from developing a visualization tool to developing an importer script which can be used to import Arriba calls into an existing platform. I have already developed a conversion script, which converts Arriba calls into VCF format. This should make Arriba calls much more interoperable with existing platforms. I am also currently working on a converter to import Arriba fusions into cBioPortal, which I could share if desired (once it is finished).
  4. From the looks of the platform you linked, it seems you are asking for a tool to interactively explore all the different variants of a patient integratively (fusions, SNVs, indels, etc.). This is beyond the scope of this project - which is exclusively focused on fusions. (See also my previous point, which addresses this issue.) The interactive data exploration capabilities provided by Arriba are therefore centered around fusions. For example, you can load the alignments into IGV and interrogate the fusion-supporting alignments. You can inspect the transcripts that are expressed this way. You can also load a protein domain track to take a look at retained protein domains.
lavauxt commented 3 years ago

thks for those answers, the conversion to vcf will be a good addition. the pdf to svg conversion is also a good point, i should have think of it before asking my question for the interactive part indeed it's beyond the arriba project, i was thinking of a way to display the graphs in a shiny R interface for ex, but it can be a silly idea ;-) because of the delay to compute the graphs

senzhaocode commented 2 years ago

thks for those answers, the conversion to vcf will be a good addition. the pdf to svg conversion is also a good point, i should have think of it before asking my question for the interactive part indeed it's beyond the arriba project, i was thinking of a way to display the graphs in a shiny R interface for ex, but it can be a silly idea ;-) because of the delay to compute the graphs

Hello,

I think this link (https://github.com/senzhaocode/FuSViz) maybe interesting for you - a shiny app to show SVs interactively, by combining RNA-seq and DNA-seq data together.