Class: Ranker

Inherits:
Object
  • Object
show all
Defined in:
lib/NetAnalyzer/ranker.rb

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize ⇒ Ranker

Returns a new instance of Ranker.



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# File 'lib/NetAnalyzer/ranker.rb', line 9

def initialize()
  @matrix = nil
  @nodes = [] # kernel_nodes
  @seeds = {} # genes_seed
  @reference_nodes = {}
  @ranking = {} # ranked_genes
end

Instance Attribute Details

#matrix ⇒ Object

Returns the value of attribute matrix.



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# File 'lib/NetAnalyzer/ranker.rb', line 7

def matrix
  @matrix
end

#nodes ⇒ Object

Returns the value of attribute nodes.



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# File 'lib/NetAnalyzer/ranker.rb', line 7

def nodes
  @nodes
end

#ranking ⇒ Object

Returns the value of attribute ranking.



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# File 'lib/NetAnalyzer/ranker.rb', line 7

def ranking
  @ranking
end

#seeds ⇒ Object

Returns the value of attribute seeds.



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# File 'lib/NetAnalyzer/ranker.rb', line 7

def seeds
  @seeds
end

Instance Method Details

#add_absolute_rank_column(ranking) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 134

def add_absolute_rank_column(ranking)
  ranking_with_new_column = []
  absolute_rank = 1
  n_rows = ranking.length
  n_rows.times do |row_pos|
    if row_pos == 0
      new_row = ranking[row_pos] << absolute_rank
      ranking_with_new_column << new_row
    else
      prev_val = ranking[row_pos-1][2]
      val = ranking[row_pos][2]
      if val > prev_val
        absolute_rank +=1
      end
      new_row = ranking[row_pos] << absolute_rank
      ranking_with_new_column << new_row
    end
  end
  return ranking_with_new_column
end

#array2hash(arr, key, values) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 217

def array2hash(arr, key, values)
  h = {}
  arr.each{|els| h[els[0]] = els[values]}
  return h
end

#do_ranking(leave_one_out: false, threads: 0) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 49

def do_ranking(leave_one_out: false, threads: 0)
  get_seed_leave_one_out() if leave_one_out
  seed_indexes = get_seed_indexes
  seed_groups = @seeds.to_a # Array conversion needed for parallelization
  ranked_lists = Parallel.map(seed_groups, in_processes: threads) do |seed_name, seed|
    # The code in this block CANNOT modify nothing outside
    if leave_one_out and @reference_nodes[seed_name].length <= 1
       rank_list = get_individual_rank(seed,@reference_nodes[seed_name][0])
    else
       rank_list = rank_by_seed(seed_indexes, seed) # Production mode
    end
    [seed_name, rank_list] 
  end
  ranked_lists.each do |seed_name, rank_list| # Transfer resuls to hash
    @ranking[seed_name] = rank_list
  end
end

#get_individual_absolute_rank(values_list, ref_value) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 184

def get_individual_absolute_rank(values_list,ref_value)
  ref_pos = nil
  values_list = values_list.sort.reverse.uniq
  values_list.each_with_index do |value,pos|
    if value == ref_value
      ref_pos = pos+1
      break
    end
  end
  return ref_pos
end

#get_individual_rank(seed_genes, node_of_interest) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 155

def get_individual_rank(seed_genes, node_of_interest)
  genes_pos = get_nodes_indexes(seed_genes)
  node_of_interest_pos = @nodes.find_index(node_of_interest)
  ordered_gene_score = []

  if !genes_pos.empty? && !node_of_interest_pos.nil?

    subsets_gen_values = @matrix[genes_pos,true]
    integrated_gen_values = subsets_gen_values.sum(0)
    integrated_gen_values = 1.fdiv(genes_pos.length) * integrated_gen_values.inplace

    ref_value = integrated_gen_values[node_of_interest_pos]

    members_below_test = 0
    integrated_gen_values.each do |gen_value|
      members_below_test += 1 if gen_value >= ref_value
    end

    rank_percentage = members_below_test.fdiv(@nodes.length)
    rank = members_below_test
    rank_absolute = get_individual_absolute_rank(integrated_gen_values.to_a,ref_value)

    ordered_gene_score << [node_of_interest, ref_value, rank_percentage, rank, rank_absolute]
  end

  return ordered_gene_score

end

#get_nodes_indexes(nodes) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 231

def get_nodes_indexes(nodes)
  node_indxs = []
  nodes.each do |node|
    index_node = @nodes.find_index(node)
    node_indxs << index_node if !index_node.nil?
  end
  return node_indxs
end

#get_position_for_items_with_same_score(pos, val, prev_val, gen_list, n_elements, ordered_gene_score) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 122

def get_position_for_items_with_same_score(pos, val, prev_val, gen_list, n_elements, ordered_gene_score)
    members_behind = 0
    if !prev_val.nil?
      if prev_val < val
        members_behind = pos
      else 
        members_behind = n_elements - ordered_gene_score.last[3]
      end
    end
    return members_behind
end

#get_reference_ranks ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 196

def get_reference_ranks
  filtered_ranked_genes = {}
  
  @ranking.each do |seed_name, ranking|
    next if @reference_nodes[seed_name].nil? or ranking.empty?

    ranking = array2hash(ranking,0,(1..ranking[0].length))
    references = @reference_nodes[seed_name]
    filtered_ranked_genes[seed_name] = []

    references.each do |reference|
      rank = ranking[reference]
      if !rank.nil?
        filtered_ranked_genes[seed_name] << [reference] + rank
      end
    end
    filtered_ranked_genes[seed_name].sort_by!{|rank| -rank[1]}
  end
  return filtered_ranked_genes
end

#get_seed_indexes ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 240

def get_seed_indexes
  indexes = {}
  @seeds.values.flatten.each do |node|
    if !indexes.include?(node)
      indx = @nodes.index(node)
      indexes[node] = indx if !indx.nil?
    end
  end
  return indexes
end

#get_seed_leave_one_out ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 67

def get_seed_leave_one_out()
  new_seeds = {}
  genes2predict = {}
  all_genes = @seeds.values.flatten.uniq
  @seeds.each do |seed_name, seeds| 
    group_number = seeds.length - 1
    one_out_seeds = seeds.combination(group_number).to_a

    one_out_seeds.each_with_index do |one_out_seed, indx|
      seed_name_one_out = seed_name.to_s + "_iteration_" + indx.to_s
      new_seeds[seed_name_one_out] = one_out_seed
      genes2predict[seed_name_one_out] = seeds - one_out_seed
      genes2predict[seed_name_one_out] += @reference_nodes[seed_name] if !@reference_nodes[seed_name].nil?
      genes2predict[seed_name_one_out].uniq!
    end
  end
  @seeds = new_seeds
  @reference_nodes = genes2predict
end

#get_top(top_n) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 223

def get_top(top_n)
	top_ranked_genes = {}
	@ranking.each do |seed_name, ranking|
      top_ranked_genes[seed_name] = ranking[0..top_n-1] if !ranking.nil?
	end
	return top_ranked_genes
end

#load_node_groups_from_file(file, sep: ',') ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 34

def load_node_groups_from_file(file, sep: ',')
  group_nodes = {}
  File.open(file).each do |line|
    set_name, nodes = line.chomp.split("\t")
    group_nodes[set_name] = nodes.split(sep)
  end
  return group_nodes
end

#load_nodes_by_group(node_groups, sep: ',') ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 25

def load_nodes_by_group(node_groups, sep: ',')
  if File.exist?(node_groups) 
    group_nodes = load_node_groups_from_file(node_groups, sep: sep)
  else
    group_nodes = {"seed_genes" => node_groups.split(sep)}
  end
  return group_nodes
end

#load_nodes_from_file(file) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 43

def load_nodes_from_file(file)
  File.open(file).each do |line|
    @nodes << line.chomp!
  end
end

#load_references(node_groups, sep: ',') ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 21

def load_references(node_groups, sep: ',')
  @reference_nodes = load_nodes_by_group(node_groups, sep: sep)
end

#load_seeds(node_groups, sep: ',') ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 17

def load_seeds(node_groups, sep: ',')
  @seeds = load_nodes_by_group(node_groups, sep: sep)
end

#rank_by_seed(seed_indexes, seeds) ⇒ Object 



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# File 'lib/NetAnalyzer/ranker.rb', line 87

def rank_by_seed(seed_indexes, seeds)
  ordered_gene_score = []
  genes_pos = seeds.map{|s| seed_indexes[s]}.compact
  number_of_seed_genes = genes_pos.length
  number_of_all_nodes = @nodes.length
  
  if number_of_seed_genes > 0
    subsets_gen_values = @matrix[genes_pos,true]
    integrated_gen_values = subsets_gen_values.sum(0)
    gen_list = 1.fdiv(number_of_seed_genes) * integrated_gen_values.inplace

    ordered_indexes = gen_list.sort_index # from smallest to largest
    
    last_val = nil
    n_elements = ordered_indexes.shape.first 
    n_elements.times do |pos|
      order_index = ordered_indexes[pos]    
      val = gen_list[order_index]
      node_name = @nodes[order_index]

      rank = get_position_for_items_with_same_score(pos, val, last_val, gen_list, n_elements, ordered_gene_score) # number of items behind
      rank = n_elements - rank # number of nodes below or equal
      rank_percentage = rank.fdiv(number_of_all_nodes)

      ordered_gene_score << [node_name, val, rank_percentage, rank]
      last_val = val
    end

    ordered_gene_score = ordered_gene_score.reverse # from largest to smallest
    ordered_gene_score = add_absolute_rank_column(ordered_gene_score)
  end
  
  return ordered_gene_score
end