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:
note how it plots the different exons, introns and UTRs using standard ucsc-like conventions. How can this be done with R?
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3 answers
Try GenomeGraphs: integrated genomic data visualization with R
Also, have a look at Drawing Chromosome Ideogams With Data for pointers
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.
In addition to GenomeGraphs, take a look at ggbio and Gviz.
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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