lib/CXGN/Trial/TrialDesign/Plugin/RowColumn.pm

   1
   2 package CXGN::Trial::TrialDesign::Plugin::RCD;
   3
   4 use Moose::Role;
   5
   6 sub create_design {
   7   my $self = shift;
   8   my %rcd_design;
   9   my $rbase = R::YapRI::Base->new();
  10   my @stock_list;
  11   my $number_of_blocks;
  12   my $stock_data_matrix;
  13   my $control_data_matrix;
  14   my $r_block;
  15   my $result_matrix;
  16   my @plot_numbers;
  17   my @stock_names;
  18   my @control_names_crbd;
  19   my @block_numbers;
  20   my @converted_plot_numbers;
  21   my @control_list;
  22   my %control_names_lookup;
  23   my $fieldmap_row_number;
  24   my @fieldmap_row_numbers;
  25   my $fieldmap_col_number;
  26   my $plot_layout_format;
  27   my @col_number_fieldmaps;
  28
  29   if ($self->has_stock_list()) {
  30     @stock_list = @{$self->get_stock_list()};
  31   } else {
  32     die "No stock list specified\n";
  33   }
  34   if ($self->has_control_list()) {
  35     @control_list = @{$self->get_control_list()};
  36     %control_names_lookup = map { $_ => 1 } @control_list;
  37     $self->_check_controls_and_accessions_lists;
  38   }
  39   if ($self->has_number_of_blocks()) {
  40     $number_of_blocks = $self->get_number_of_blocks();
  41   } else {
  42     die "Number of blocks not specified\n";
  43   }
  44
  45   if ($self->has_fieldmap_col_number()) {
  46     $fieldmap_col_number = $self->get_fieldmap_col_number();
  47   }
  48   if ($self->has_fieldmap_row_number()) {
  49     $fieldmap_row_number = $self->get_fieldmap_row_number();
  50     my $colNumber = ((scalar(@stock_list) * $number_of_blocks)/$fieldmap_row_number);
  51     $fieldmap_col_number = CXGN::Trial::TrialDesign::validate_field_colNumber($colNumber);
  52   }
  53   if ($self->has_plot_layout_format()) {
  54     $plot_layout_format = $self->get_plot_layout_format();
  55   }
  56
  57   $stock_data_matrix =  R::YapRI::Data::Matrix->new(
  58                               {
  59                            name => 'stock_data_matrix',
  60                            rown => 1,
  61                            coln => scalar(@stock_list),
  62                            data => \@stock_list,
  63                               }
  64                              );
  65
  66   $control_data_matrix =  R::YapRI::Data::Matrix->new(
  67                                                        {
  68                                                         name => 'control_data_matrix',
  69                                                         rown => 1,
  70                                                         coln => scalar(@control_list),
  71                                                         data => \@control_list,
  72                                                        }
  73                                                       );
  74
  75
  76   my $plot_start = $self->get_plot_start_number();
  77   my $serie;
  78   if($plot_start == 1){
  79       $serie = 1;
  80   }elsif($plot_start == 101){
  81       $serie = 2;
  82   }elsif($plot_start == 1001){
  83       $serie = 3;
  84   }
  85
  86   $r_block = $rbase->create_block('r_block');
  87   $stock_data_matrix->send_rbase($rbase, 'r_block');
  88   $control_data_matrix->send_rbase($rbase, 'r_block');
  89   $r_block->add_command('library(agricolae)');
  90   $r_block->add_command('library(blocksdesign)');
  91   $r_block->add_command('treatments <- stock_data_matrix[1,]');
  92   $r_block->add_command('controls <- control_data_matrix[1,]');
  93   $r_block->add_command('number_of_blocks <- '.$number_of_blocks);
  94   $r_block->add_command('number_of_rows <- '.$fieldmap_row_number);
  95   $r_block->add_command('number_of_cols <- '.$fieldmap_col_number);
  96
  97   $r_block->add_command('RCDblocks <- data.frame(
  98     block = gl(number_of_blocks,length(treatments)),
  99     row = gl(number_of_rows,1),
 100     col = gl(number_of_cols,number_of_rows)
 101   )');
 102   $r_block->add_command('RCD <- design(treatments, RCDblocks)$Design');
 103   # $r_block->add_command('RCD <- transform(RCD, is_a_control = ifelse(RCD$treatments %in% controls, TRUE, FALSE))');
 104
 105   $r_block->run_block();
 106   $result_matrix = R::YapRI::Data::Matrix->read_rbase( $rbase,'r_block','RCD');
 107   print STDERR Dumper $result_matrix;
 108   @plot_numbers = $result_matrix->get_column("plots");
 109   print STDERR Dumper \@plot_numbers;
 110   @block_numbers = $result_matrix->get_column("block");
 111   @stock_names = $result_matrix->get_column("treatments");
 112   @fieldmap_row_numbers = $result_matrix->get_column("row");
 113   @col_number_fieldmaps = $result_matrix->get_column("col");
 114
 115   # alter plot numbers for serpentine or custom start number
 116
 117     my %seedlot_hash;
 118     if($self->get_seedlot_hash){
 119         %seedlot_hash = %{$self->get_seedlot_hash};
 120     }
 121   for (my $i = 0; $i < scalar(@plot_numbers); $i++) {
 122     my %plot_info;
 123     $plot_info{'stock_name'} = $stock_names[$i];
 124     $plot_info{'seedlot_name'} = $seedlot_hash{$stock_names[$i]}->[0];
 125     if ($plot_info{'seedlot_name'}){
 126         $plot_info{'num_seed_per_plot'} = $self->get_num_seed_per_plot;
 127     }
 128     $plot_info{'block_number'} = $block_numbers[$i];
 129     $plot_info{'plot_name'} = $plot_numbers[$i];
 130     $plot_info{'rep_number'} = $block_numbers[$i];
 131     #$plot_info{'plot_num_per_block'} = $plot_numbers[$i];
 132     $plot_info{'plot_number'} = $plot_numbers[$i];
 133     $plot_info{'plot_num_per_block'} = $plot_numbers[$i];
 134     $plot_info{'is_a_control'} = exists($control_names_lookup{$stock_names[$i]});
 135     #$plot_info_per_block{}
 136       if ($fieldmap_row_numbers[$i]){
 137       $plot_info{'row_number'} = $fieldmap_row_numbers[$i];
 138       $plot_info{'col_number'} = $col_number_fieldmaps[$i];
 139     }
 140     $rcd_design{$plot_numbers[$i]} = \%plot_info;
 141   }
 142   %rcd_design = %{$self->_build_plot_names(\%rcd_design)};
 143   return \%rcd_design;
 144 }
 145
 146 1;