Module: Heatmap

Defined in:
lib/rbbt/plots/heatmap.rb

Class Method Summary collapse

Class Method Details

.heatmap(values, filename, options = {}) ⇒ Object 



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# File 'lib/rbbt/plots/heatmap.rb', line 5

def self.heatmap(values, filename, options = {})
  scale, take_log, add_to_height, colors = Misc.process_options options, 
    :scale, :take_log, :add_to_height, :colors

  width = 200 + (values.fields.length * 16)
  height = 200 + (values.length * 16)
  size = [width, height].max
  size = [size, 10000].min

  heatmap_script = <<-EOF 
  #{ take_log ? "data <- log(data)" : ""}
      my.hclust <- function(d){ hclust(d, method="ward") }; 
      my.hclust <- function(d){ hclust(d) }; 
      rbbt.png_plot(
        '#{filename}', 
  #{ size }, 
  #{ (defined?(add_to_height) and not add_to_height.nil?) ? (size + (add_to_height * 16 * [1, (height.to_f / width)].max).to_i) : size }, 
        'heatmap(as.matrix(data),
  #{
  case scale.to_s
  when "true", 'row'
    'scale="row",' 
  when 'column' 
    'scale="column",' 
  when "none", ""
    'scale="none",'
  end
  }
  #{colors.nil? ? "" : "ColSideColors=#{colors},"} 
        hclustfun=my.hclust, 
        )',
        pointsize=12, type='cairo', res=150)
      data = NULL;
  EOF

  values.R heatmap_script
  
  filename
end

.heatmap2(values, filename, options = {}) ⇒ Object 



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# File 'lib/rbbt/plots/heatmap.rb', line 45

def self.heatmap2(values, filename, options = {})
  scale, take_log, add_to_height, colors = Misc.process_options options, 
    :scale, :take_log, :add_to_height, :colors

  width = 1200 + (values.fields.length * 100)
  height = 1000 + (values.length * 50)
  size = [width, height].max
  size = [size, 20000].min
  width = [size, width].min
  height = [size, height].min

  take_log = take_log ? "TRUE" : "FALSE"
  heatmap_script = <<-EOF 
library(ggplot2);
rbbt.heatmap('#{filename}', #{ width }, #{ height }, data, take_log=#{take_log});
  EOF

  values.R heatmap_script
  
  filename
end

.heatmap3(values, filename, options = {}) ⇒ Object 



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# File 'lib/rbbt/plots/heatmap.rb', line 67

def self.heatmap3(values, filename, options = {})
  scale, take_log, add_to_height, colors = Misc.process_options options, 
    :scale, :take_log, :add_to_height, :colors

  width = 1200 + (values.fields.length * 100)
  height = 1000 + (values.length * 50)
  size = [width, height].max
  size = [size, 2000].min
  width = [size, width].min
  height = [size, height].min

  take_log = take_log ? "TRUE" : "FALSE"

  map = options.delete :map

  if map
    values = values.slice(map.keys)
    clab = TSV.setup(map.keys, :type => :list, :fields => [], :key_field => map.key_field)

    options[:keys] = []
    options[:colors] = []
    map.fields.each do |field|
      color = Colorize.tsv map.slice(field)
      clab.add_field field do |k, values|
        color[k].to_rgb
      end
      options[:keys] << "" unless options[:keys].empty?
      options[:keys].concat map.values.uniq
      options[:colors] << "#000" unless options[:colors].empty?
      options[:colors].concat color.values_at(*map.keys).collect{|c| c.to_rgb}.uniq
    end

    if options[:keys].length > 20 
      options.delete :keys
      options.delete :colors
    end

    options[:ColSideColors] = clab
  end

  other_params = ", " << options.collect{|k,v| [R.ruby2R(k), R.ruby2R(v)] * "="} * ", " if options.any?

  heatmap_script = <<-EOF 
library(ggplot2, quietly = TRUE, warn.conflicts = TRUE);
source('#{Rbbt.share.R["heatmap.3.R"].find}');

rbbt.heatmap.3('#{filename}', #{ width }, #{ height }, data, take_log=#{take_log}#{other_params});
  EOF

  values.R heatmap_script
  
  filename
end