Class: Bio::Graphics::Page

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/graphics/page.rb

Overview

The Bio::Graphics::Page class represents the page of the final rendered SVG and is the top level container into which Bio::Graphics::Tracks are added. It will contain a scale and all the tracks along with their features. The scale is calculated will start at the genomic co-ordinates of the start of the first feature and stop at the end of the last feature)

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(args) ⇒ Page

Creates a new Page object.

args

  • :height = the minimum height of the rendered page

  • :width = the minimum width of the rendered page

  • :background_color = the background color of the page (default none), can be any SVG colour eg rgb(256,0,0) or #FF0000



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# File 'lib/bio/graphics/page.rb', line 16

def initialize(args)
  @height = args[:height]
  @width = args[:width]
  args[:style] = "background-color:#{args[:background_color]};" if args[:background_color]
  @svg = SVGEE.new(args)
  @scale_start = 1.0/0.0
  @scale_stop = -1.0/0.0
  @tracks = [] #array of track objects with loads of features in it...
  @nt_per_percent = 1;
  @num_intervals = args[:number_of_intervals]
  @track_top = 30

  def @svg.update_height(height)
    @height = height
  end

  #def @svg.update_width(width)
  #  @width = width
  #end
end

Class Method Details

.from_json(args) ⇒ Object

Takes a custom-written json file and uses it to generate an SVG document based on the information in that page.

  • :json a JSON file describing the parameters and files needed to build an SVG document



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# File 'lib/bio/graphics/page.rb', line 39

def self.from_json(args)
  require 'rubygems'
  require 'json'
  data = JSON.parse(File.open(args[:json], 'r').read)
  p = Page.new(:width => data["Page"]["width"],
               :height => data["Page"]["height"],
               :number_of_intervals => data["Page"]["intervals"])
  data["Tracks"].each do |track|
    #prep the track args
    track_args = track.dup
    track_args.delete("file")
    track_args.delete("file_type")
    track_args = track_args.inject({}) { |memo, (k, v)| memo[k.to_sym] = v; memo }
    ##convert any of the pre-made gradient strings in the keys to symbol
    track_args.each_key do |k|
      next unless track_args[k].respond_to?(:to_sym)
      track_args[k] = track_args[k].to_sym if Glyph.gradients.include?(track_args[k].to_sym)
    end

    svg_track = p.add_track(track_args)
    features = [] ##set up the features...

    case track["file_type"] ##deal with the gff and data files
      when "gff"
        groups = {}
        parentless_features = []
        Page.parse_gff(track["file"]).each do |gff| #gets features in a list and links their children to them as members of the array at the key
          parent_id = gff.attributes.select { |a| a.first == 'Parent' }
          if parent_id.empty?
            parentless_features << gff
          else
            if groups[parent_id.first.last].nil?
              groups[parent_id.first.last] = []
              groups[parent_id.first.last] << gff
            else
              groups[parent_id.first.last] << gff
            end
          end
        end
        #now flick through the parentless features and add any exons / UTRs
        parentless_features.each do |plf|
          require 'pp'
          #pp parentless_features
          gff_id = plf.attributes.select { |a| a.first == 'ID' }
          gff_id = gff_id.first.last
          exons = []
          utrs = []
          children = groups[gff_id] || children = []
          children.each do |child|
            if child.feature == 'exon' or child.feature == 'CDS'
              exons += [child.start, child.end]
            elsif child.feature =~ /utr/i
              utrs += [child.start, child.end]
            end
          end
          features << MiniFeature.new(:start => plf.start, :end => plf.end, :exons => exons, :utrs => utrs, :strand => plf.strand, :id => gff_id)
        end #parentless features end
      when "data"
        ##each line is a data feature
        File.open(track["file"], "r").each do |line|
          start, stop, value = line.split(/\t/)
          features << MiniFeature.new(:start => start.to_i, :end => stop.to_i, :segment_height => value.to_f)
        end
    end #data end
    features.each { |f| svg_track.add(f) }
  end #track end
  p.write(args[:outfile])
end

.parse_gff(gff_file) ⇒ Object

Parses a GFF file into an Array of Bio::GFF::GFF3::Record objects



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# File 'lib/bio/graphics/page.rb', line 111

def self.parse_gff(gff_file)
  require 'bio'
  a = []
  File.open(gff_file).each do |line|
    next if line =~ /^#/
    a << Bio::GFF::GFF3::Record.new(line)
  end
  a
end

.update_height(height) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 28

def @svg.update_height(height)
  @height = height
end

Instance Method Details

#add_track(args) ⇒ Object

adds a new Bio::Graphics::Track object to the current Bio::Graphics::Page object

args

  • :glyph = one of Bio::Graphics::Glyphs#glyphs currently

:generic, :directed, :transcript, :scale, :label, :histogram, :circle, :down_triangle, :up_triangle, :span

  • :stroke_color = the outline colour of the glyphs in the track (default = “black”), can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :fill_color = the fill colour of the glyphs in the track (default = ‘red’), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bio::Graphics::Glyph#gradients

:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial

or a custom definition of a gradient {: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
     }, ]

}

  • :track_height = minimum height for the track, will be modified automatically if more space is needed e.g for overlapping features (default = auto),

  • :name = a displayed name for the track (default = ‘feature_track’)

  • :label = display the name given to the track (default = true),

  • :stroke_width = width in pixels of the outline of the glyphs (default=1)

  • :x_round = x radius of the ellipse used to round off the corners of rectangles (default = 1)

  • :y_round = y radius of the ellipse used to round off the corners of rectangles (default = 1)

:utr_fill_color = the fill colour of the utr part of the glyph (default = ‘black’), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bio::Graphics::Glyph#gradients

:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial

or a custom definition of a gradient {: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
     }, ]

}

  • :utr_stroke = the outline colour of the utr part of the glyph (default = “black”), can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :utr_stroke_width = The width of the outline stroke for the utr part of the glyph (default = 1)

  • :exon_fill_color = the fill colour of the utr part of the glyph (default = ‘red’), can be any SVG colour eg rgb(256,0,0) or #FF0000, or one of the built in gradient types Bio::Graphics::Glyph#gradients or a custom definition of a gradient

:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial

or a custom definition of a gradient {: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
     }, ]

  • :exon_stroke = the outline colour of the exon part of the glyph (default = “black”) can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :exon_stroke_width = The width of the outline stroke for the exon part of the glyph (default = 1)

  • :line_color = the colour for the line part that joins the blocks (default = ‘black’) can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :line_width = the width ffor the line part that joins the blocks (default = 1)

  • :exon_style = an arbitrary SVG compliant style string eg “fill-opacity:0.4;”

  • :utr_style = an arbitrary SVG compliant style string eg “fill-opacity:0.4;”

  • :line_style = an arbitrary SVG compliant style string eg “fill-opacity:0.4;”

  • :gap_marker = style of the line between blocks - either angled or straight

returns

a new Bio::Graphics::Track object



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# File 'lib/bio/graphics/page.rb', line 206

def add_track(args)
  #sort out the colour/gradient options
  [:fill_color, :exon_fill_color, :utr_fill_color].each do |colour_tag|
    if Glyph.gradients.include?(args[colour_tag])
      @svg.gradient(Glyph.gradient(args[colour_tag]))
      args[colour_tag] = "url(##{args[colour_tag]})"
    elsif args[colour_tag].instance_of?(Hash)
      @svg.gradient(args[colour_tag])
      args[colour_tag] = "url(##{args[colour_tag][:id]})"
    end
  end
  @tracks << Track.new(args)
  return @tracks.last
end

#compute_boundaries(feature) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 244

def compute_boundaries(feature)
  feat_end = feature.end
  feat_end += (8 * @nt_per_px_x * feature.id.to_s.length).to_i if feature.id and @nt_per_px_x
  [feature.start, feat_end]
end

#draw ⇒ Object

Prints the svg text to STDOUT



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# File 'lib/bio/graphics/page.rb', line 411

def draw
  puts get_markup
end

#draw_circle(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 275

def draw_circle(args)
  Glyph.circle(args).each { |g| @svg.add_primitive(g) }
end

#draw_directed(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 271

def draw_directed(args)
  Glyph.directed(args).each { |g| @svg.add_primitive(g) }
end

#draw_down_triangle(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 291

def draw_down_triangle(args)
  Glyph.down_triangle(args).each { |g| @svg.add_primitive(g) }
end

#draw_features(track) ⇒ Object

Takes a Bio::Graphics::Track object and does the work to draw features

It examines the the type of track and calculates the required parameters

  • args - an Array of Bio::Graphics::Track object



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# File 'lib/bio/graphics/page.rb', line 303

def draw_features(track)
  if [:histogram, "histogram"].include?(track.glyph) #do different stuff for data tracks...

    y = @track_top + (track.track_height)
    max = track.max_y ? track.max_y : track.features.sort { |a, b| a.segment_height <=> b.segment_height }.last.segment_height
    min = 0
    if track.label
      draw_label(:text => track.name, :y => @track_top += 30, :x => 3)
    end
    draw_label(:text => max, :x => to_px(@scale_stop - @scale_start) + 5, :y => @track_top + 5)
    draw_label(:text => min, :x => to_px(@scale_stop - @scale_start) + 5, :y => @track_top + track.track_height + 5)
    data_interval = max - min
    data_per_px = track.track_height.to_f / data_interval.to_f
    track.features.each do |f|
      x = to_px(f.start - @scale_start)
      width = to_px((f.end - @scale_start) - (f.start - @scale_start))
      height = f.segment_height.to_f * data_per_px
      y = @track_top + track.track_height - height + 5
      #$stderr.puts f.segment_height, data_per_px, data_interval, max, min, "------"
      self.send("draw_#{track.glyph}", {:x => x,
                                        :y => y,
                                        :width => width,
                                        :height => height}.merge!(track.args))
    end
    @track_top += (track.track_height) + 20
  else ##following stuff for the features
    if track.label
      draw_label(:text => track.name, :y => @track_top += 30, :x => 3)
    end
    track.get_rows(self) ##work out how many rows and which features belong in each row...
    track.features.each_with_index do |f, index|
      x = to_px(f.start - @scale_start) #bottom left of feature
      all_sub_blocks = []

      #convert the exon and utr start stops to px start stops and px widths
      exons = []
      if f.exons
        f.exons.each_slice(2).each do |exon|
          all_sub_blocks << exon
          next if exon.nil?
          exons << [to_px(exon[0] - @scale_start), to_px((exon[1] - @scale_start) - (exon[0] - @scale_start))]
        end
      end
      f.exons = exons

      utrs = []
      if f.utrs
        f.utrs.each_slice(2).each do |utr|
          all_sub_blocks << utr
          next if utr.nil?
          utrs << [to_px(utr[0] - @scale_start), to_px((utr[1] - @scale_start) - (utr[0] - @scale_start))]
        end
      end
      f.utrs = utrs

      #if there are any intron like gaps.. get where they would be
      if not all_sub_blocks.empty?
        all_sub_blocks = all_sub_blocks.sort { |a, b| a.first <=> b.first }
        all_sub_blocks.each_index do |i|
          next if i + 1 == all_sub_blocks.length or all_sub_blocks[i].last >= all_sub_blocks[i + 1].first #skip if there is no gap
          f.block_gaps << [to_px(all_sub_blocks[i].last - @scale_start), to_px((all_sub_blocks[i + 1].first - @scale_start) - (all_sub_blocks[i].last - @scale_start))]
        end
      end

      width = to_px((f.end - @scale_start) - (f.start - @scale_start))
      if track.min_width and width < track.min_width
        width = track.min_width
      end
      y = @track_top + (track.feature_rows[index] * 2 * track.feature_height)

      self.send("draw_#{track.glyph}", {:x => x,
                                        :y => y,
                                        :width => width,
                                        :strand => f.strand,
                                        :exons => f.exons,
                                        :utrs => f.utrs,
                                        :block_gaps => f.block_gaps,
                                        :height => track.feature_height,
                                        :params => f.params
      }.merge!(track.args))

      if f.id
        draw_label(:y => y, :x => x + width +2, :text => f.id)
      end
    end
    @track_top += (track.feature_height * track.number_rows * 2) + 20
  end

  @height = @track_top + 100 #fudge...
  @svg.update_height(@height)
                         #@svg.update_width(@width + 200)

end

#draw_generic(args) ⇒ Object

remember presentation info comes from track@args when the track is defined



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# File 'lib/bio/graphics/page.rb', line 267

def draw_generic(args) #remember presentation info comes from track@args when the track is defined
  Glyph.generic(args).each { |g| @svg.add_primitive(g) }
end

#draw_histogram(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 283

def draw_histogram(args)
  Glyph.generic(args).each { |g| @svg.add_primitive(g) }
end

#draw_label(args) ⇒ Object

Adds the Bio::Graphics::Primitive objects to the SVGEE object

  • args - an Array of Bio::Graphics::Primitive object



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# File 'lib/bio/graphics/page.rb', line 260

def draw_label(args)
  Glyph.label(:text => args[:text],
              :x => args[:x],
              :y => args[:y]).each { |g| @svg.add_primitive(g) }
end

#draw_scale ⇒ Object

Adds scale bar to the list of objects to be rendered in the final



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# File 'lib/bio/graphics/page.rb', line 252

def draw_scale
  Glyph.scale(:start => @scale_start,
              :stop => @scale_stop,
              :number_of_intervals => @num_intervals, :page_width => @width).each { |g| @svg.add_primitive(g) }
end

#draw_span(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 295

def draw_span(args)
  Glyph.span(args).each { |g| @svg.add_primitive(g) }
end

#draw_transcript(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 279

def draw_transcript(args)
  Glyph.transcript(args).each { |g| @svg.add_primitive(g) }
end

#draw_up_triangle(args) ⇒ Object 



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# File 'lib/bio/graphics/page.rb', line 287

def draw_up_triangle(args)
  Glyph.up_triangle(args).each { |g| @svg.add_primitive(g) }
end

#get_limits ⇒ Object

Calculates the Page scale-start and scale-stop position and the nucleotides per pixel for the current Page



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# File 'lib/bio/graphics/page.rb', line 222

def get_limits
  @tracks.each do |track|
    lowest = track.features.sort { |x, y| x.start <=> y.start }.first.start
    highest = track.features.sort { |x, y| y.end <=> x.end }.first.end
    @scale_start = lowest if lowest < @scale_start
    @scale_stop = highest if highest > @scale_stop
    @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
  end
  begin
    old_nt_per_px_x = @nt_per_px_x
    @tracks.each do |track|
      highest = track.features.map { |feat|
        compute_boundaries(feat)[1]
      }.max
      if highest > @scale_stop
        @scale_stop = highest
        @nt_per_px_x = (@scale_stop - @scale_start).to_f / @width.to_f
      end
    end
  end while (@nt_per_px_x - old_nt_per_px_x).abs > 1
end

#get_markup ⇒ Object

generates the SVG text



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# File 'lib/bio/graphics/page.rb', line 402

def get_markup
  get_limits
  draw_scale
  @tracks.each do |track|
    draw_features(track)
  end
  @svg.draw
end

#to_px(num) ⇒ Object

Calculates the pixel value for a given number



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# File 'lib/bio/graphics/page.rb', line 397

def to_px(num)
  (num.to_f / @nt_per_px_x.to_f)
end

#write(file) ⇒ Object

Writes the SVG text to a file



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# File 'lib/bio/graphics/page.rb', line 416

def write(file)
  File.open(file, 'w').write(get_markup)
end