Class: RbbtMatrix

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

Class Attribute Summary collapse

Instance Attribute Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(data_file, labels = nil, value_type = nil, format = nil, organism = nil, identifiers = nil) ⇒ RbbtMatrix

Returns a new instance of RbbtMatrix.



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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

#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

#labels ⇒ Object

Returns the value of attribute labels.



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

def labels
  @labels
end

#organism ⇒ Object

Returns the value of attribute organism.



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

def organism
  @organism
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

Instance Method Details

#activity_cluster(outfile, clusters = 2) ⇒ Object 



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

def activity_cluster(outfile, clusters = 2)

  clusters = Array === clusters ? clusters : (2..clusters).to_a

  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 key_field}, #{R.ruby2R clusters})
  EOF

  R.run(cmd)
end

#all_fields ⇒ Object 



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

def all_fields
  @all_fields ||= TSV.parse_header(@data_file).all_fields
end

#barcode(outfile, 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 109

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 => RbbtMatrix.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

#fields ⇒ Object 



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

def fields
  all_fields[1..-1]
end

#key_field ⇒ Object 



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

def key_field
  all_fields.first
end

#samples ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 44

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

#subsets ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 52

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 48

def subsets=(subsets)
  @subsets = subsets
end

#to_activity(clusters = 2) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 223

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

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

  file = Persist.persist(data_file, :tsv, :prefix => "Activity #{clusters.inspect}", :check => [data_file],  :dir => RbbtMatrix.matrix_dir.barcode, :no_load => true) do |filename|
    activity_cluster(filename, clusters)
  end
  subsets = self.subsets
  matrix = RbbtMatrix.new file, labels, value_type, key_field, organism
  matrix.subsets = subsets
  matrix
end

#to_average(identifiers = nil) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 143

def to_average(identifiers = nil)
  name = data_file =~ /:>/ ? File.basename(data_file) : data_file

  file = Persist.persist(data_file, :tsv, :prefix => "Average", :check => [data_file],  :dir => RbbtMatrix.matrix_dir.values, :no_load => true) do

    data = data_file.tsv(:cast => :to_f, :type => :double)

    data.to_list{|v| v.length > 1 ? Misc.mean(v) : v }
  end
  subsets = self.subsets
  matrix = RbbtMatrix.new file, labels, value_type, key_field, organism
  matrix.subsets = subsets
  matrix
end

#to_barcode(factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 211

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

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

#to_barcode_ruby(factor = 2) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 199

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

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

#to_gene(identifiers = nil) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 158

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", :check => [data_file], :dir => RbbtMatrix.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 = RbbtMatrix.new file, labels, value_type, "Ensembl Gene ID", organism
  matrix.subsets = subsets
  matrix
end

#to_name(identifiers = nil) ⇒ Object 



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# File 'lib/rbbt/matrix.rb', line 179

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

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

  file = Persist.persist(data_file, :tsv, :prefix => "Name", :check => [data_file], :dir => RbbtMatrix.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("Associated Gene Name", :identifiers => identifiers.reverse) do |v|
      Misc.mean(v.compact)
    end
  end
  subsets = self.subsets
  matrix = RbbtMatrix.new file, labels, value_type, "Associated Gene Name", organism
  matrix.subsets = subsets
  matrix
end

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



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# File 'lib/rbbt/matrix.rb', line 237

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