[BioRuby] new release Bio::Graphics

Jan Aerts jan.aerts at bbsrc.ac.uk
Mon Jan 28 14:47:59 UTC 2008


I've uploaded a new version of Bio::Graphics on
http://bio-graphics.rubyforge.org. Current version now is 1.4. Most
notable new features:
* drawing of composite features (such as transcripts)
* drawing of vertical pictures
* easier assignment of optional arguments: these now use keywords
* users can easily create their own glyphs just by creating a file
describing them

A small example (adapted from the homepage):
  # Load the library
  gem 'bio-graphics' # or require 'bio-graphics' or require_gem 'bio-graphics'
  # Create the panel
  my_panel = Bio::Graphics::Panel.new(500, :width => 1000)
  # Create the tracks
  generic_track = my_panel.add_track('generic', :label => false)
  directed_spliced_track = my_panel.add_track('directed_spliced', :label => false, :glyph => :directed_spliced, :colour => [1,0,1])

  # Add features to each track
  generic_track.add_feature(Bio::Feature.new('clone', '250..375'), :link => 'http://www.newsforge.com')
  generic_track.add_feature(Bio::Feature.new('clone', '54..124'), :glyph => :line)
  generic_track.add_feature(Bio::Feature.new('clone', '100..449'), :colour => [1,1,0], :glyph => :box)
  directed_spliced_track.add_feature(Bio::Feature.new('cds','join(34..52,109..183)'), :link => 'http://www.google.com')
  directed_spliced_track.add_feature(Bio::Feature.new('cds', 'complement(join(170..231,264..299,350..360,409..445))'), :link => 'http://bioinformatics.roslin.ac.uk')


A major effort has been put into this release by Charles Comstock.
Thanks Charles.

I'll try and find some time to further improve the library. But if
anyone is willing to put a bit of effort in it: that'd be great. There
are still a few things to be done, including speeding things up and
drawing continuous features (e.g. GC content).

Any questions/suggestions, please let me know.

Dr Jan Aerts
Bioinformatics Group
Roslin Institute
Roslin EH25 9PS
Scotland, UK
tel: +44 131 527 4198

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