From 0813b486bc6b107a6970bae7cfb4ca262d7c5697 Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Mon, 12 Dec 2016 13:02:29 +0100
Subject: 5 repeated cvs for enm

---
 lib/crossvalidation.rb | 33 ---------------------------------
 lib/model.rb           |  4 ++--
 2 files changed, 2 insertions(+), 35 deletions(-)

diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index 5a05955..bcb3ccf 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -96,39 +96,6 @@ module OpenTox
         crossvalidation_ids.collect{|id| CrossValidation.find(id)}
       end
 
-      def correlation_plot format: "png"
-        #unless correlation_plot_id
-          feature = Feature.find(crossvalidations.first.model.prediction_feature)
-          title = feature.name
-          title += "[#{feature.unit}]" if feature.unit and !feature.unit.blank?
-          tmpfile = "/tmp/#{id.to_s}_correlation.#{format}"
-          images = []
-          crossvalidations.each_with_index do |cv,i|
-            x = []
-            y = []
-            cv.predictions.each do |sid,p|
-              x << p["measurements"].median
-              y << p["value"]
-            end
-            R.assign "measurement", x
-            R.assign "prediction", y
-            R.eval "all = c(measurement,prediction)"
-            R.eval "range = c(min(all), max(all))"
-            R.eval "image#{i} = qplot(prediction,measurement,main='#{title} #{i}',xlab='Prediction',ylab='Measurement',asp=1,xlim=range, ylim=range)"
-            R.eval "image#{i} = image#{i} + geom_abline(intercept=0, slope=1)"
-            images << "image#{i}"
-            
-            R.eval "ggsave(file='/home/ist/lazar/test/tmp#{i}.pdf', plot=image#{i})"
-          end
-          R.eval "pdf('#{tmpfile}')"
-          R.eval "grid.arrange(#{images.join ","},ncol=#{images.size})"
-          R.eval "dev.off()"
-          file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{id.to_s}_correlation_plot.#{format}")
-          correlation_plot_id = $gridfs.insert_one(file)
-          update(:correlation_plot_id => correlation_plot_id)
-        #end
-      $gridfs.find_one(_id: correlation_plot_id).data
-      end
     end
   end
 
diff --git a/lib/model.rb b/lib/model.rb
index 5a1c191..9c4a93f 100644
--- a/lib/model.rb
+++ b/lib/model.rb
@@ -395,7 +395,7 @@ module OpenTox
         
         # find/import training_dataset
         training_dataset ||= Dataset.where(:name => "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first
-        unless training_dataset # try to import from json dump
+        unless training_dataset # try to import 
           Import::Enanomapper.import
           training_dataset = Dataset.where(name: "Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles").first
           bad_request_error "Cannot import 'Protein Corona Fingerprinting Predicts the Cellular Interaction of Gold and Silver Nanoparticles' dataset" unless training_dataset
@@ -410,7 +410,7 @@ module OpenTox
         )
         model = LazarRegression.create prediction_feature: prediction_feature, training_dataset: training_dataset, algorithms: algorithms
         model_validation[:model_id] = model.id
-        repeated_cv = OpenTox::Validation::RepeatedCrossValidation.create model
+        repeated_cv = OpenTox::Validation::RepeatedCrossValidation.create model, 10, 5
         model_validation[:repeated_crossvalidation_id] = repeated_cv.id
         model_validation.save
         model_validation
-- 
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