diff options
| -rw-r--r-- | README.md | 3 | ||||
| -rw-r--r-- | ext/lazar/rinstall.R | 7 | ||||
| -rw-r--r-- | lib/crossvalidation.rb | 12 |
3 files changed, 15 insertions, 7 deletions
@@ -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 |