1 files changed, 0 insertions, 61 deletions
diff --git a/loael-variability.rb b/loael-variability.rb
deleted file mode 100644
index 5a8f1ca..0000000
--- a/loael-variability.rb
+++ /dev/null
@@ -1,61 +0,0 @@
-require_relative '../../lazar/lib/lazar'
-include OpenTox
-#$mongo.database.drop
-#$gridfs = $mongo.database.fs # recreate GridFS indexes
-# compare duplicates within datasets
-#old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mmol_corrected_smiles.csv")
-old = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL_mg_corrected_smiles_mmol.csv")
-#new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL.csv")
-new = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","swissRat_chron_LOAEL_mmol.csv")
-#combined = Dataset.from_csv_file File.join(File.dirname(__FILE__),"regression","LOAEL-rat-combined.csv")
-
-compound_vector = []
-value_vector = []
-dataset_vector = []
-
-vars = []
-
-[old, new].each do |dataset|
-  vars << []
-  #vars[dataset.name] = []
-  p dataset.name
-  p dataset.compounds.size
-  p dataset.duplicates(dataset.features.first).size
-  dataset.duplicates.each do |cid,values|
-    R.assign "values", values
-    var = R.eval("var(-log(values))").to_f
-    vars.last << var
-    #smi = Compound.find(cid).smiles
-    smi = cid.to_s
-    values.each do |val|
-      compound_vector << smi
-      value_vector << - Math.log(val)
-      dataset_vector << dataset.name
-    end
-    #vars << { :var => var, :values => values, :smiles => smi }
-  end
-  #vars.sort!{|a,b| a[:var] <=> b[:var]}
-  #vars.each do |dup|
-    #dup[:values].each do |v|
-      #compound_vector << dup[:smiles]
-      #value_vector << v
-    #end
-  #end
-end
-p vars
-# TODO statistical test for variances
-R.assign "vars1", vars[0]
-R.assign "vars2", vars[1]
-print "p-value: #{R.eval("t.test(vars1,vars2)$p.value").to_f}"
-
-R.assign "smi", compound_vector
-R.assign "values", value_vector
-R.assign "dataset", dataset_vector
-R.eval "df <- data.frame(factor(smi),values,factor(dataset))"
-R.eval "df$smi <- reorder(df$factor.smi,df$values)"
-R.eval "img <- ggplot(df, aes(smi,values,ymin = min(values), ymax=max(values),color=dataset))"
-R.eval "img <- img + ylab('-log(LOAEL mg/kg_bw/day)') + xlab('Compound') + theme(axis.text.x = element_blank())"
-R.eval "img <- img + geom_point()"
-#R.eval "img <- img + scale_x_discrete(breaks=NULL) + geom_point() + coord_flip()"# + xlab('-log(LOAEL)'), ylab('Compound')"
-#R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael_variance.svg', plot=img)"
-R.eval "ggsave(file='/home/ch/opentox/lazar-nestec-data/loael-variance.svg', plot=img,width=12, height=8)"