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# File 'lib/publisci/dataset/dataset_for.rb', line 73
def self.r_object(object, options={}, ask_on_ambiguous=true)
if object.is_a? String
con = Rserve::Connection.new
vars = con.eval("load('#{File.absolute_path object}')")
if vars.to_ruby.size > 1 && ask_on_ambiguous
puts "Which variable? #{vars.to_ruby}"
var = vars.to_ruby[gets.to_i]
else
var = vars.to_ruby[0]
end
r_classes = con.eval("class(#{var})").to_ruby
if r_classes.include? "data.frame"
df = PubliSci::Readers::Dataframe.new
unless options[:dimensions] || !ask_on_ambiguous
dims = con.eval("names(#{var})").to_ruby
puts "Which dimensions? #{dims}"
selection = gets.chomp
if selection.size > 0
options[:dimensions] = selection.split(',').map(&:to_i).map{|i| dims[i]}
end
end
unless options[:measures] || !ask_on_ambiguous
meas = con.eval("names(#{var})").to_ruby
puts "Which measures? #{meas} "
selection = gets.chomp
if selection.size > 0
options[:measures] = selection.split(',').map(&:to_i).map{|i| meas[i]}
end
end
df.generate_n3(con.eval(var),var,options)
elsif r_classes.include? "cross"
bc = PubliSci::Readers::RCross.new
unless options[:measures] || !ask_on_ambiguous
pheno_names = con.eval("names(#{var}$pheno)").to_ruby
puts "Which phenotype traits? #{pheno_names}"
selection = gets.chomp
if selection.size > 0
options[:measures] = selection.split(',').map(&:to_i).map{|i| pheno_names[i]}
end
end
base = var
if ask_on_ambiguous
puts "Output file base?"
base = gets.chomp
base = var unless base.size > 0
end
bc.generate_n3(con, var, base, options)
elsif r_classes.include? "matrix"
mat = PubliSci::Readers::RMatrix.new
unless options[:measures] || !ask_on_ambiguous
puts "Row label"
rows = gets.chomp
rows = "row" unless rows.size > 0
puts "Column label"
cols = gets.chomp
cols = "column" unless cols.size > 0
puts "Entry label"
vals = gets.chomp
vals = "value" unless vals.size > 0
options[:measures] = [cols,rows,vals]
end
base = var
if ask_on_ambiguous
puts "Output file base?"
base = gets.chomp
base = var unless base.size > 0
end
mat.generate_n3(con, var, base, options)
else
raise "no PubliSci::Readers found for #{r_classes}"
end
elsif object.is_a? Rserve::REXP
if object.attr.payload["class"].payload.first
df = PubliSci::Readers::Dataframe.new
var = nil
if ask_on_ambiguous
var = interact("Dataset name?",nil)
end
unless options[:dimensions] || !ask_on_ambiguous
dims = object.payload.names
selection = interact("Which dimensions?","row",dims){|s| puts s; nil}
options[:dimensions] = selection if selection
end
unless options[:measures] || !ask_on_ambiguous
meas = object.payload.names
options[:measures] = interact("Which measures?",meas,meas)
end
df.generate_n3(object,var,options)
else
raise "support for other Rserve objects coming shortly"
end
else
raise "#{object} is not an R object"
end
end
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