plain R version of test.rb

Author: Juul

.gitignore

@@ -0,0 +1,2 @@
+*~
+output/**/*

README

@@ -10,18 +10,25 @@ It outputs three types of data:
 
 We use this tool to analyze the data from our Millipore Guava easyCyte, and some of the code may be specific to the fcs files produced by this device.
 
+Running using R directly:
+
+  R --vanilla < test.r
+
+Running using R through Ruby:
+
+  ruby test.rb
+
 Requirements:
 
   BioConductor libraries: flowCore, flowClust and flowViz
-  Ruby libraries: rubygems, rsruby
+  For Ruby: rubygems, rsruby
 
 ToDo:
 
-  R script to run this without Ruby.
   Support for specifying channel (red or green) per fcs file in batch mode.
 
 Note:
 
-The test.rb file runs in batch mode.
-You can also run this for a single fcs file using the "run" function in fcs3_analysis/run.r
+  The test.rb file runs in batch mode.
+  You can also run this for a single fcs file using the "run" function in fcs3_analysis/run.r
 

test.r

@@ -0,0 +1,29 @@
+
+root.path = getwd()
+script.path = file.path(root.path, 'fcs3_analysis')
+main.script = file.path(script.path, 'fcs3_analysis.r')
+replicate.path = file.path(root.path, 'example_replicate')
+out.path = file.path(root.path, 'output')
+dump.file = file.path(out.path, 'out.dump')
+
+fluo.channel = 'GRN' # or 'RED'
+init.gate = 'ellipse' # or 'rectangle
+
+setwd(script.path)
+source(main.script)
+
+fcs.file.paths = c()
+files = list.files(replicate.path)
+
+for(i in 1:length(files)) {
+  if(length(grep(".+\\.fcs$", files[i], perl=TRUE)) > 0) {
+    fcs.file.paths = c(fcs.file.paths, file.path(replicate.path, files[i]))
+  }
+}
+
+data.set = batch(out.path, fcs.file.paths, fluo.channel=fluo.channel, init.gate=init.gate, verbose=TRUE)
+
+cat("Analysis completed.\n")
+cat("Cleaned fcs files and plots in: ", out.path, "\n")
+cat("Output data not dumped (not implemented).\n")
+

test.rb

@@ -13,8 +13,6 @@
 out_path = File.join(root_path, 'output')
 dump_file = File.join(out_path, 'out.dump')
 
-fluo_channel = 'GRN'
-init_gate = 'ellipse'
 
 begin
 
@@ -33,7 +31,7 @@
     next if (fcs_file == '.') || (fcs_file == '..')
     fcs_file_path = File.join(replicate_path, fcs_file)
     next if File.directory?(fcs_file_path)
-    next if !fcs_file.match(/.*\.fcs3?$/i)
+    next if !fcs_file.match(/.+\.fcs3?$/i)
     fcs_file_paths << fcs_file_path
   end
 
@@ -45,11 +43,10 @@
   f = File.new(dump_file, 'w+')
   f.puts(data_set.inspect)
   f.close
-  puts "Output data dumped to: #{dump_file}"
 
   puts "Analysis completed."
-  puts "Data available in: #{dump_file}"
   puts "Cleaned fcs files and plots in: #{out_path}"
+  puts "Output data dumped to: #{dump_file}"
 
 rescue Exception => e
   if(e.message[:r_msg])