R.rb in rbbt-util-5.3.0

- old
+ new

@@ -5,11 +5,16 @@
 
   LIB_DIR = File.join(File.expand_path(File.dirname(__FILE__)),'../../../share/lib/R')
   UTIL    = File.join(LIB_DIR, 'util.R')
 
   def self.run(command, options = {})
-    cmd = "source('#{UTIL}');\n"
+    cmd =<<-EOF
+# Loading basic rbbt environment
+source('#{UTIL}');
+
+    EOF
+
     case
     when IO === command
       cmd << command.read
     when File.exists?(command)
       cmd << File.open(command, 'r') do |f| f.read end
@@ -17,37 +22,54 @@
       cmd << command
     end
 
     Log.debug "R Script:\n#{ cmd }"
 
-    CMD.cmd('R --vanilla --slave --quiet', options.merge(:in => cmd))
+    if options.delete :monitor
+      io = CMD.cmd('R --vanilla --slave --quiet', options.merge(:in => cmd, :pipe => true))
+      while line = io.gets
+        puts line
+      end
+      nil
+    else
+      CMD.cmd('R --vanilla --slave --quiet', options.merge(:in => cmd))
+    end
   end
 
   def self.interactive(init_file, options = {})
     CMD.cmd("env R_PROFILE='#{init_file}' xterm R")
   end
 
   def self.interactive(script, options = {})
     TmpFile.with_file do |init_file|
         Open.write(init_file) do |file|
-          profile = File.join(ENV["HOME"], ".Rprofile")
-          file.puts "source('#{profile}');\n" if File.exists? profile
+          file.puts "# Loading basic rbbt environment"
           file.puts "source('#{R::UTIL}');\n"
+          file.puts 
           file.puts script
         end
         CMD.cmd("env R_PROFILE='#{init_file}' xterm R")
     end
   end
 
   def self.ruby2R(object)
     case object
+    when nil
+      "NULL"
+    when TSV
+      #"as.matrix(data.frame(c(#{object.transpose("Field").collect{|k,v| "#{k}=" << R.ruby2R(v)}.flatten * ", "}), row.names=#{R.ruby2R object.keys}))"
+      "matrix(#{R.ruby2R object.values},dimnames=list(#{R.ruby2R object.keys}, #{R.ruby2R object.fields}))"
+    when Symbol
+      "#{ object }"
     when String
       "'#{ object }'"
-    when Fixnum
+    when Fixnum, Float
       object
     when Array
       "c(#{object.collect{|e| ruby2R(e) } * ", "})"
+    else
+      raise "Type of object not known: #{ object.inspect }"
     end
   end
 
 end
 
@@ -56,16 +78,24 @@
   def R(script, open_options = {})
     TmpFile.with_file do |f|
       Open.write(f, self.to_s)
       Log.debug(R.run(
       <<-EOF
+## Loading tsv into data
 data = rbbt.tsv('#{f}');
+
 #{script.strip}
+
+## Resaving data
 if (! is.null(data)){ rbbt.tsv.write('#{f}', data); }
       EOF
       ).read)
       open_options = Misc.add_defaults open_options, :type => :list
-      TSV.open(f, open_options) unless open_options[:ignore_output]
+      if open_options[:raw]
+        Open.read(f)
+      else
+        TSV.open(f, open_options) unless open_options[:ignore_output]
+      end
     end
   end
 
   def R_interactive(open_options = {})
     TmpFile.with_file do |f|