diff options
| author | Christoph Helma <helma@in-silico.ch> | 2015-08-27 20:28:25 +0200 |
|---|---|---|
| committer | Christoph Helma <helma@in-silico.ch> | 2015-08-27 20:28:25 +0200 |
| commit | 66c34e4682965272060a121b6e362af67ed4be5f (patch) | |
| tree | 61350c4ada8cbb6ca724f3af221f229ffcd70560 /lib/crossvalidation.rb | |
| parent | d542e9fe92567c54423f39904111bd5293236416 (diff) | |
Initial GUI for Nestec models
Diffstat (limited to 'lib/crossvalidation.rb')
| -rw-r--r-- | lib/crossvalidation.rb | 24 |
1 files changed, 21 insertions, 3 deletions
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb index 58a9664..a10dc1d 100644 --- a/lib/crossvalidation.rb +++ b/lib/crossvalidation.rb @@ -105,9 +105,9 @@ module OpenTox field :mae, type: Float field :weighted_rmse, type: Float field :weighted_mae, type: Float - field :weighted_mae, type: Float field :r_squared, type: Float field :correlation_plot_id, type: BSON::ObjectId + field :confidence_plot_id, type: BSON::ObjectId def self.create model, n=10 cv = self.new @@ -147,7 +147,7 @@ module OpenTox predictions.each do |pred| compound_id,activity,prediction,confidence = pred if activity and prediction - error = Math.log(prediction)-Math.log(activity) + error = Math.log10(prediction)-Math.log10(activity) rmse += error**2 weighted_rmse += confidence*error**2 mae += error.abs @@ -224,9 +224,27 @@ module OpenTox end end + def confidence_plot + tmpfile = "/tmp/#{id.to_s}_confidence.svg" + sorted_predictions = predictions.sort{|a,b| b[3]<=>a[3]}.collect{|p| [(Math.log10(p[1])-Math.log10(p[2]))**2,p[3]]} + R.assign "error", sorted_predictions.collect{|p| p[0]} + #R.assign "p", predictions.collect{|p| p[2]} + R.assign "confidence", predictions.collect{|p| p[2]} + #R.eval "diff = log(m)-log(p)" + R.eval "library(ggplot2)" + R.eval "svg(filename='#{tmpfile}')" + R.eval "image = qplot(confidence,error)"#,main='#{self.name}',asp=1,xlim=range, ylim=range)" + R.eval "ggsave(file='#{tmpfile}', plot=image)" + R.eval "dev.off()" + file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.svg") + plot_id = $gridfs.insert_one(file) + update(:confidence_plot_id => plot_id) + $gridfs.find_one(_id: confidence_plot_id).data + end + def correlation_plot unless correlation_plot_id - tmpfile = "/tmp/#{id.to_s}.svg" + tmpfile = "/tmp/#{id.to_s}_correlation.svg" x = predictions.collect{|p| p[1]} y = predictions.collect{|p| p[2]} attributes = Model::Lazar.find(self.model_id).attributes |