From 6117375fdc800fd071fc4983896c26700bf2acd7 Mon Sep 17 00:00:00 2001
From: gebele <gebele@in-silico.ch>
Date: Mon, 21 Mar 2016 09:50:12 +0000
Subject: added install script for R packages, updated README with install
 instructions; changed plot format from svg to png

---
 README.md              |  3 ++-
 ext/lazar/rinstall.R   |  7 +++++++
 lib/crossvalidation.rb | 12 ++++++------
 3 files changed, 15 insertions(+), 7 deletions(-)
 create mode 100644 ext/lazar/rinstall.R

diff --git a/README.md b/README.md
index e0b17d1..4de5a12 100644
--- a/README.md
+++ b/README.md
@@ -8,7 +8,7 @@ Dependencies
 
   lazar depends on a couple of external programs and libraries. On Debian 7 "Wheezy" systems you can install them with
 
-   `sudo apt-get install build-essential ruby ruby-dev git cmake swig r-base r-base-dev r-cran-rserve openjdk-7-jre libgsl0-dev libxml2-dev zlib1g-dev libcairo2-dev`
+   `sudo apt-get install build-essential ruby ruby-dev git cmake swig r-base r-base-dev openjdk-7-jre libgsl0-dev libxml2-dev zlib1g-dev libcairo2-dev`
   
   You will also need at least mongodb version 3.0, but Debian "Wheezy" provides version 2.4. Please follow the instructions at http://docs.mongodb.org/manual/tutorial/install-mongodb-on-debian/:
 
@@ -30,6 +30,7 @@ Installation
   git clone https://github.com/opentox/lazar.git
   cd lazar
   ruby ext/lazar/extconf.rb
+  sudo Rscript ext/lazar/rinstall.R
   bundle install
   ```
 
diff --git a/ext/lazar/rinstall.R b/ext/lazar/rinstall.R
new file mode 100644
index 0000000..7c1510d
--- /dev/null
+++ b/ext/lazar/rinstall.R
@@ -0,0 +1,7 @@
+chooseCRANmirror(ind=19);
+install.packages("Rserve");
+install.packages("gridExtra");
+install.packages("ggplot2");
+install.packages("pls");
+install.packages("caret");
+install.packages("doMC");
diff --git a/lib/crossvalidation.rb b/lib/crossvalidation.rb
index 08a5ad3..29e208c 100644
--- a/lib/crossvalidation.rb
+++ b/lib/crossvalidation.rb
@@ -132,7 +132,7 @@ module OpenTox
 
     def confidence_plot
       unless confidence_plot_id
-        tmpfile = "/tmp/#{id.to_s}_confidence.svg"
+        tmpfile = "/tmp/#{id.to_s}_confidence.png"
         accuracies = []
         confidences = []
         correct_predictions = 0
@@ -149,7 +149,7 @@ module OpenTox
         R.assign "confidence", confidences
         R.eval "image = qplot(confidence,accuracy)+ylab('accumulated accuracy')+scale_x_reverse()"
         R.eval "ggsave(file='#{tmpfile}', plot=image)"
-        file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.svg")
+        file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.png")
         plot_id = $gridfs.insert_one(file)
         update(:confidence_plot_id => plot_id)
       end
@@ -244,7 +244,7 @@ module OpenTox
     end
 
     def confidence_plot
-      tmpfile = "/tmp/#{id.to_s}_confidence.svg"
+      tmpfile = "/tmp/#{id.to_s}_confidence.png"
       sorted_predictions = predictions.collect{|p| [(Math.log10(p[1])-Math.log10(p[2])).abs,p[3]] if p[1] and p[2]}.compact
       R.assign "error", sorted_predictions.collect{|p| p[0]}
       R.assign "confidence", sorted_predictions.collect{|p| p[1]}
@@ -252,7 +252,7 @@ module OpenTox
       R.eval "image = qplot(confidence,error)"
       R.eval "image = image + stat_smooth(method='lm', se=FALSE)"
       R.eval "ggsave(file='#{tmpfile}', plot=image)"
-      file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.svg")
+      file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_confidence_plot.png")
       plot_id = $gridfs.insert_one(file)
       update(:confidence_plot_id => plot_id)
       $gridfs.find_one(_id: confidence_plot_id).data
@@ -260,7 +260,7 @@ module OpenTox
 
     def correlation_plot
       unless correlation_plot_id
-        tmpfile = "/tmp/#{id.to_s}_correlation.svg"
+        tmpfile = "/tmp/#{id.to_s}_correlation.png"
         x = predictions.collect{|p| p[1]}
         y = predictions.collect{|p| p[2]}
         attributes = Model::Lazar.find(self.model_id).attributes
@@ -273,7 +273,7 @@ module OpenTox
         R.eval "image = qplot(-log(prediction),-log(measurement),main='#{self.name}',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 => "#{self.id.to_s}_correlation_plot.svg")
+        file = Mongo::Grid::File.new(File.read(tmpfile), :filename => "#{self.id.to_s}_correlation_plot.png")
         plot_id = $gridfs.insert_one(file)
         update(:correlation_plot_id => plot_id)
       end
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