Question: browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
0
gravatar for James Perkins
4.5 years ago by
Spain
James Perkins60 wrote:

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

ADD COMMENTlink modified 2.6 years ago by maximilianh10 • written 4.5 years ago by James Perkins60

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

 

Thanks!

ADD REPLYlink written 4.1 years ago by shrutiisarda0
Answer: browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
0
gravatar for shrutiisarda
4.1 years ago by
shrutiisarda0 wrote:

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

 

Thanks!

ADD COMMENTlink written 4.1 years ago by shrutiisarda0
Answer: browseGenome rtracklayer, save / export UCSC genome browser image e.g. as pdf
0
gravatar for maximilianh
2.6 years ago by
maximilianh10
UCSC
maximilianh10 wrote:

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

ADD COMMENTlink written 2.6 years ago by maximilianh10
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