This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How To Draw Genome Features Along Chromosome

hi, all
I try to draw features like genes, transposable elemets, GC content along chromosomes
are there any R packages available?

genome visualization
• 11,996 views • link
updated by ALchEmiXt ALchEmiXt • written by Plantae Plantae

If you're not tied to R, I would highly recommend AnnotationSketch (part of GenomeTools). They have a web service, but you can download and compile the code on your local system. It's a C library, but they have bindings for Python, Ruby, and Lua as well.

• 0 views • link
written by Daniel Standage Daniel Standage

2 answers

Have a look at genoplotR. It might be able to do what you want from R. It is highly tunable.

Just a random example below;

• 123 views • link
written by ALchEmiXt ALchEmiXt

This is awesome! I have been looking for a tool like this. Thanks!

• 0 views • link
written by Ericc • Ericc

In no particular order:

  1. Base R plotting and grid
  2. ggplot2
  3. Bioconductor ggbio
  4. Bioconductor Gviz
  5. Bioconductor GenomeGraphs
  6. Bioconductor geneplotter
• 2 views • link
written by Sean Davis Sean Davis

Log in to answer this question.

More posts like this