From f7e87b45f15083e5fcdea64821f06ed93ece4c4e Mon Sep 17 00:00:00 2001
From: Christoph Helma <helma@in-silico.ch>
Date: Tue, 7 Jun 2016 18:07:28 +0200
Subject: (repeated)crossvalidation plots

---
 lib/crossvalidation.rb       | 35 +++++++++++++++++++++++++++++++++++
 lib/nanoparticle.rb          |  1 -
 lib/regression.rb            |  2 +-
 lib/validation-statistics.rb |  6 +++---
 4 files changed, 39 insertions(+), 5 deletions(-)

(limited to 'lib')

diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index 15e25a5..7aae3d2 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -71,6 +71,8 @@ module OpenTox
 
     class RepeatedCrossValidation < Validation
       field :crossvalidation_ids, type: Array, default: []
+      field :correlation_plot_id, type: BSON::ObjectId
+
       def self.create model, folds=10, repeats=3
         repeated_cross_validation = self.new
         repeats.times do |n|
@@ -80,9 +82,42 @@ module OpenTox
         repeated_cross_validation.save
         repeated_cross_validation
       end
+
       def crossvalidations
         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["value"]
+              y << p["measurements"].median
+            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}',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}"
+          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/nanoparticle.rb b/lib/nanoparticle.rb
index c1bf1b5..d6261ee 100644
--- a/lib/nanoparticle.rb
+++ b/lib/nanoparticle.rb
@@ -10,7 +10,6 @@ module OpenTox
     attr_accessor :scaled_values
  
     def physchem_neighbors min_sim: 0.9, dataset_id:, prediction_feature_id:, relevant_features:
-      p name
       dataset = Dataset.find(dataset_id)
       #relevant_features = {}
       measurements = []
diff --git a/lib/regression.rb b/lib/regression.rb
index c4c83d2..51317ac 100644
--- a/lib/regression.rb
+++ b/lib/regression.rb
@@ -122,7 +122,7 @@ module OpenTox
           pc_ids.compact!
           prediction = r_model_prediction method, data_frame, pc_ids.collect{|i| "\"#{i}\""}, weights, query_descriptors
           if prediction.nil?
-            prediction = local_weighted_average substance, neighbors
+            prediction = local_weighted_average(substance: substance, neighbors: neighbors)
             prediction[:warning] = "Could not create local PLS model. Using weighted average of similar substances."
           end
           p prediction
diff --git a/lib/validation-statistics.rb b/lib/validation-statistics.rb
index 6b252b1..9aa9cff 100644
--- a/lib/validation-statistics.rb
+++ b/lib/validation-statistics.rb
@@ -136,9 +136,9 @@ module OpenTox
         }
       end
 
-      def correlation_plot 
+      def correlation_plot format: "png"
         unless correlation_plot_id
-          tmpfile = "/tmp/#{id.to_s}_correlation.pdf"
+          tmpfile = "/tmp/#{id.to_s}_correlation.#{format}"
           x = []
           y = []
           feature = Feature.find(predictions.first.last["prediction_feature_id"])
@@ -155,7 +155,7 @@ module OpenTox
           R.eval "image = qplot(prediction,measurement,main='#{title}',xlab='Prediction',ylab='Measurement',asp=1,xlim=range, ylim=range)"
           R.eval "image = image + geom_abline(intercept=0, slope=1)"
           R.eval "ggsave(file='#{tmpfile}', plot=image)"
-          file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{id.to_s}_correlation_plot.png")
+          file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{id.to_s}_correlation_plot.#{format}")
           plot_id = $gridfs.insert_one(file)
           update(:correlation_plot_id => plot_id)
         end
-- 
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