Class: Bio::Graphics::Glyph

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

Overview

A glyph is a particular shape that represents a genomic feature. Bio::Graphics::Glyph objects represent glyphs. Bio::Graphics::Glyphs are created internally according to specification from the Bio::Graphics::Track and not instantiated directly by the user. Internally, these are constructed as an array of Bio::Graphics::Primitive objects, which are collections of simple shapes, combined appropriately to make a glyph

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Attribute Details

#glyphs ⇒ Object (readonly)

The different type of Glyphs are:

  • :generic

  • :circle

  • :directed

  • :down_triangle

  • :up_triangle

  • :span

  • :transcript

  • :scale

  • :label

  • :histogram



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# File 'lib/bio/graphics/glyph.rb', line 21

def glyphs
  @glyphs
end

Class Method Details

.circle(args) ⇒ Object

A circular glyph centered on the start of the feature it represents

args

  • :radius = the radius of the circle (default = 10)

  • :fill_color = the fill colour 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

: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
     }, ]

} #* :stroke = the outline colour of the Glyph (default = “black”), can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000

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

  • :x = base x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = base y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 103

def self.circle(args) 
  args = { 
    :radius => 10, 
    :fill_color => 'red', 
    :stroke => "black", 
    :stroke_width => 1, 
    :style => ""}.merge!(args)
    args[:x_center] = args[:x]
    args[:y_center] = args[:y]
    [:x, :y].each {|e| args.delete(e)}
  [Bio::Graphics::Primitive.new(:circle, args)]
end

.directed(args) ⇒ Object

A polygon glyph with a point on the end that represents the features strand and direction

args

  • :width = the width of the feature in px

  • :fill_color = the fill colour 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

: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
     }, ]

}

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

  • :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000

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

  • :strand = the strand on which the feature is located. May be ‘+’ or ‘-’

  • :points = the x and y axis coordinates that make up the corners of the polygon, calculated and added by the Bio::Graphics::Page object

  • :x = base x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = base y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

The points of the polygon are calculated form the :x and :y co-ordinates

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 151

def self.directed(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
  args = {
    
    :height => 10, 
    :fill_color => 'red', 
    :stroke => "black", 
    :stroke_width => 1, 
    :style => "fill-opacity:0.4;"}.merge!(args)
    
    if args[:strand] == '-'
      args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + args[:height] } #{args[:x]},#{args[:y] + (args[:height])} #{args[:x] - (args[:height] * 0.2)},#{args[:y] + (args[:height]/2)}"
    else
      args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y]} #{args[:x] + args[:width]},#{args[:y] + (args[:height]/2) } #{args[:x] + args[:width] - (args[:height] * 0.2)},#{args[:y] + args[:height]} #{args[:x]},#{args[:y] + args[:height]}"

    end
  [Bio::Graphics::Primitive.new(:polygon, args)]
end

.down_triangle(args) ⇒ Object

A downward-pointing triangle glyph

args

  • :height = the height of the Glyph (default = 10)

  • :fill_color = the fill colour 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

: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
     }, ]

} #* :stroke = the outline colour of the Glyph (default = “black”), can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000

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

  • :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 200

def self.down_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
  args = {
    
    :height => 10, 
    :fill_color => 'red', 
    :stroke => "black", 
    :stroke_width => 1, 
    :style => "fill-opacity:0.4;"}.merge!(args)

    args[:points] = "#{args[:x]},#{args[:y]} #{args[:x] + args[:width]},#{args[:y]} #{ args[:x] + (args[:width]/2) },#{(args[:y] + args[:height]) }"
  [Bio::Graphics::Primitive.new(:polygon, args)]
end

.generic(args) ⇒ Object

A generic glyph is a block of colour that displays no specific directional information attached.

args

  • :height = the height of the Glyph (default = 10)

  • :fill_color = the fill colour 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

: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
     }, ]

} #* :stroke = the outline colour of the Glyph (default = “black”), can be any SVG colour eg rgb(256,0,0) or #FF0000

  • :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000

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

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

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

  • :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 59

def self.generic(args)
  args = { 
    :height => 10, 
    :fill_color => 'red', 
    :stroke => "black", 
    :stroke_width => 1, 
    :x_round => 1, 
    :y_round => 1, 
    :style => "fill-opacity:0.4;"}.merge!(args)
  [Bio::Graphics::Primitive.new(:rectangle, args)]
end

.gradient(gradient) ⇒ Object

Sets the the type (linear or radial) and colours for a pre-defined gradient

args

  • gradient = a pre-defined gradient type, one of

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


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# File 'lib/bio/graphics/glyph.rb', line 536

def self.gradient(gradient)
  type, color = case gradient
  when :red_white_h
    [:linear, "red"]
  when :green_white_h
    [:linear, "green"]
  when :blue_white_h
    [:linear, "blue"]
  when :yellow_white_h
    [:linear, "yellow"]
  when :red_white_radial
    [:radial, "red"]
  when :green_white_radial
    [:radial, "green"]
  when :blue_white_radial
    [:radial, "blue"]
  when :yellow_white_radial
    [:radial, "yellow"]
  end
  
  case type
  when :linear
          {:type => :linear, 
     :id => gradient, 
     :x1 => 0, :y1 => 0, 
     :x2 => 0, :y2 => 100, 
     :stops => [
       {
        :color => color, 
        :offset => 0, 
        :opacity=> 1
        },
        {
         :color => "white", 
         :offset => 100, 
         :opacity=> 1 
         }
        ]
      }
  when :radial
    {
     :type => :radial, 
     :id => gradient, 
     :cx => 50, :cy => 50, 
     :r => 50, :fx => 50, :fy => 50, 
     :stops => [ 
       {:offset => 0, 
        :color => "white", 
        :opacity => 0
        },  
        {
        :offset => 100, 
        :color => color, 
        :opacity => 1
        }
      ]
    }
  end
  
end

.gradients ⇒ Object

The list of pre-defined gradients



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# File 'lib/bio/graphics/glyph.rb', line 527

def self.gradients #needs to know which of its gradients are predefined
  [:red_white_h, :green_white_h, :blue_white_h, :yellow_white_h, :red_white_radial, :green_white_radial, :blue_white_radial, :yellow_white_radial ]
end

.label(args) ⇒ Object

Creates a label Glyph to write text

args

  • :text = the text to write

  • :fill = the colour of the text (“black”)

  • :style = the style of writing (“font-family:monospace;”)

  • :x = the co-ordinates of the Glyph for the x-axis

  • :y = the co-ordinates of the Glyph for the y-axis



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# File 'lib/bio/graphics/glyph.rb', line 517

def self.label(args)
  [Bio::Graphics::Primitive.new(:text, 
                 :text => args[:text], 
                 :x => args[:x], 
                 :y => args[:y], 
                 :fill => "black", 
                 :style => "font-family:monospace;")]
end

.scale(args) ⇒ Object

Glyph for the scale across the top of the rendered page

args

  • :start = the start of the scale, usually added by the Bio::Graphics::Page object

  • :stop = the end of the scale, usually added by the Bio::Graphics::Page object

  • :number_of_intervals = the number of tick-marks the scale will marked with

  • :page_width = the minimum width of the page, usually updated by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects (of type ‘line’, ‘rectangle’ and ‘text’)



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# File 'lib/bio/graphics/glyph.rb', line 472

def self.scale(args)
  first_mark = args[:start]
  last_mark = args[:stop] 
  #(num.to_f / @nt_per_px_x.to_f)
  full_dist = last_mark - first_mark
  interval_width =  full_dist / (args[:number_of_intervals] - 1) 


  a = [Bio::Graphics::Primitive.new(:line, 
                             :stroke => 'black', 
                             :stroke_width => 1, 
                             :x1 => 1, :x2 => args[:page_width],# * 1.1, 
                             :y1 => "20", :y2 => "20"  )]


  marks = (first_mark..last_mark).step(interval_width).to_a

  px_per_nt =  args[:page_width].to_f / full_dist.to_f
  marks.each do |mark|
    x =   (mark.to_f - first_mark ).to_f * px_per_nt
    a << Bio::Graphics::Primitive.new(:rectangle, 
                       :x => x, 
                       :y => 20, 
                       :stroke => 'black', 
                       :stroke_width => 1, 
                       :width => 1, 
                       :height => 5 )
                       
    a << Bio::Graphics::Primitive.new(:text, 
                       :x => x, 
                       :y => 40, :fill => 'black', 
                       :text => mark, 
                       :style => "font-family:Arial;font-style:italic")
  end
  return a
end

.span(args) ⇒ Object

A line (span) glyph

args

  • :height = the height of the Glyph (default = 10)

  • :fill_color = the fill colour 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

: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
     }, ]

}

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

  • :stroke_width = The width of the outline stroke (default = 1)

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

  • :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 289

def self.span(args)
  args = {
    :height => 10,
    :fill_color => 'red',
    :stroke => "black",
    :stroke_width => 1,
    :style => "fill-opacity:1;"
  }.merge!(args)
  args[:x1] = args[:x]
  args[:x2] = args[:x] + args[:width]
  args[:y1] = args[:y]
  args[:y2] = args[:y]
  [Bio::Graphics::Primitive.new(:line, args)]
end

.transcript(args) ⇒ Object

Creates a transcript glyph, which is a composite glyph containing generic glyphs for the exons/utrs and a directed glyph at the end. The glyphs are joined by lines.

args

  • :height = the height of the Glyph (default = 10)

  • :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;”

  • :block_gaps = gaps between the rendered blocks - calculated internally by Bio::Graphics::Page object

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

  • :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 366

def self.transcript(args)
    args = {
    :height => 10, 
    :utr_fill_color => 'black', 
    :utr_stroke => "black", 
    :utr_stroke_width => 1, 
    :exon_fill_color => 'red', 
    :exon_stroke => "black", 
    :exon_stroke_width => 1, 
    :line_color => 'black',
    :line_width => 1, 
    :exon_style => "fill-opacity:0.4;",
    :utr_style => "",
    :line_style => "",
    :block_gaps => "",
    :gap_marker => ""
    }.merge!(args)
    
    composite = []

    if not args[:utrs].empty?  ##draw the utr as terminal element...##terminal utr is the one with the point on...
      x,width =  args[:strand] == '-' ? args[:utrs].shift : args[:utrs].pop 
      composite += Glyph.directed(:x => x, 
                                  :y => args[:y], 
                                  :width => width, 
                                  :strand => args[:strand], 
                                  :height => args[:height], 
                                  :fill_color => args[:utr_fill_color], 
                                  :stroke =>args[:utr_stroke], 
                                  :stroke_width => args[:utr_stroke_width], 
                                  :style => args[:utr_style] )
      ##draw the other(s!) 
      args[:utrs].each do |utr|
        composite <<  Bio::Graphics::Primitive.new(:rectangle, {
                                                  :x => utr.first, 
                                                  :width => utr.last, 
                                                  :y => args[:y], 
                                                  :height => args[:height], 
                                                  :fill_color => args[:utr_fill_color], 
                                                  :stroke =>args[:utr_stroke], 
                                                  :stroke_width => args[:utr_stroke_width], 
                                                  :style => args[:utr_style]} )
      end
    else ## draw the terminal exon as terminal element  
      points = nil      
      x,width =  args[:strand] == '-' ? args[:exons].shift : args[:exons].pop 
      composite += Glyph.directed(:x => x, 
                                  :y => args[:y], 
                                  :width => width, 
                                  :strand => args[:strand], 
                                  :height => args[:height], 
                                  :fill_color => args[:exon_fill_color], 
                                  :stroke =>args[:exon_stroke], 
                                  :stroke_width => args[:exon_stroke_width], 
                                  :style => args[:exon_style] )
    end
    #draw any remaining exons
    args[:exons].each do |exon|
        composite <<  Bio::Graphics::Primitive.new(:rectangle, {
                                                  :x => exon[0], 
                                                  :width => exon[1], 
                                                  :y => args[:y], 
                                                  :height => args[:height], 
                                                  :fill_color => args[:exon_fill_color], 
                                                  :stroke =>args[:exon_stroke], 
                                                  :stroke_width => args[:exon_stroke_width], 
                                                  :style => args[:exon_style]} )
    end
    if not args[:block_gaps].empty?
      if args[:gap_marker] == "angled"
        args[:block_gaps].each do |gap|
          points = "#{gap.first},#{args[:y] + (args[:height]/2) } #{gap.first + (gap.last/2)},#{args[:y]} #{gap.first + gap.last},#{args[:y] + (args[:height]/2)}"
          composite << Bio::Graphics::Primitive.new(:polyline, {
                                                :points => points, 
                                                :stroke => args[:line_color], 
                                                :stroke_width => args[:line_width], 
                                                :fill => "none", 
                                                :line_style => args[:line_style]})
        end
      else
      #add line
        composite << Bio::Graphics::Primitive.new(:line, {
                                            :x1 => args[:x], 
                                            :x2 => "#{args[:x] + args[:width]}", 
                                            :y1 => args[:y] + (args[:height]/2), 
                                            :y2 => args[:y] + (args[:height]/2), 
                                            :stroke => args[:line_color], 
                                            :stroke_width => args[:line_width], 
                                            :line_style => args[:line_style]})

      end
    end
    composite
end

.up_triangle(args) ⇒ Object

An upward-pointing triangle glyph

args

  • :height = the height of the Glyph (default = 10)

  • :fill_color = the fill colour 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

: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
     }, ]

}

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

  • :stroke_width = The width of the outline stroke (default = 1), can be any SVG colour eg rgb(256,0,0) or #FF0000

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

  • :x = x coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

  • :y = y coordinate of the feature in pixels, usually added by the Bio::Graphics::Page object

returns

  • An Array of Bio::Graphic::Primitive objects



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# File 'lib/bio/graphics/glyph.rb', line 245

def self.up_triangle(args) #:x, :y, :width :fill, :stroke :stroke_width, :style, :height
  args = {
    :height => 10, 
    :fill_color => 'red', 
    :stroke => "black", 
    :stroke_width => 1, 
    :style => "fill-opacity:0.4;"}.merge!(args)
    args[:points] = "#{args[:x]},#{args[:y] + args[:height]} #{args[:x] + args[:width]},#{args[:y] + args[:height]} #{ args[:x] + (args[:width]/2) },#{args[:y] }"
  [Bio::Graphics::Primitive.new(:polygon, args)]
end