Class: Matrix

Inherits:
Object
  • Object
show all
Extended by:
Resource
Defined in:
lib/rbbt/matrix.rb,
lib/rbbt/matrix/barcode.rb,
lib/rbbt/matrix/differential.rb,
lib/rbbt/expression_old/matrix.rb

Constant Summary collapse

MATRIX_DIR = 
Matrix.root.find

Class Attribute Summary collapse

Instance Attribute Summary collapse

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data, identifiers, labels = nil, key_field = nil, organism = nil, log2 = false, channel = false) ⇒ Matrix

Returns a new instance of Matrix.



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# File 'lib/rbbt/matrix.rb', line 14

def initialize(data_file, labels = nil, value_type = nil, format = nil, organism=nil, identifiers=nil)
  @data_file = data_file
  @labels = labels 
  @value_type = value_type || 'count'
  @format = format
  _header = nil
  @format ||=  begin
                 _header ||= TSV.parse_header(@data_file)
                 _header.key_field || "ID"
               end
  @organism = organism 
  @organism ||=  begin
                   _header ||= TSV.parse_header(@data_file)
                   _header.namespace || Organism.default_code("Hsa")
                 end
  @identifiers = identifiers 
end

Class Attribute Details

.matrix_dir ⇒ Object

Returns the value of attribute matrix_dir.



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# File 'lib/rbbt/matrix.rb', line 7

def matrix_dir
  @matrix_dir
end

Instance Attribute Details

#channel ⇒ Object

Returns the value of attribute channel.



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# File 'lib/rbbt/expression_old/matrix.rb', line 28

def channel
  @channel
end

#data ⇒ Object

Returns the value of attribute data.



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# File 'lib/rbbt/expression_old/matrix.rb', line 28

def data
  @data
end

#data_file ⇒ Object

Returns the value of attribute data_file.



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# File 'lib/rbbt/matrix.rb', line 13

def data_file
  @data_file
end

#format ⇒ Object

Returns the value of attribute format.



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# File 'lib/rbbt/matrix.rb', line 13

def format
  @format
end

#identifiers ⇒ Object

Returns the value of attribute identifiers.



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# File 'lib/rbbt/matrix.rb', line 13

def identifiers
  @identifiers
end

#key_field ⇒ Object

Returns the value of attribute key_field.



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# File 'lib/rbbt/expression_old/matrix.rb', line 28

def key_field
  @key_field
end

#labels ⇒ Object

Returns the value of attribute labels.



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# File 'lib/rbbt/matrix.rb', line 13

def labels
  @labels
end

#log2 ⇒ Object

Returns the value of attribute log2.



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# File 'lib/rbbt/expression_old/matrix.rb', line 28

def log2
  @log2
end

#organism ⇒ Object

Returns the value of attribute organism.



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# File 'lib/rbbt/matrix.rb', line 13

def organism
  @organism
end

#samples ⇒ Object

Returns the value of attribute samples.



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# File 'lib/rbbt/matrix.rb', line 32

def samples
  @samples ||= TSV.parse_header(@data_file).fields
end

#value_type ⇒ Object

Returns the value of attribute value_type.



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# File 'lib/rbbt/matrix.rb', line 13

def value_type
  @value_type
end

Class Method Details

.geo_matrix_for(gds, key_field = nil, organism = nil) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 15

def self.geo_matrix_for(gds, key_field = nil, organism = nil)
  data    = GEO[gds].values.produce.find
  samples = GEO[gds].samples.produce.find

  dataset_info = GEO[gds]['info.yaml'].produce.yaml
  platform     = dataset_info[:platform]
  identifiers  = GEO[platform].codes.produce.find

  log2         = ["count"].include? dataset_info[:value_type]

  Matrix.new(data, identifiers, samples, key_field, organism, log2)
end

Instance Method Details

#activity_cluster(outfile, factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix/barcode.rb', line 48

def activity_cluster(outfile, factor = 2)

  FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
  cmd =<<-EOF
source('#{Rbbt.share.R['barcode.R'].find}')
rbbt.GE.activity_cluster(#{ R.ruby2R self.data_file }, #{ R.ruby2R outfile }, #{R.ruby2R value_type})
  EOF

  R.run(cmd)
end

#average_label(value, field = nil) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 69

def average_label(value, field = nil)
  samples = find_samples(value, field)
  samples = remove_missing(samples)
  average_samples(samples)
end

#average_samples(samples) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 51

def average_samples(samples)
  path = Persist.persistence_path(matrix_file, {:dir => File.join(Matrix::MATRIX_DIR, 'averaged_samples')}, {:samples => samples})
  Persist.persist(data, :tsv, :file => path, :no_load => true, :check => [matrix_file]) do
    Expression.average_samples(matrix_file, samples)
  end
  path
end

#barcode(path = nil, factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix/barcode.rb', line 4

def barcode(outfile, factor = 2)

  FileUtils.mkdir_p File.dirname(outfile) unless outfile.nil? or File.exists? File.dirname(outfile)
  cmd =<<-EOF
source('#{Rbbt.share.R['barcode.R'].find}')
rbbt.GE.barcode.mode(#{ R.ruby2R self.data_file }, #{ R.ruby2R outfile }, #{ R.ruby2R factor })
  EOF

  R.run(cmd)
end

#barcode_ruby(outfile, factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix/barcode.rb', line 15

def barcode_ruby(outfile, factor = 2)
  parser = TSV::Parser.new self.data_file
  dumper = TSV::Dumper.new parser.options.merge(:type => :list, :cast => :to_i)
  dumper.init

  TSV.traverse parser, :into => dumper, :bar => "Barcoding #{self.data_file}" do |key,values|
    clean_values = values.flatten.compact.collect{|v| v.to_f}
    modes = R.eval("rbbt.get.modes(#{R.ruby2R clean_values})$modes")
    mode = Array === modes ? modes.first : modes
    mode_values = clean_values.select{|v| v.to_f <= mode}
    mode_values.concat mode_values.collect{|v| v+mode}
    sd = Misc.sd mode_values 
    if sd.nil?
      [key, [nil] * values.length]
    else
      threshold = mode + sd
      bars = if Array === values.compact.first 
        values.collect do |v|
          Misc.mean(v.compact.collect{|v| v.to_f}) > threshold ? 1 : 0
        end
      else
        values.collect do |v|
          v.to_f > threshold ? 1 : 0
        end
      end
      key = key.first if Array === key
    [key, bars]
    end
  end

  Misc.sensiblewrite(outfile, dumper.stream)
end

#comparison(main, contrast, subsets = nil) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 97

def comparison(main, contrast, subsets = nil)
  subsets ||= self.subsets

  if main.index "="
    main_factor, main_value = main.split "=" 
    raise ParameterException, "Main selection not understood" if subsets[main_factor].nil? or subsets[main_factor][main_value].nil?
    value = subsets[main_factor][main_value]
    main_samples = String === value ? value.split(',') : value
  else
    main_samples = main.split(/[|,\n]/)
  end

  if contrast
    if contrast.index "="
      contrast_factor, contrast_value = contrast.split "=" 
      raise ParameterException, "Contrast selection not understood" if subsets[contrast_factor].nil? or subsets[contrast_factor][contrast_value].nil?
      value = subsets[contrast_factor][contrast_value]
      contrast_samples = String === value ? value.split(',') : value
    else
      contrast_samples = contrast.split(/[|,\n]/)
    end
  else
    if subsets and main_factor
      contrast_samples = subsets[main_factor].values.flatten.collect{|s| s.split ',' }.flatten.uniq - main_samples
    else
      contrast_samples = samples - main_samples
    end
  end
  main_samples = main_samples.compact.reject{|m| m.empty? }.collect{|m| m.strip }
  contrast_samples = contrast_samples.compact.reject{|m| m.empty? }.collect{|m| m.strip }

  [main_samples, contrast_samples]
end

#differential(main, contrast, path = nil) ⇒ Object 



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# File 'lib/rbbt/matrix/differential.rb', line 4

def differential(main, contrast, path = nil)
  all_samples = self.samples
  if Array === main and Array === contrast
    main_samples, contrast_samples = main, contrast
  else
    main_samples, contrast_samples = comparison main, contrast
  end

  name = data_file =~ /:>/ ? File.basename(data_file) : data_file
  main_samples = main_samples & all_samples
  contrast_samples = contrast_samples & all_samples
  raise "No main samples found" if main_samples.empty?
  raise "No contrast samples found" if contrast_samples.empty?

  Persist.persist(name, :tsv, :persist => true, :file => path,
                  :other => {:main => main_samples, :contrast => contrast_samples}, 
                  :prefix => "Diff", :dir => Matrix.matrix_dir.differential, :no_load => true) do |file|

    raise if file.nil?

    case value_type
    when 'two_channel'
      log2 = true
      trend = false
      two_channel = true
    when nil, 'count', 'counts'
      log2 = true
      trend = false
      two_channel = false
    when 'fpkm'
      log2 = true
      trend = true
      two_channel = false
    when 'log2 ratio', 'transformed count'
      log2 = false
      trend = false
      two_channel = false
    else
      Log.warn "Unkown value_type: #{value_type}"
      log2 = true
      trend = false
      two_channel = false
    end

    file = file.find if Path === file
    FileUtils.mkdir_p File.dirname(file) unless file.nil? or File.exists? File.dirname(file)

    cmd = <<-EOS

source('#{Rbbt.share.R["MA.R"].find(:lib)}')

data = rbbt.dm.matrix.differential(#{ R.ruby2R data_file }, 
main = #{R.ruby2R(main_samples)}, 
contrast = #{R.ruby2R(contrast_samples)}, 
log2=#{ R.ruby2R log2 }, 
outfile = #{R.ruby2R file}, 
key.field = #{R.ruby2R format}, 
two.channel = #{R.ruby2R two_channel},
namespace = #{R.ruby2R organism},
eBayes.trend = #{R.ruby2R trend}
)
      EOS

      R.run(cmd, :monitor => true)
  end
end

#find_samples(value, field = nil) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 59

def find_samples(value, field = nil)
  labels.select(field){|k,v|
    Array === v ? v.flatten.include?(value) : v == value
  }.keys
end

#label_differences(main, contrast = nil, field = nil) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 92

def label_differences(main, contrast = nil, field = nil)
  all_samples = labels.keys
  main_samples = find_samples(main, field)
  if contrast
    contrast_samples = find_samples(contrast, field)
  else
    contrast_samples = all_samples - main_samples
  end

  main_samples = remove_missing(main_samples)
  contrast_samples = remove_missing(contrast_samples)

  sample_differences(main_samples, contrast_samples)
end

#matrix_file(path = nil) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 41

def matrix_file(path = nil)
  path ||= Persist.persistence_path(data, {:dir => Matrix::MATRIX_DIR}, {:identifiers => identifiers, :labels => labels, :key_field => key_field, :organism => organism})
  Persist.persist(data, :tsv, :file => path, :check => [data], :no_load => true) do
    matrix = Expression.load_matrix(data, identifiers, key_field, organism)
    matrix = matrix.select(:key => Organism.sanctioned_genes(organism).list) if matrix.key_field == "Ensembl Gene ID"
    matrix
  end
  path
end

#random_forest_importance(main, contrast = nil, field = nil, options = {}) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 125

def random_forest_importance(main, contrast = nil, field = nil, options = {})
  features = Misc.process_options options, :features
  features ||= []

  path = Persist.persistence_path(matrix_file, {:dir => File.join(Matrix::MATRIX_DIR, 'random_forest_importance')}, {:main => main, :contrast => contrast, :field => field, :features => features})
  Persist.persist(data, :tsv, :file => path, :no_load => false, :check => [matrix_file]) do
    all_samples = labels.keys
    main_samples = find_samples(main, field)
    if contrast
      contrast_samples = find_samples(contrast, field)
    else
      contrast_samples = all_samples - main_samples
    end


    main_samples     = remove_missing(main_samples)
    contrast_samples = remove_missing(contrast_samples)

    TmpFile.with_file do |result|
      R.run <<-EOF
library(randomForest);
orig = rbbt.tsv('#{matrix_file}');
main = c('#{main_samples * "', '"}')
contrast = c('#{contrast_samples * "', '"}')
features = c('#{features * "', '"}')

features = intersect(features, rownames(orig));
data = t(orig[features, c(main, contrast)])
data = cbind(data, Class = 0)
data[main, "Class"] = 1

rf = randomForest(factor(Class) ~ ., data, na.action = na.exclude)
rbbt.tsv.write(rf$importance, filename='#{ result }', key.field = '#{@key_field}')
      EOF

      TSV.open(result, :type => :single, :cast => :to_f)
    end
  end
end

#remove_missing(samples) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 65

def remove_missing(samples)
  @samples & samples
end

#sample_differences(main, contrast) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 84

def sample_differences(main, contrast)
  path = Persist.persistence_path(matrix_file, {:dir => File.join(Matrix::MATRIX_DIR, 'sample_differences')}, {:main => main, :contrast => contrast, :log2 => log2, :channel => channel})
  Persist.persist(data, :tsv, :file => path, :no_load => true, :check => [matrix_file]) do
    Expression.differential(matrix_file, main, contrast, log2, channel)
  end
  path
end

#signature_set(field, cast = nil) ⇒ Object 



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# File 'lib/rbbt/expression_old/matrix.rb', line 107

def signature_set(field, cast = nil)
  path = Persist.persistence_path(matrix_file, {:dir => File.join(Matrix::MATRIX_DIR, 'signature_set')}, {:field => field, :cast => cast})
  Persist.persist(data, :tsv, :file => path, :no_load => true, :check => [matrix_file]) do
    signatures = TSV.open(matrix_file, :fields => [], :type => :list, :cast => cast)
    labels.values.flatten.uniq.sort.each do |value|
      begin
        s = Signature.tsv_field(label_differences(value), field, cast)
        s.fields = [value]
        signatures.attach s
      rescue Exception
        Log.warn("Signature for #{ value } did not compute")
      end
    end
    signatures
  end
  path
end

#subsets ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 40

def subsets
  @subsets ||= begin
                 subsets = {}
                 case @labels
                 when Path
                   if @labels.exists?
                    labels = @labels.tsv
                    factors = labels.fields
                    labels.through do |sample,values|
                      factors.zip(values).each do |factor,value|
                        subsets[factor] ||= {}
                        subsets[factor][value] ||= []
                        subsets[factor][value] << sample
                      end
                    end
                   end

                 when TSV
                   factors = @labels.fields
                   @labels.through do |sample,values|
                     factors.zip(values).each do |factor,value|
                       subsets[factor] ||= {}
                       subsets[factor][value] ||= []
                       subsets[factor][value] << sample
                     end
                   end
                 when Hash
                   @labels.each do |factor,info|
                     subsets[factors] ||= {}
                     info.each do |value, samples|
                       subsets[factors][value] = case samples
                                                 when Array 
                                                   samples
                                                 when String
                                                   samples.split ','
                                                 else
                                                   raise "Format of samples not understood: #{Misc.finguerprint samples}"
                                                 end

                     end
                   end
                 end

                 clean_subsets = {}
                 subsets.each do |factor,values|
                   next if values.nil? or values.size < 2
                   values.each do |level,samples|
                     next if samples.nil? or samples.length < 2
                     clean_subsets[factor] ||= {}
                     clean_subsets[factor][level] = samples
                   end
                 end

                 clean_subsets
               end
end

#subsets=(subsets) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 36

def subsets=(subsets)
  @subsets = subsets
end

#to_activity(factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 177

def to_activity(factor = 2)
  require 'rbbt/tsv/change_id'

  name = data_file =~ /:>/ ? File.basename(data_file) : data_file

  file = Persist.persist(data_file, :tsv, :prefix => "Activity #{factor}", :dir => Matrix.matrix_dir.barcode, :no_load => true) do |filename|
    activity_cluster(filename, factor)
  end
  subsets = self.subsets
  matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
  matrix.subsets = subsets
  matrix
end

#to_barcode(factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 165

def to_barcode(factor = 2)
  name = data_file =~ /:>/ ? File.basename(data_file) : data_file

  file = Persist.persist(data_file, :tsv, :prefix => "Barcode R #{factor}", :dir => Matrix.matrix_dir.barcode, :no_load => true) do |filename|
    barcode(filename, factor)
  end
  subsets = self.subsets
  matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
  matrix.subsets = subsets
  matrix
end

#to_barcode_ruby(factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 153

def to_barcode_ruby(factor = 2)
  name = data_file =~ /:>/ ? File.basename(data_file) : data_file

  file = Persist.persist(data_file, :tsv, :prefix => "Barcode #{factor}", :dir => Matrix.matrix_dir.barcode, :no_load => true) do |filename|
    barcode_ruby(filename, factor)
  end
  subsets = self.subsets
  matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
  matrix.subsets = subsets
  matrix
end

#to_gene(identifiers = nil) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 132

def to_gene(identifiers = nil)
  require 'rbbt/tsv/change_id'

  name = data_file =~ /:>/ ? File.basename(data_file) : data_file

  file = Persist.persist(data_file, :tsv, :prefix => "Gene", :dir => Matrix.matrix_dir.values, :no_load => true) do

    data = data_file.tsv(:cast => :to_f)

    identifiers = [identifiers, @identifiers, data.identifiers, Organism.identifiers(organism)].flatten.compact.uniq

    data.change_key("Ensembl Gene ID", :identifiers => identifiers.reverse) do |v|
      Misc.mean(v.compact)
    end
  end
  subsets = self.subsets
  matrix = Matrix.new file, labels, value_type, "Ensembl Gene ID", organism
  matrix.subsets = subsets
  matrix
end

#tsv(to_gene = true, identifiers = nil) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 191

def tsv(to_gene=true, identifiers = nil)
  if to_gene and TSV.parse_header(self.data_file).key_field != "Ensembl Gene ID"
    file =  self.to_gene(identifiers).data_file
    file.tsv :persist => true, :persist_dir => Matrix.matrix_dir.persist, :type => :double, :merge => true
  else
    self.data_file.tsv :persist => true, :persist_dir => Matrix.matrix_dir.persist, :merge => true
  end
end