Plotting Read Densities And Gene Tracks In R?
3
4
Entering edit mode
11.3 years ago
user ▴ 940

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
ADD COMMENT
3
Entering edit mode
ADD COMMENT
2
Entering edit mode
11.3 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.

ADD COMMENT
1
Entering edit mode
11.3 years ago

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

ADD COMMENT
0
Entering edit mode

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?

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2719 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6