Plotting Read Densities And Gene Tracks In R?

Question

[user]

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?

Answer 1

[Sukhi Singh]

Try GenomeGraphs: integrated genomic data visualization with R

Also, have a look at Drawing Chromosome Ideogams With Data for pointers

Answer 2

[Sean Davis]

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.

Answer 3

[Steve Lianoglou]

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

[user]

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?

[Steve Lianoglou]

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.