How To Draw Genome Features Along Chromosome

Question

[Plantae]

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

[Zhidkov]

Did you look on Bioconductor packages - http://www.bioconductor.org/

[Daniel Standage]

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.

Answer 1

[ALchEmiXt]

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;

[Ericc]

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

Answer 2

[Sean Davis]

In no particular order:

1. Base R plotting and grid
2. ggplot2
3. Bioconductor ggbio
4. Bioconductor Gviz
5. Bioconductor GenomeGraphs
6. Bioconductor geneplotter