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example.rb
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example.rb
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#!/usr/bin/env ruby
#
# example.rb
#
# Created by Dan MacLean (TSL) on 2012-09-28.
# Copyright (c) . All rights reserved.
###################################################
##A very straightforward example that creates all the features and tracks explicitly.
require 'bio-svgenes'
##create the page
p = Bio::Graphics::Page.new(:width => 800,
:height => 200,
:number_of_intervals => 10
)
##add a generic glyph track
generic_track = p.add_track(:glyph => :generic,
:name => 'generic_features',
:label => true )
##and some features
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '+', :id => "MyFeature")
generic_track.add(feature1)
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
##another generic track
generic_track = p.add_track(:glyph => :generic, :name => 'more_generic_features', :label => true, :fill_color => 'green' )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
generic_track.add(feature1)
feature1 = Bio::Graphics::MiniFeature.new(:start => 3935, :end => 4212)
generic_track.add(feature1)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)
##another generic
generic_track = p.add_track(:glyph => :generic,
:name => 'yet_more_generic_features',
:label => true,
:fill_color => 'yellow',
:stroke_width => '1',
:x_round => 10 )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
generic_track.add(feature1)
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)
directed_track = p.add_track(:glyph => :directed,
:name => 'directed_features gradient',
:label => true,
:fill_color => :red_white_h )
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234, :strand => '+')
directed_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '-')
directed_track.add(feature1)
generic_track = p.add_track(:glyph => :generic,
:name => 'generic_features',
:label => true )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '+')
generic_track.add(feature1) # will be Bio::Feature object
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 2030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
generic_track = p.add_track(:glyph => :generic,
:name => 'more_generic_features',
:label => true,
:fill_color => 'green' )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
generic_track.add(feature1)
feature1 = Bio::Graphics::MiniFeature.new(:start => 3935, :end => 4212)
generic_track.add(feature1)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)
generic_track = p.add_track(:glyph => :generic,
:name => 'yet_more_generic_features',
:label => true,
:fill_color => 'yellow',
:stroke_width => '1',
:x_round => 1 )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
generic_track.add(feature1) # will be Bio::Feature object
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)
directed_track = p.add_track(:glyph => :directed,
:name => 'directed_features',
:label => true )
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234, :strand => '+')
directed_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '-')
directed_track.add(feature1)
generic_track = p.add_track(:glyph => :generic,
:name => 'generic_features',
:label => true )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '+')
generic_track.add(feature1) # will be Bio::Feature object
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
generic_track = p.add_track(:glyph => :generic,
:name => 'more_generic_features',
:label => true,
:fill_color => 'green' )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
generic_track.add(feature1)
feature1 = Bio::Graphics::MiniFeature.new(:start => 3935, :end => 4212)
generic_track.add(feature1)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)
generic_track = p.add_track(:glyph => :generic,
:name => 'yet_more_generic_features',
:label => true,
:fill_color => :yellow_white_radial,
:stroke_width => '1',
:x_round => 4 )
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212)
generic_track.add(feature1) # will be Bio::Feature object
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature2 = Bio::Graphics::MiniFeature.new(:start => 12000, :end => 12030)
generic_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 15000)
generic_track.add(feature1)
directed_track = p.add_track(:glyph => :directed,
:name => 'directed_features fat ones',
:label => true,
:feature_height => 32,
:fill_color => :red_white_h)
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234, :strand => '+' )
directed_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '-')
directed_track.add(feature1)
feature2 = Bio::Graphics::MiniFeature.new(:start => 467, :end => 1234, :strand => '+')
directed_track.add(feature2)
feature1 = Bio::Graphics::MiniFeature.new(:start => 923, :end => 2212, :strand => '-')
directed_track.add(feature1)
transcript_track = p.add_track(:glyph => :transcript,
:name => 'transcripts (grouped models)',
:label => true,
:exon_fill_color => 'green',
:utr_fill_color => {:type => :radial, :id => :custom, :cx => 5, :cy => 5, :r => 50, :fx => 50, :fy => 50, :stops => [ {:offset => 0, :color => 'rgb(255,255,255)', :opacity => 0}, {:offset => 100, :color => 'rgb(0,127,200)', :opacity => 1},]},
:line_color => 'black',
:feature_height => 20 )
feature3 = Bio::Graphics::MiniFeature.new(:start => 923,
:end => 2345,
:strand => '-',
:exons => [1000,1200,1800,2000],
:utrs => [923,1000,2000,2345])
transcript_track.add(feature3)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467,
:end => 15000,
:exons => [1500,2500, 3000,7000, 9000,12000],
:utrs => [467, 1000, 13500,14000, 14400, 14900],
:id => 'MyTranscript')
transcript_track.add(feature1)
transcript_track = p.add_track(:glyph => :transcript,
:name => 'transcripts (grouped models)',
:label => true,
:exon_fill_color => :green_white_h,
:utr_fill_color => :blue_white_h,
:line_color => 'black',
:gap_marker => 'angled',
:feature_height => 20 )
feature3 = Bio::Graphics::MiniFeature.new(:start => 923,
:end => 2345,
:strand => '-',
:exons => [1000,1200,1800,2000],
:utrs => [923,1000,2000,2345])
transcript_track.add(feature3)
feature1 = Bio::Graphics::MiniFeature.new(:start => 467,
:end => 15000,
:exons => [1500,2500, 3000,7000, 9000,12000],
:utrs => [467, 1000, 13500,14000])
transcript_track.add(feature1)
data_track = p.add_track(:glyph => :histogram, #might also be :density or heatmap ##page doesn't know how to deal with individual file types, rather page object takes a list of values (e.g bar heights) from pre-processed data source and renders those
:stroke_color => 'black',
:fill_color => 'gold',
:track_height => 150,
:name => 'data track',
:label => true,
:stroke_width => '1',
:x_round => 1,
:y_round => 1
)
##generate a load of data, each data point becomes a feature...
data = (400..25000).step(1000) do |start|
data_feature = Bio::Graphics::MiniFeature.new(:start => start,
:end => start + 999,
:segment_height => rand(30)
)
data_track.add(data_feature)
end
data_track1 = p.add_track(:glyph => :histogram, #might also be :density or heatmap ##page doesn't know how to deal with individual file types, rather page object takes a list of values (e.g bar heights) from pre-processed data source and renders those
:stroke_color => 'black',
:fill_color => :red_white_radial,
:track_height => 150,
:name => 'data track',
:label => true,
:stroke_width => '1',
:x_round => 1,
:y_round => 1
)
##generate a load of data, each data point becomes a feature...
data = (400..25000).step(200) do |start|
data_feature = Bio::Graphics::MiniFeature.new(:start => start,
:end => start + 200,
:segment_height => rand(30)
)
data_track1.add(data_feature)
end
p.draw