Question: How To Draw Genome Features Along Chromosome
5
gravatar for Plantae
7.2 years ago by
Plantae380
Plantae380 wrote:

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

genome visualization • 7.7k views
ADD COMMENTlink modified 7.2 years ago by ALchEmiXt1.9k • written 7.2 years ago by Plantae380
1

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

ADD REPLYlink written 7.2 years ago by Zhidkov570

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.

ADD REPLYlink written 7.2 years ago by Daniel Standage3.8k
8
gravatar for ALchEmiXt
7.2 years ago by
ALchEmiXt1.9k
The Netherlands
ALchEmiXt1.9k wrote:

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;

ADD COMMENTlink written 7.2 years ago by ALchEmiXt1.9k

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

ADD REPLYlink written 7.2 years ago by Ericc50
6
gravatar for Sean Davis
7.2 years ago by
Sean Davis25k
National Institutes of Health, Bethesda, MD
Sean Davis25k wrote:

In no particular order:

  1. Base R plotting and grid
  2. ggplot2
  3. Bioconductor ggbio
  4. Bioconductor Gviz
  5. Bioconductor GenomeGraphs
  6. Bioconductor geneplotter
ADD COMMENTlink written 7.2 years ago by Sean Davis25k
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