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?
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?
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.