User: willbradshaw

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Posts by willbradshaw

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Extracting read coverage data from a Gviz AlignmentsTrack
... I'm using Gviz to make read-coverage and Sashimi plots for a paper, and I'd like to extract information about how many reads contribute to each splice junction in the Sashimi plot. These numbers must be inferred at some point since Gviz is generating the AlignmentsTrack object directly from the BAM ...
gviz sashimi written 3 months ago by willbradshaw0 • updated 12 weeks ago by Robert Ivanek660
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Comment: C: Gviz: decreasing tick resolution
... Hi Robert, Strange, I restarted everything and it seems to work now. Sorry for wasting your time! Will ...
written 8 months ago by willbradshaw0
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Comment: C: Gviz: decreasing tick resolution
... Hi Robert, I was checking over my figures again just now and noticed that the tick labels are back to the overlapping state they were in before. Checking my R script it seems like the `ticksAt` argument has stopped working; changing the values to the argument in `plotTracks` doesn't seem to have an ...
written 8 months ago by willbradshaw0
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Comment: C: Gviz: decreasing tick resolution
... Hi Robert, I just installed Gviz 1.27.5 and then realised I didn't actually ask how to use the new parameter to do what I want. Whoops. I tried adding ticksAt = 2000 and ticksAt=seq(0, <end>, 2000) to my GenomeAxisTrack call and it didn't seem to make any difference. Could you give me a quic ...
written 11 months ago by willbradshaw0
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Comment: C: Gviz: decreasing tick resolution
... That sounds ideal, thanks! :-) ...
written 11 months ago by willbradshaw0
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Comment: C: Gviz: decreasing tick resolution
... Hi Robert, Thanks for the quick and helpful answer; great to know this will be available soon! Just to check (I'm not used to working with dev versions), since this is in Bioc 3.9 and R 3.6 isn't released yet, I'll need to set up r-devel to use it, right? Thanks again, Will ...
written 11 months ago by willbradshaw0
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Gviz: decreasing tick resolution
... Hi everyone! I'm currently mapping out a genomic locus with Gviz, and I'm running into an issue in one of my sub-figures where the Genome Axis Track tick labels are mashing into each other: It seems to have automatically decided to show ticks every 1kb due to the relatively short range being plo ...
gviz gviz-package written 11 months ago by willbradshaw0 • updated 11 months ago by Robert Ivanek660

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