Module: Wrnap::Graphing::R

Defined in:
lib/wrnap/graphing/r.rb

Class Method Summary collapse

Class Method Details

.graph(width: 8, height: 6, &block) ⇒ Object 



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# File 'lib/wrnap/graphing/r.rb', line 5

def graph(width: 8, height: 6, &block)
  if const_defined?(:RinRuby)
    begin
      generate_graph(r_instance = RinRuby.new(false), width, height, &block).tap { r_instance.close }
    rescue RuntimeError => e
      raise unless e.message == "Unsupported data type on R's end"
    end
  else
    raise RuntimeError.new("Your system does not appear to have R installed, and thus the RinRuby gem was not loaded.")
  end
end

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



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# File 'lib/wrnap/graphing/r.rb', line 121

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

  graph do |r|
    r.assign("histogram.data", data)
    r.assign("histogram.breaks", breaks)

    r.eval <<-STR
      hist(
        histogram.data,
        breaks   = histogram.breaks,
        xlab     = #{expressionify(x_label)},
        main     = #{expressionify(title || "Histogram")},
        freq     = #{relative ? 'F' : 'T'},
        cex.main = 0.9,
        cex.lab  = 0.9,
        cex.axis = 0.9
      )
    STR

    r.eval("abline(v = #{x_arrow}, lty = 'dashed')") if x_arrow
  end
end

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



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# File 'lib/wrnap/graphing/r.rb', line 74

def line_graph(data, title: nil, type: ?l, x_label: "Independent", y_label: "Dependent", filename: false)
  overlay([{ data: data }], title: title, type: type, x_label: x_label, y_label: y_label, legend: false, filename: filename)
end

.matrix_heatmap(x, y, z, title: nil, x_label: "Column index", y_label: "Row index", filename: false, num_colors: 64) ⇒ Object 



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# File 'lib/wrnap/graphing/r.rb', line 147

def matrix_heatmap(x, y, z, title: nil, x_label: "Column index", y_label: "Row index", filename: false, num_colors: 64)
  graph do |r|
    if r.pull("ifelse('Matrix' %in% rownames(installed.packages()), 1, -1)") > 0
      if forced_square = (x.max != y.max)
        x << [x, y].map(&:max).max
        y << [x, y].map(&:max).max
        z << 0
      end

      r.assign("matrix.i", x)
      r.assign("matrix.j", y)
      r.assign("matrix.x", z)
      r.eval <<-STR
        require("Matrix")
        matrix.data <- sparseMatrix(
        i      = matrix.i,
        j      = matrix.j,
        x      = matrix.x,
        index1 = F
        )
        
        filtered.values <- Filter(function(i) { is.finite(i) & i != 0 }, matrix.x)
        print(apply(as.matrix(matrix.data), 2, rev))
        print(c(sort(filtered.values)[2], max(filtered.values)))

        image(
          x    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])),
          y    = 1:max(c(dim(matrix.data)[[1]], dim(matrix.data)[[2]])),
          z    = as.matrix(matrix.data),
          col  = rev(heat.colors(#{num_colors})),
          zlim = #{forced_square ? "c(sort(filtered.values)[2], max(filtered.values))" : "c(min(filtered.values), max(filtered.values))"},
          xlab = "#{x_label} (1-indexed)",
          ylab = "#{y_label} (1-indexed)"
        )
        title(#{expressionify(title || "Matrix Heatmap")})
      STR
    else
      puts "Please install the Matrix package for R before using this function."
    end
  end
end

.overlay(data, title: nil, type: ?l, x_label: "Independent", y_label: "Dependent", legend: "topleft", filename: false) ⇒ Object 



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# File 'lib/wrnap/graphing/r.rb', line 17

def overlay(data, title: nil, type: ?l, x_label: "Independent", y_label: "Dependent", legend: "topleft", filename: false)
  # data: [{ data: [[x_0, y_0], ..., [x_n, y_n]], legend: "Line 1" }, ...]

  x_points = data.map { |hash| hash[:data].map(&:first) }
  y_points = data.map { |hash| hash[:data].map(&:last) }
  x_range  = Range.new(x_points.map(&:min).min.floor, x_points.map(&:max).max.ceil)
  y_range  = Range.new(y_points.map(&:min).min.floor, y_points.map(&:max).max.ceil)

  graph do |r|
    r.assign("legend.titles", data.each_with_index.map { |hash, index| hash[:legend] || "Line #{index + 1}" })
    r.eval("line.colors <- rainbow(%d)" % data.size)
    r.eval("plot(0, 0, type = 'n', cex = .75, cex.axis = .9, xlab = '', ylab = '', xlim = c(%d, %d), ylim = c(%d, %d))" % [
      x_range.min, x_range.max, y_range.min, y_range.max
    ])

    data.each_with_index do |hash, index|
      r.assign("line_graph.x.%d" % index, x_points[index])
      r.assign("line_graph.y.%d" % index, y_points[index])

      r.eval <<-STR
        lines(
          line_graph.x.#{index},
          line_graph.y.#{index},
          col  = line.colors[#{index + 1}],
          type = "#{type}",
          pch  = #{index}
        )
      STR
    end

    r.eval <<-STR
      title(
        xlab     = #{expressionify(x_label)},
        ylab     = #{expressionify(y_label)},
        main     = #{expressionify(title || "Line Graph")},
        cex.main = .9,
        cex.lab  = .9
      )
    STR

    if legend
      r.eval <<-STR
        legend(
          "#{legend}",
          legend.titles,
          bty = "o",
          bg  = rgb(1, 1, 1, .5, 1),
          col = line.colors,
          lty = rep(1, #{data.size}),
          pch = 0:#{data.size},
          cex = .6
        )
      STR
    end
  end
end

.roc(data, title: nil, baseline: true, filename: false) ⇒ Object 



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# File 'lib/wrnap/graphing/r.rb', line 82

def roc(data, title: nil, baseline: true, filename: false)
  # data: [[-0.894, 1.0], [-0.950, 1.0], [0.516, -1.0], ..., [0.815, -1.0], [0.740, -1.0]]
  auc            = ROC.auc(data)
  title_with_auc = title ? "%s (AUC: %.4f)" % [title, auc] : "AUC: %.4f" % auc
  overlay(
    [{ data: ROC.curve_points(data) }, { data: [[0, 0], [1, 1]] }],
    title:    title_with_auc,
    x_label:  "False positive rate",
    y_label:  "True positive rate",
    legend:   false,
    filename: filename
  )
end

.roc_overlay(data, title: nil, auc_in_legend: true, filename: false) ⇒ Object 



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# File 'lib/wrnap/graphing/r.rb', line 96

def roc_overlay(data, title: nil, auc_in_legend: true, filename: false)
  # [{ data: [[-0.894, 1.0], [-0.950, 1.0], [0.516, -1.0], ..., [0.815, -1.0], [0.740, -1.0]], legend: "ROC 1" }, ...]
  formatted_data = data.map do |hash|
    curve_points = ROC.curve_points(hash[:data])

    if auc_in_legend
      auc    = ROC.auc(hash[:data])
      legend = hash[:legend] ? "%s (AUC: %.4f)" % [hash[:legend], auc] : "AUC: %.4f" % auc

      hash.merge({ data: curve_points, legend: legend })
    else
      hash.merge({ data: curve_points })
    end
  end

  overlay(
    formatted_data,
    title:    title,
    x_label:  "False positive rate",
    y_label:  "True positive rate",
    legend:   "bottomright",
    filename: filename
  )
end

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



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# File 'lib/wrnap/graphing/r.rb', line 78

def scatterplot(data, title: nil, x_label: "Independent", y_label: "Dependent", filename: false)
  line_graph(data, title: title || "Scatterplot", type: ?p, x_label: x_label, y_label: y_label, filename: filename)
end