TUTORIAL

Path: TUTORIAL
Last Update: Mon Jun 30 11:39:50 +0100 2008

Bio::Graphics tutorial

Copyright (C) 2007, 2008 Jan Aerts <jan.aerts@gmail.com>

License: The Ruby License

Homepage: bio-graphics.rubyforge.org

(If you‘d like to know how the code itself works, please see the README.DEV)

Overview and terms used

This Bio::Graphics library allows for drawing overviews of genomic regions, similar to the pictures drawn by gbrowse. Basically, it allows creating simple images that display features on a linear map, including the position of subdomains in a protein (see picture). It‘s now also possible to create vertical pictures.

Any Bio::Graphics image consists of the following parts (concepts and nomenclature identical to that from bioperl):

  • one panel: container of all tracks
  • one or more tracks: container of the features. Multiple tracks can exist in the same graphic to allow for differential visualization of different feature types (e.g. genes as blue rectangles and polymorphisms as red triangles)
  • one or more features in each track: these are the actual features that you want to display (e.g. ‘gene 1’, ‘SNP 123445’)
  • a ruler on top of the panel: is added automatically

Schematically:

 panel
  +-> track 1
  |     +-> feature 1
  |     +-> feature 2
  |     +-> feature 3
  +-> track 2
  |     +-> feature 4
  |     +-> feature 5
  +-> ruler

Below is an annotated version of the picture at the top of the page. The whole picture makes up the panel, which contains one ruler and 3 tracks (‘scaffolds’, ‘markers’ and ‘clones’). Each of these tracks has zero or more features.

Glyphs

According to Wikipedia, a glyph is "the shape given in a particular typeface to a specific grapheme or symbol". In the context of Bio::Graphics, a glyph is just the thing that represents one single feature. Several kinds of glyph exist to allow for features that are on a particular strand as well as for spliced features. See the picture below for an overview.

If the view is really zoomed out, arrow on the directed glyphs are not shown, as they would be bigger than the glyph itself.

Use

The code below was used to create the picture showing all the different glyphs mentioned above. This is not the nicest piece of code, but it is the simplest. It is straightforward to parse a GFF file and create a picture based on that. See my blog for an nicer example.

For an explanation of the arguments with each method for this example, see the Bio::Graphics::Panel and Bio::Graphics::Track object documentation.

  1   # Load the library
  2   require 'bio-graphics' # or require_gem 'bio-graphics' or gem 'bio-graphics'
  3
  4   # Create the panel
  5   my_panel = Bio::Graphics::Panel.new(500, :width => 1000)
  6
  7   # Create the tracks
  8   generic_track = my_panel.add_track('generic', :label => false)
  9   line_track = my_panel.add_track('line', :label => false, :glyph => :line, :colour => [0,0,1])
 10   line_with_handles_track = my_panel.add_track('line_with_handles', :label => false, :glyph => :line_with_handles, [1,0,0])
 11   directed_track = my_panel.add_track('directed', :label => false, :glyph => :directed_generic, :colour => [0,1,0])
 12   triangle_track = my_panel.add_track('triangle', :label => false, :glyph => :triangle, :colour => [1,0,0])
 13   spliced_track = my_panel.add_track('spliced', :label => false, :glyph => :spliced, :colour => [1,0,0])
 14   directed_spliced_track = my_panel.add_track('directed_spliced', :label => false, :glyph => :directed_spliced, :colour => [1,0,1])
 15   composite_track = my_panel.add_track('composite_features', :label => false, :glyph => { 'utr' => :line, 'cds' => :directed_spliced})
 16
 17   # Add features to each track
 18   generic_track.add_feature(Bio::Feature.new('clone', '250..375'), :link => 'http://www.newsforge.com')
 19   generic_track.add_feature(Bio::Feature.new('clone', '54..124'), :link => 'http://www.thearkdb.org')
 20   generic_track.add_feature(Bio::Feature.new('clone', '100..449'), :link => 'http://www.google.com')
 21
 22   line_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
 23   line_track.add_feature(Bio::Feature.new('utr', '355..480'), :link => 'http://www.zdnet.co.uk')
 24
 25   line_with_handles_track.add_feature(Bio::Feature.new('utr', 'complement(200..320)'))
 26   line_with_handles_track.add_feature(Bio::Feature.new('utr', '355..480'), :link => 'http://www.zdnet.co.uk')
 27
 28   directed_track.add_feature(Bio::Feature.new('primer', '50..60'), :link => 'http://www.google.com')
 29   directed_track.add_feature(Bio::Feature.new('primer', 'complement(80..120)'), :link => 'http://www.sourceforge.net')
 30
 31   triangle_track.add_feature(Bio::Feature.new('snp', '56'))
 32   triangle_track.add_feature(Bio::Feature.new('snp', '103'), :link => 'http://digg.com')
 33
 34   spliced_track.add_feature(Bio::Feature.new('spliced', 'join(34..52,109..183)'), :link => 'http://news.bbc.co.uk')
 35   spliced_track.add_feature(Bio::Feature.new('spliced', 'complement(join(170..231,264..299,350..360,409..445))'))
 36   spliced_track.add_feature(Bio::Feature.new('spliced', 'join(134..152,209..283)'))
 37
 38   directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(34..52,109..183)'), :link => 'http://www.vrtnieuws.net')
 39   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')
 40   directed_spliced_track.add_feature(Bio::Feature.new('cds', 'join(134..152,209..283)'))
 41
 42   utr5 = Bio::Feature.new('utr', '100..150')
 43   cds = Bio::Feature.new('cds', 'join(150..225, 250..275, 310..330)')
 44   utr3 = Bio::Feature.new('utr', '330..375')
 45
 46   transcript = Bio::Feature.new('transcript', 'join(100..150, 150..225, 250..275, 310..330, 330..375)', [], nil, [utr5,cds,utr3])
 47   composite_track.add_feature(transcript, :label => 'my_transcript')
 48
 49   # Draw the thing
 50   my_panel.draw('glyph_showcase.png')

Let‘s walk through this:

  • Line 2: load the actual library code. Make sure that the library is in your RUBYLIB path.
  • Line 5: Create the panel, which is nothing more than the canvas you‘ll be working on. The following parameters were used:
    • The sequence is 500 bp long.
    • The width of the picture will be 1000 points.
  • Lines 8-15: Create the different tracks. Parameters are:
    • name.
    • flag if feature labels should be drawn (here: false)
    • the default glyph for features in this track. This can be overridden on a feature-by-feature basis. See the picture above and Bio::Graphics::Track#new for allowed values.
    • the default colour for features in this track. This can also be overridden on a feature-by-feature basis. At the moment in RGB. (This will probably change to colour names in the future).
  • Lines 18-47: Add features to each track. Parameters are:
  • Line 50: Create the actual picture. If the the initial Panel#new call contains the parameter ":clickable => true" (in line 5), a HTML file is created as well.

That‘s pretty clear, but what‘s happening with the composite_track (on lines 15 and 42-47)?

To set the glyph for a feature (or the default glyph in a track), you normally use a symbol, like :generic or :directed_spliced. For composite features, however, we‘ve made it possible to have different subfeatures drawn in different ways. In this example: we want to draw the UTRs as thin lines, while the CDS is big boxes connected with thin lines. How does this work? See lines 42 to 47. If the feature you‘re adding to a track has subfeatures, you can use the type of the subfeature to direct the glyph to use. In the example above: the utr5 and utr3 have ‘utr’ as the first argument in the Bio::Feature#new, and the cds object has ‘cds’. The transcript that gets created in line 46 takes these three Bio::Feature objects as subfeatures (the last argument). Now up in line 15 we set the glyph of this track to the hash {‘utr’ => :line, ‘cds’ => :directed_spliced}. What this does, is it takes each subfeature in turn, and draws it using the glyph that matches its type.

Hyperlinks

There are no graphic formats that are inherently clickable (SVG is a special case and the display of it is not the SVG itself). Therefore, in case the user wants a clickable graphic, an accompanying HTML file is created with the same name as the picture but obviously the .html extension. This file contains the map and will display a clickable picture when loaded in a webbrowser.

Custom glyphs

The user can easily create custom glyphs to add to the functionality of the Bio::Graphics library. The only thing that has to be done is add a file to lib/bio/graphics/glyphs. The file should look like this:

  module Bio::Graphics::Glyph
    class Bio::Graphics::Glyph::SomeName < Bio::Graphics::Glyph::Common
      def draw
        @feature_context.rectangle(x1, y1, x2, y2).fill
      end
    end
  end

What are the properties of that file?

  • It‘s name has to be the same as the class name specified on the second line, but in snake_case instead of CamelCase. The above file therefore should be called some_name.rb.
  • Give the class a sensible name (in CamelCase).
  • Just define the draw method. Have a look at the other files in the glyphs/ directory for examples. Some values you can use:
    • Bio::Graphics::FEATURE_HEIGHT = default height in pixels for a glyph
    • Bio::Graphics::FEATURE_ARROW_LENGTH = default width in pixels of arrows on features

Setting options dynamically

In some circumstances, you might want to have the colour of a feature depend on some characteristic of the feature itself. A prime example is the score of a BLAST hit: the higher the score, the more ‘red’ the bar should be; the lower the score, the more ‘pink’. This is easily achievable: instead of just setting the default feature colour within a track to a fixed colour (e.g. [0,1,0]), use a lambda function.

An example. Suppose we want to show a bunch of features that should be red if they‘re longer than 1000 bp and green if they‘re shorter than 1000 bp. The following code will do that:

  generic_track = my_panel.add_track('generic', :label => false,
                                     :colour => lambda do |feature|
                                         if (feature.stop - feature.start) > 1000
                                           return [1,0,0] # i.e. 'red'
                                         else
                                           return [0,1,0] # i.e. 'green's
                                         end
                                     )

Download and installation

As of May 2008, development of the library has moved from rubyforge to github at github.com/jandot/bio-graphics. I‘ve moved away from SVN and embraced git as the new source control system.

There are different ways to install the library.

  • The easiest way: gem install bio-graphics (although this will get you the last version on rubyforge which will probably not be updated)
  • The other way: "git clone git://github.com/jandot/bio-graphics.git" or use the download button at github.com/jandot/bio-graphics

Prerequisites

You‘ll need to have the following installed to use this library:

Ubuntu

  • gem install bio
  • sudo apt-get install libcairo-ruby

Windows (thanks to Naohisa Goto)

Install Ruby-GNOME2 Win32 GUI Installer, which contains rcairo-1.2.6. Get it from ruby-gnome2.sourceforge.jp/?News_20070212_1 (ruby-gnome2-0.16.0-1-i386-mswin32.exe)

During installation, check the "Register enviroment variables" option.

Mac OSX (thanks to Ed Allen and _why)

I‘ve been successful in installing Bio::Graphics on a Mac by meticulously following the steps from code.whytheluckystiff.net/shoes/wiki/BuildingShoesOnOsx. After that, I got the ruby-bindings for pango by installing ruby-gnome2 from ruby-gnome2.sourceforge.jp. Unfortunately, the compilation step returns an error, complaining about a file rbpangolayoutiter.c. Changing line 22 in that file to "if 0" solves this problem. YMMV.

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