Plotting Read Densities And Gene Tracks In R?
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11.7 years ago
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What are some standard tools in R for plotting gene annotations/gene tracks and read densities on top of them? A tool that takes a gene track annotation in GTF/GFF format or something similar and reads in BAM format or bigWig/bedGraph and produces something like this:

enter image description here

note how it plots the different exons, introns and UTRs using standard ucsc-like conventions. How can this be done with R?

gff genes rna-seq next-gen bam visualization r • 14k views
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11.7 years ago

The SRAdb package enables communication with the IGV browser including loading data and annotation tracks, changing the view in the browser, and, importantly, capturing the current view to a file.

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11.7 years ago

In addition to GenomeGraphs, take a look at ggbio and Gviz.

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Thanks. Is it obvious which one of those was used for the above figure or could they all make something as pretty just as easily?

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It may not have been made with any of these packages :-) I suggest reading through the vignettes for each package and pick one you thin you'll get the most mileage out of.

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