Question: Plotting Read Densities And Gene Tracks In R?
4
gravatar for user
6.9 years ago by
user840
United States
user840 wrote:

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?

ADD COMMENTlink modified 6.9 years ago by Sean Davis25k • written 6.9 years ago by user840
3
gravatar for Sukhdeep Singh
6.9 years ago by
Sukhdeep Singh10.0k
Netherlands
Sukhdeep Singh10.0k wrote:

Try GenomeGraphs: integrated genomic data visualization with R

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

ADD COMMENTlink written 6.9 years ago by Sukhdeep Singh10.0k
2
gravatar for Sean Davis
6.9 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

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 COMMENTlink written 6.9 years ago by Sean Davis25k
1
gravatar for Steve Lianoglou
6.9 years ago by
Steve Lianoglou5.0k
US
Steve Lianoglou5.0k wrote:

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

ADD COMMENTlink modified 6.9 years ago • written 6.9 years ago by Steve Lianoglou5.0k

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 REPLYlink written 6.9 years ago by user840

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 REPLYlink written 6.9 years ago by Steve Lianoglou5.0k
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