Module: Score

Defined in:
lib/MARQ/score.rb

Constant Summary collapse

COLORS = 
{
  :red =>   PNG::Color::Red,
  :green => PNG::Color::Green,
  :white => PNG::Color::White,
  :black => PNG::Color::Black,

}

Class Method Summary collapse

Class Method Details

.add_pvalues(scores, null_scores) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 142

def self.add_pvalues(scores, null_scores)
  null_scores = null_scores.sort
  times       = null_scores.length

  scores.each do |experiment, info|
    info[:pvalue] = (times - null_scores.count_smaller(info[:score].abs)).to_f / times
  end

  scores
end

.combine(up, down) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 97

def self.combine(up, down)
  return down if up == 0
  return up if down == 0

  return up - down
  if (up > 0) == (down > 0)
    return 0
  else
    up - down
  end
end

.draw_hits(hits, total, filename = nil, options = {}) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 161

def self.draw_hits(hits, total, filename = nil, options = {})

  size = options[:size] || total
  bg_color = options[:bg_color] || :white
  width = options[:width] || 20
  sections = options[:sections] || []

  size = [size, total].min

  hits = hits.collect{|h| h - 1}
  if size < total
    hits = hits.collect{|h| (h.to_f * size / total).to_i}
  end

  canvas = PNG::Canvas.new size, width, COLORS[bg_color]

  sections.each{|color, info|
    start = info[0]
    finish = info[1]
    (start..finish).each{|x|
      (0..width - 1).each{|y|
        canvas[x,y] = COLORS[color]
      }
    }
  }

  hits.each{|hit|
    canvas.line hit, 0, hit , width - 1, PNG::Color::Black
  }

  png = PNG.new canvas

  if filename
    png.save filename
  else
    png.to_blob
  end
end

.null_scores(up_size, down_size, times = 10000) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 135

def self.null_scores(up_size, down_size, times = 10000)
  up_perm   = permutations(up_size, times)
  down_perm = permutations(down_size, times)

  up_perm.zip(down_perm).collect{|p| up, down = p; combine(up, down).abs}
end

.permutations(size, times) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 124

def self.permutations(size, times)
  total = 10000
  if size == 0
    [0] * times
  else
    (1..times).collect do
      fast_score_scale(Array.new(size){ (rand * total).to_i }.sort, total, 0)
    end
  end
end

.score(*args) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 67

def self.score(*args)
  self.fast_score_scale(*args)
end

.scores(dataset, genes) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 71

def self.scores(dataset, genes)
  positions   = MADB.load_positions(dataset, genes)
  values      = MADB.num_values(dataset)

  experiments = positions.keys

  scores      = {}
  experiments.each do |experiment|
    hits  = positions[experiment].compact
    total = values[experiment]
    if hits.nil? || hits.empty?
      score = 0
    else
      missing = genes.length - hits.length
      score = self.fast_score_scale(hits.sort, total, missing) 
    end
    scores[experiment] = {
      :positions => positions[experiment],
      :score     => score,
      :total     => total,
    }
  end

  scores
end

.scores_up_down(dataset, up, down) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 109

def self.scores_up_down(dataset, up, down)
  scores_up   = scores(dataset, up)
  scores_down = scores(dataset, down)

  scores      = {}
  scores_up.keys.each do |experiment|
    scores[experiment] = {}
    scores[experiment][:up]    = scores_up[experiment]
    scores[experiment][:down]  = scores_down[experiment]
    scores[experiment][:score] = combine(scores_up[experiment][:score], scores_down[experiment][:score])
  end

  scores
end