How To Draw Genome Features Along Chromosome
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12.1 years ago
Plantae ▴ 390

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

genome visualization • 11k views
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Did you look on Bioconductor packages - http://www.bioconductor.org/

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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.

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12.1 years ago
ALchEmiXt ★ 1.9k

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;

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

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12.1 years ago

In no particular order:

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