Module: ViennaRna::Graphing::R

Defined in:
lib/vienna_rna/modules/graphing.rb

Class Method Summary collapse

Class Method Details

.graph(&block) ⇒ Object 



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# File 'lib/vienna_rna/modules/graphing.rb', line 5

def graph(&block)
  begin
    (yield (r_instance = RinRuby.new)).tap { r_instance.close }
  rescue RuntimeError => e
    raise unless e.message == "Unsupported data type on R's end"
  end
end

.histogram(data, title: nil, x_label: "Bins", bin_size: 1, relative: false, filename: false) ⇒ Object 



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# File 'lib/vienna_rna/modules/graphing.rb', line 33

def histogram(data, title: nil, x_label: "Bins", bin_size: 1, relative: false, filename: false)
  half     = bin_size / 2.0
  range    = Range.new((data.min - half).floor, (data.max + half).ceil)
  breaks   = (range.min + half).step(range.max + half, bin_size).to_a
  
  graph do |r|
    r.assign("histogram.data", data)
    r.assign("histogram.breaks", breaks)

    if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
      r.eval <<-STR
        pdf("#{filename}", 6, 6)
        hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}", freq = #{relative ? 'FALSE' : 'TRUE'})
        dev.off()
      STR
    else
      r.eval <<-STR
        quartz("Histogram", 6, 6)
        hist(histogram.data, breaks = histogram.breaks, xlab = "#{x_label} (width: #{bin_size})", main = "#{title || 'Histogram'}", freq = #{relative ? 'FALSE' : 'TRUE'})
      STR
    end
  end
end

.line_graph(data, title: nil, type: "l", x_label: "Independent", y_label: "Dependent", filename: false) ⇒ Object 



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# File 'lib/vienna_rna/modules/graphing.rb', line 13

def line_graph(data, title: nil, type: "l", x_label: "Independent", y_label: "Dependent", filename: false)
  graph do |r|
    r.assign("line_graph.x", data.map(&:first))
    r.assign("line_graph.y", data.map(&:last))

    if filename && (filename = filename.end_with?(".pdf") ? filename : filename + ".pdf")
      r.eval <<-STR
        pdf("#{filename}", 6, 6)
        plot(line_graph.x, line_graph.y, xlab = "#{x_label}", ylab = "#{y_label}", main = "#{title || 'Line Graph'}", type = "#{type}")
        dev.off()
      STR
    else
      r.eval <<-STR
        quartz("Histogram", 6, 6)
        plot(line_graph.x, line_graph.y, xlab = "#{x_label}", ylab = "#{y_label}", main = "#{title || 'Line Graph'}", type = "#{type}")
      STR
    end
  end
end

.roc(data, title = "", options = {}) ⇒ Object 



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# File 'lib/vienna_rna/modules/graphing.rb', line 57

def roc(data, title = "", options = {})
  # data = [[true_score_1, true_score_2, ...], [false_score_1, false_score_2, ...]]

  if R.pull("ifelse('ROCR' %in% rownames(installed.packages()), 1, -1)") > 0

  else
    puts "Please install the ROCR package for R before using this function."
  end

  # roc_curve = ROC.curve_points({ 1 => data[0], -1 => data[1] }.inject([]) { |data, (truth, values)| data.concat(values.map { |i| [i, truth] })})
  # area      = roc_curve.each_cons(2).inject(0) do |sum, (a, b)| 
  #   delta_x, delta_y = b[0] - a[0], b[1] - a[1]
  #   sum + (delta_x * delta_y / 2 + delta_x * [a[1], b[1]].min)
  # end
  
  # options.merge!(output: "file") if options[:filename]
  # options.merge!({ plot: { title: "%s %s %.4f" % [title, "AUC:", area] } })
    
  # plot([{ x: roc_curve.map(&:first), y: roc_curve.map(&:last), style: "lines" }], options)
end