browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
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@james-perkins-6126
Last seen 5.5 years ago
Spain

I would like to be able to save the UCSC genome browser image view generated by the browserView method in rtracklayer without having to manually do it from the browser. Is this possible?

I.e.   for the example:

session <- browserSession()
  browserView(session,
              GRangesForUCSCGenome("hg19", "chr2", IRanges(20000, 50000)))
  ## only view "knownGene" track
  browserView(session, track = "knownGene")

Something like

browserView(session, track = "knownGene", save = "UCSCview.pdf")

Is that possible? Or is there a similar solution? I know tracks can be exported as bed files.

Many thanks.

Jim

rtracklayer browseGenome save file image UCSC • 1.1k views
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Did you figure out how to save an image of the UCSC browserView using rtracklayer?

 

Thanks!

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@shrutiisarda-8853
Last seen 5.9 years ago

Did you figure out how to save an image of the UCSC browserView using rtracklayer?

 

Thanks!

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maximilianh ▴ 10
@maximilianh-11016
Last seen 4.4 years ago
UCSC

you can use genome.ucsc.edu/cgi-bin/hgRenderTracks to obtain only the image for a given configuration. 

the parameters are documented here:

https://genome.ucsc.edu/goldenpath/help/customTrack.html#SHARE

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