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

.average(list) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 17

def self.average(list)
  clean = list.compact
  clean.inject(0){|acc, e| acc += e}.to_f / clean.length
end

.combine(up, down) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 5

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 316

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

.permutations(genes, total, times = 10000) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 286

def self.permutations(genes, total, times = 10000)
  scores = []
  times.times{
    positions = Array.new(genes){ (rand * total).to_i }
    scores << score(positions, total)[:score]
  }
  scores
end

.pvalues(scores, up, down, total, options = {}) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 295

def self.pvalues(scores, up, down, total, options = {})
  times = options[:times]|| 1000

  permutations_up = permutations(up, total, times)
  permutations_down = permutations(down, total, times )
  permutations = permutations_up.zip(permutations_down).collect{|p| combine(*p).abs }.sort

  scores.collect{|score| 
    num = permutations.count_smaller(score.abs)
    (times - num).to_f / times
  }
end

.scale_score1(positions, platform_entries) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 85

def self.scale_score1(positions, platform_entries)

  mean = platform_entries/2
  max_top = 0
  max_bottom = 0

  top_list = []
  bottom_list = []

  weights = positions.sort.collect{|position| 
    rel_pos = ((position - mean).abs.to_f / mean);
    0.3 * rel_pos + 0.7 * Math::exp(30*rel_pos)/Math::exp(30)
  }
  weights.unshift(0)
  total_weights = weights.inject(0){|v,acc| acc += v}
  weights.collect!{|v| v / total_weights}

  rel_qt = 0
  rel_qb = 0
  positions.sort.each_with_index{|position, idx|

    rel_qt += weights[idx + 1] 
    rel_qb += weights[idx]     
    rel_p   = position.to_f    / platform_entries
 
    top    = (rel_qt - rel_p);
    bottom = (rel_p - rel_qb);

    top_list << top
    bottom_list << bottom

    if (top > max_top) 
      max_top = top;
    end
    if (bottom > max_bottom) 
      max_bottom = bottom;
    end
  }

  p [top_list, bottom_list]
  if (max_top > max_bottom)
    return max_top;
  else
    return -max_bottom;
  end           
end

.score_area(positions, platform_entries, missing = 0) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 22

def self.score_area(positions, platform_entries, missing = 0)
  return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?

  clean_positions = positions.compact.sort

  total_tags      = positions.length + missing
  extra           = total_tags - clean_positions.length

  top = 0
  bottom = 0

  clean_positions.each_with_index{|p,i|
    rel_qt = (i + 1).to_f / total_tags
    rel_qb = ( i + extra ).to_f / total_tags
    rel_p  = p.to_f / platform_entries


    top    += rel_qt - rel_p if rel_qt > rel_p
    bottom += rel_p - rel_qb if rel_p > rel_qb
  }


  {
    :top => top,
    :bottom => bottom,
    :score => top > bottom ? top.to_f / total_tags : - bottom.to_f / total_tags, 
  }
end

.score_max(positions, platform_entries, missing = 0) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 246

def self.score_max(positions, platform_entries, missing = 0)
  return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?

  clean_positions = positions.compact.sort

  extra           = missing + (positions.length - clean_positions.length)
  total_tags      = extra + clean_positions.length


  values = [0]

  clean_positions.each_with_index{|p,i| 
    
    up   = (i + 1).to_f / total_tags
    down = p.to_f       / platform_entries

    values << up - down
  }

  top    = values.max
  bottom = values.min + ((extra - 1).to_f/ total_tags)


  {
    :score => top.abs > bottom.abs ? top : bottom, 
  }
end

.score_max_norm(positions, platform_entries, missing = 0) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 51

def self.score_max_norm(positions, platform_entries, missing = 0)
  return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?

  clean_positions = positions.compact.sort

  extra           = missing + (positions.length - clean_positions.length)
  total_tags      = extra + clean_positions.length

  mean = platform_entries / 2

  values_top = [0]
  values_bottom = [0]

  clean_positions.each_with_index{|p,i| 
    rel_qt = (i + 1).to_f / total_tags
    rel_qb = ( i + extra ).to_f / total_tags
    rel_p  = p.to_f / platform_entries


    values_top << (rel_qt - rel_p) * ((p - mean).abs.to_f / mean)**2
    values_bottom << (rel_p - rel_qb) * ((p - mean).abs.to_f / mean)**2
  }

  top    = values_top.max
  bottom = values_bottom.max 


  {
    :score => top > bottom ? top : -bottom, 
  }


end

.score_norm_fast(positions, platform_entries, missing = 0) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 233

def self.score_norm_fast(positions, platform_entries, missing = 0)
  return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?

  clean_positions = positions.compact.sort

  extra           = missing + (positions.length - clean_positions.length)
  total_tags      = extra + clean_positions.length

  {
    :score => fast_norm_score(clean_positions, total_tags, extra, platform_entries)
  }
end

.score_scale_fast(positions, platform_entries, missing = 0) ⇒ Object Also known as: score 



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# File 'lib/MARQ/score.rb', line 221

def self.score_scale_fast(positions, platform_entries, missing=0)
  return {:score => 0, :top => 0, :bottom => 0} if positions.nil? || positions.empty? || positions.compact.empty?

  clean_positions = positions.compact.sort
  missing = missing + positions.length - clean_positions.length

  {
    :score => fast_score_scale(clean_positions,  platform_entries, missing)
  }
end

.score_up_down(up, down, total, missing_up = 0, missing_down = 0) ⇒ Object 



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# File 'lib/MARQ/score.rb', line 279

def self.score_up_down(up, down, total, missing_up = 0, missing_down = 0)
  up = score(up, total, missing_up)
  down = score(down, total, missing_down)

  {:up =>  up[:score], :down => down[:score], :score => combine(up[:score], down[:score])}
end