rbbt-dm 1.1.44 → 1.1.49

checksums.yaml

@@ -1,7 +1,7 @@
 ---
-SHA1:
-  metadata.gz: fa73301479755273960bc84aec02ba3684d834ba
-  data.tar.gz: 5ea346bea9926dda33f3ccdb78651f5987abfb96
+SHA256:
+  metadata.gz: 73f692fa2323508c640c594a056975f7bd24659aaffe8e9c4fb5e1c19d5b4ee9
+  data.tar.gz: 9cc5cb88059630f1c65e6e2c6e9b9af5e1766aa97cc1192f088ee7043ee2cbef
 SHA512:
-  metadata.gz: f7f3774226a153552bf323ed058b21f405767810dce814166b605a87a6c7473ec5b38a4a56df82ba553c7f5d1521e2c04c401ae7a2b4df00281bf3d9d4ddc5dd
-  data.tar.gz: c48a92abf268fe4acf1a7d405df8e93446fff00a7ccdbca16b4e0e1ffae8607a40eb67f2495e1908dc34dba2ba61d6079c9b2849078712786036d95f06531ca3
+  metadata.gz: bab237c5d577abab5e4fed7f4567f15a95c20faa64dfbc3ba58dfb4054dc715093c2685e9166ce0df91148a3de0ea60aba1ea3de20a40120eb563806f15dd5a2
+  data.tar.gz: 20fe2789e521288b50ff070b5f4ad930115ffcc782fbb656048a601f17e8f7408cbdc14181023e3430194855e40fd3dee8fbea2cb7d28981296ceafa10c6abc7

data/lib/rbbt/matrix.rb

@@ -176,6 +176,26 @@ class RbbtMatrix
     matrix
   end
 
+  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
   def to_barcode_ruby(factor = 2)
     name = data_file =~ /:>/ ? File.basename(data_file) : data_file
 

data/lib/rbbt/matrix/barcode.rb

@@ -38,7 +38,7 @@ rbbt.GE.barcode.mode(#{ R.ruby2R self.data_file }, #{ R.ruby2R outfile }, #{ R.r
           end
         end
         key = key.first if Array === key
-      [key, bars]
+        [key, bars]
       end
     end
 

data/lib/rbbt/ml_task.rb

@@ -0,0 +1,7 @@
+class MLTask
+  def initialize
+  end
+
+  def pre_process
+  end
+end

data/lib/rbbt/vector/model.rb

@@ -4,6 +4,20 @@ class VectorModel
   attr_accessor :directory, :model_file, :extract_features, :train_model, :eval_model
   attr_accessor :features, :labels
 
+  def self.R_run(model_file, features, labels, code)
+    TmpFile.with_file do |feature_file|
+      Open.write(feature_file, features.collect{|feats| feats * "\t"} * "\n")
+      Open.write(feature_file + '.class', labels * "\n")
+
+      R.run <<-EOF
+features = read.table("#{ feature_file }", sep ="\\t", stringsAsFactors=FALSE);
+labels = scan("#{ feature_file }.class");
+features = cbind(features, class = labels);
+#{code}
+      EOF
+    end
+  end
+
   def self.R_train(model_file, features, labels, code)
     TmpFile.with_file do |feature_file|
       Open.write(feature_file, features.collect{|feats| feats * "\t"} * "\n")
@@ -57,6 +71,11 @@ cat(paste(label, sep="\\n"));
     @labels = []
   end
 
+  def clear
+    @features = []
+    @labels = []
+  end
+
   def add(element, label = nil)
     @features << extract_features.call(element)
     @labels << label unless label.nil?
@@ -67,16 +86,20 @@ cat(paste(label, sep="\\n"));
     when Proc === train_model
       train_model.call(@model_file, @features, @labels)
     when String === train_model
-      SVMModel.R_train(@model_file,  @features, @labels, train_model)
+      VectorModel.R_train(@model_file,  @features, @labels, train_model)
     end
   end
 
+  def run(code)
+    VectorModel.R_run(@model_file,  @features, @labels, code)
+  end
+
   def eval(element)
     case 
     when Proc === eval_model
       eval_model.call(@model_file, extract_features.call(element), false)
     when String === eval_model
-      SVMModel.R_eval(@model_file,  extract_features.call(element), false, eval_model)
+      VectorModel.R_eval(@model_file,  extract_features.call(element), false, eval_model)
     end
   end
 
@@ -119,4 +142,53 @@ cat(paste(label, sep="\\n"));
 
     acc
   end
+
+  def cross_validation(folds = 10)
+
+    res = TSV.setup({}, "Fold~TP,TN,FP,FN,P,R,F1#:type=:list")
+
+    feature_folds = Misc.divide(@features, folds)
+    labels_folds = Misc.divide(@labels, folds)
+
+    folds.times do |fix|
+
+      test_set = feature_folds[fix]
+      train_set = feature_folds.values_at(*((0..9).to_a - [fix])).inject([]){|acc,e| acc += e; acc}
+
+      test_labels = labels_folds[fix]
+      train_labels = labels_folds.values_at(*((0..9).to_a - [fix])).flatten
+
+      tp, fp, tn, fn, pr, re, f1 = [0, 0, 0, 0, nil, nil, nil]
+
+      @features = train_set
+      @labels = train_labels
+      self.train
+      predictions = self.eval_list test_set, false
+
+      test_labels.zip(predictions).each do |gs,pred|
+        gs = gs.to_i
+        pred = pred > 0.5 ? 1 : 0
+        tp += 1 if gs == pred && gs == 1
+        tn += 1 if gs == pred && gs == 0
+        fp += 1 if gs == 0 && pred == 1
+        fn += 1 if gs == 1 && pred == 0
+      end
+
+      p = tp + fn
+      pp = tp + fp
+
+      pr = tp.to_f / pp
+      re = tp.to_f / p
+
+      f1 = (2.0 * tp) / (2.0 * tp + fp + fn) 
+
+      Misc.fingerprint([tp,tn,fp,fn,pr,re,f1])
+
+      Log.debug "CV Fold #{fix} P:#{"%.3f" % pr} R:#{"%.3f" % re} F1:#{"%.3f" % f1}"
+
+      res[fix] = [tp,tn,fp,fn,pr,re,f1]
+    end
+
+    res
+  end
 end

data/lib/rbbt/vector/model/svm.rb

@@ -9,7 +9,7 @@ class SVMModel < VectorModel
 
     @train_model =<<-EOF
 library(e1071);
-model = svm(class ~ ., data = features);
+model = svm(class ~ ., data = features, scale=c(0));
     EOF
  
     @eval_model =<<-EOF

data/test/rbbt/matrix/test_barcode.rb

@@ -11,7 +11,7 @@ class TestBarcode < Test::Unit::TestCase
     data["G4"] = [6,6,1,1,1,1]
 
     TmpFile.with_file(data.to_s) do |file|
-      m = Matrix.new file
+      m = RbbtMatrix.new file
       m.barcode(file+'.barcode')
       tsv =  TSV.open(file+'.barcode')
       assert tsv["G2"] = [0,1,0,1,0,1]

data/test/rbbt/test_ml_task.rb

@@ -0,0 +1,12 @@
+require File.join(File.expand_path(File.dirname(__FILE__)), '..', 'test_helper.rb')
+require 'rbbt/ml_task'
+
+class TestMLTask < Test::Unit::TestCase
+  def test_MLTask
+
+    triage = MLTask.new
+    ml_task.pre_process do
+    end
+  end
+end
+

data/test/rbbt/vector/test_model.rb

@@ -34,7 +34,7 @@ class TestVectorModel < Test::Unit::TestCase
 features = read.table("#{ feature_file }", sep ="\\t", stringsAsFactors=FALSE);
 labels = scan("#{ feature_file }.class", what=numeric());
 features = cbind(features, class = labels);
-library(e1071)
+rbbt.require('e1071')
 model = svm(class ~ ., data = features) 
 save(model, file="#{ model_file }");
           EOF

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: rbbt-dm
 version: !ruby/object:Gem::Version
-  version: 1.1.44
+  version: 1.1.49
 platform: ruby
 authors:
 - Miguel Vazquez
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2018-12-02 00:00:00.000000000 Z
+date: 2020-08-14 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: rbbt-util
@@ -39,7 +39,7 @@ dependencies:
       - !ruby/object:Gem::Version
         version: '0'
 - !ruby/object:Gem::Dependency
-  name: priority_queue_cxx
+  name: priority_queue_cxx17
   requirement: !ruby/object:Gem::Requirement
     requirements:
     - - ">="
@@ -95,6 +95,7 @@ files:
 - lib/rbbt/matrix/barcode.rb
 - lib/rbbt/matrix/differential.rb
 - lib/rbbt/matrix/knowledge_base.rb
+- lib/rbbt/ml_task.rb
 - lib/rbbt/network/paths.rb
 - lib/rbbt/plots/bar.rb
 - lib/rbbt/plots/heatmap.rb
@@ -115,6 +116,7 @@ files:
 - test/rbbt/statistics/test_fisher.rb
 - test/rbbt/statistics/test_hypergeometric.rb
 - test/rbbt/statistics/test_random_walk.rb
+- test/rbbt/test_ml_task.rb
 - test/rbbt/test_stan.rb
 - test/rbbt/vector/model/test_svm.rb
 - test/rbbt/vector/test_model.rb
@@ -137,8 +139,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
     - !ruby/object:Gem::Version
       version: '0'
 requirements: []
-rubyforge_project: 
-rubygems_version: 2.6.13
+rubygems_version: 3.0.6
 signing_key: 
 specification_version: 4
 summary: Data-mining and statistics
@@ -149,6 +150,7 @@ test_files:
 - test/rbbt/statistics/test_fisher.rb
 - test/rbbt/statistics/test_fdr.rb
 - test/rbbt/statistics/test_hypergeometric.rb
+- test/rbbt/test_ml_task.rb
 - test/rbbt/vector/test_model.rb
 - test/rbbt/vector/model/test_svm.rb
 - test/rbbt/test_stan.rb