How to plot gene names in Gviz plotTracks and get the ideogram track to work (US-based)?
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Michael • 0
@e828643d
Last seen 14 months ago
United States

Hi,

I am trying to plot some data in R using the Gviz package, but I can't seem to get the gene names to appear on the track nor can I get the ideogram function to work.

For the ideogram, I am aware that the yeast genome does not have cytobands, but I would like to plot the chromosome diagram and red bar mark indicating the region in my plots.

The error I receive when I try running IdeogramTrack is:

itrack <- IdeogramTrack(genome = gen, chromosome = chr)
Error in .local(.Object, ...) : Failed to obtain 'hguid' cookie

For gene names, I would like to have them on top of the yellow bars indicating UCSC gene locations, but I'm not sure how to do so.

enter image description here

gviz Saccharomyces_cerevisiae Gviz ideogram • 1.3k views
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You'll need to show more code, for example how you created that GeneRegionTrack, and what 'gen' and 'chr' are.

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Ideally it would also be a self-contained example that others could run, rather than using data that noboby has access to.

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I think the above mentioned error is linked to old url scheme in rtracklayer (only http) which prevents fetching the data from UCSC servers. For reference: https://github.com/lawremi/rtracklayer/issues/91

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