Class: Bio::Graphics::Panel

Inherits:
Object
  • Object
show all
Defined in:
lib/bio/graphics/panel.rb,
lib/bio/graphics/ruler.rb,
lib/bio/graphics/track.rb,
lib/bio/graphics/feature.rb

Overview

The Bio::Graphics::Panel class describes the complete graph and contains all tracks. See Bio::Graphics documentation for explanation of interplay between different classes.

Defined Under Namespace

Classes: Ruler, Track

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(length, width = DEFAULT_PANEL_WIDTH, clickable = false, display_start = nil, display_stop = nil) ⇒ Panel

Create a new Bio::Graphics::Panel object

g = Bio::Graphics::Panel.new(456)

The height of the image is calculated automatically depending on how many tracks and features it contains. The width of the image defaults to 800 pt but can be set manually by using a second argument:

g = Bio::Graphics::Panel.new(456, 400)

See also: Bio::Graphics::Track, BioExt::Graphics::Feature

Arguments:

  • length

    length of the thing you want to visualize, e.g for

    visualizing a sequence that is 3.24 kb long, use 324.

  • width

    width of the resulting image in pt. This should be a string

    and not an integer. Default = ‘800’ (Notice the quotes…).

  • clickable

    whether the picture should have clickable glyphs or not

    (default: false) If set to true, a html file will be created with the map.

  • display_start

    start coordinate to be displayed (default: 1)

  • display_stop

    stop coordinate to be displayed (default: length of sequence)

Returns

Bio::Graphics::Panel object



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

def initialize(length, width = DEFAULT_PANEL_WIDTH, clickable = false, display_start = nil, display_stop = nil)
  @length = length.to_i
  @width = width.to_i
  @tracks = Array.new
  @number_of_feature_rows = 0
  @clickable = clickable
  @image_map = ( clickable ) ? ImageMap.new : nil
  @display_start = ( display_start.nil? or display_start < 0 ) ? 0 : display_start
  @display_stop = ( display_stop.nil? or display_stop > @length ) ? @length : display_stop
  if @display_stop <= @display_start
    raise "[ERROR] Start coordinate to be displayed has to be smaller than stop coordinate."
  end
  @rescale_factor = (@display_stop - @display_start).to_f / @width
end

Instance Attribute Details

#clickable ⇒ Object

Returns the value of attribute clickable.



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# File 'lib/bio/graphics/panel.rb', line 117

def clickable
  @clickable
end

#display_start ⇒ Object

Returns the value of attribute display_start.



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# File 'lib/bio/graphics/panel.rb', line 117

def display_start
  @display_start
end

#display_stop ⇒ Object

Returns the value of attribute display_stop.



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# File 'lib/bio/graphics/panel.rb', line 117

def display_stop
  @display_stop
end

#height ⇒ Object

Returns the value of attribute height.



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# File 'lib/bio/graphics/panel.rb', line 117

def height
  @height
end

#image_map ⇒ Object

Returns the value of attribute image_map.



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# File 'lib/bio/graphics/panel.rb', line 117

def image_map
  @image_map
end

#length ⇒ Object

Returns the value of attribute length.



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# File 'lib/bio/graphics/panel.rb', line 117

def length
  @length
end

#number_of_feature_rows ⇒ Object

Returns the value of attribute number_of_feature_rows.



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# File 'lib/bio/graphics/panel.rb', line 117

def number_of_feature_rows
  @number_of_feature_rows
end

#rescale_factor ⇒ Object

Returns the value of attribute rescale_factor.



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# File 'lib/bio/graphics/panel.rb', line 117

def rescale_factor
  @rescale_factor
end

#tracks ⇒ Object

Returns the value of attribute tracks.



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# File 'lib/bio/graphics/panel.rb', line 117

def tracks
  @tracks
end

#width ⇒ Object

Returns the value of attribute width.



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# File 'lib/bio/graphics/panel.rb', line 117

def width
  @width
end

Instance Method Details

#add_track(name, label = true, feature_colour = [0,0,1], feature_glyph = 'generic') ⇒ Object

Adds a Bio::Graphics::Track container to this panel. A panel contains a logical grouping of features, e.g. (for sequence annotation:) genes, polymorphisms, ESTs, etc.

est_track = g.add_track('ESTs')
gene_track = g.add_track('genes')

Arguments:

  • name (required)

    Name of the track to be displayed (e.g. ‘genes’)

  • _label)

    Whether the feature labels should be displayed or not

  • colour

    Colour to be used to draw the features within the track.

    Default = ‘blue’

  • glyph

    Glyph to use for drawing the features. Options are:

    ‘generic’, ‘directed_generic’, ‘spliced’, ‘directed_spliced’ and ‘triangle’. Triangles can be used for features whose start and stop positions are the same (e.g. SNPs). If you try to draw a feature that is longer with triangles, an error will be shown.

Returns

Bio::Graphics::Track object that has just been created



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# File 'lib/bio/graphics/panel.rb', line 139

def add_track(name, label = true, feature_colour = [0,0,1], feature_glyph = 'generic')
  @tracks.push(Bio::Graphics::Panel::Track.new(self, name, label, feature_colour, feature_glyph))
  return @tracks[-1]
end

#draw(file_name) ⇒ Object

Create the drawing – The fact that display_start and display_stop can be set has two consequences:

1. not all features are drawn
2. the x-coordinate of all glyphs has to be corrected

++



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

def draw(file_name)
  # Create a panel that is huge vertically
  huge_height = 2000

  huge_panel_drawing = nil
  huge_panel_drawing = Cairo::ImageSurface.new(1, @width, huge_height)

  background = Cairo::Context.new(huge_panel_drawing)
  background.set_source_rgb(1,1,1)
  background.rectangle(0,0,@width,huge_height).fill

  # Add ruler
  vertical_offset = 0
  ruler = Bio::Graphics::Panel::Ruler.new(self)
  ruler.draw(huge_panel_drawing, vertical_offset)
  vertical_offset += ruler.height

  # Add tracks
  @tracks.each do |track|
    track.vertical_offset = vertical_offset
    track.draw(huge_panel_drawing)
    @number_of_feature_rows += track.number_of_feature_rows
    vertical_offset += ( track.number_of_feature_rows*(FEATURE_HEIGHT+FEATURE_V_DISTANCE+5)) + 10 # '10' is for the header
  end

  # And create a smaller version of the panel
  height = ruler.height
  @number_of_feature_rows.times do
    height += 20
  end
  @tracks.length.times do #To correct for the track headers
    height += 10
  end

  resized_panel_drawing = nil
  resized_panel_drawing = Cairo::ImageSurface.new(1, @width, height)
  resizing_context = Cairo::Context.new(resized_panel_drawing)
  resizing_context.set_source(huge_panel_drawing, 0,0)
  resizing_context.rectangle(0,0,@width, height).fill

  # And print to file
  resized_panel_drawing.write_to_png(file_name)
  if @clickable # create png and map
    html_filename = file_name.sub(/\.[^.]+$/, '.html')
    html = File.open(html_filename,'w')
    html.puts "<html>"
    html.puts "<body>"
    html.puts @image_map.to_s
    html.puts "<img border='1' src='" + file_name + "' usemap='#image_map' />"
    html.puts "</body>"
    html.puts "</html>"
  end
end