mason/solgs/population/trait.mas

   1 <%args>
   2
   3 $training_pop_id
   4 $training_pop_name
   5 $training_pop_desc =>''
   6 $show_data => 1;
   7 $accuracy_report
   8 $model_parameters
   9 $top_blups
  10 $blups_download_url
  11 $marker_effects_download_url
  12 $top_marker_effects
  13 $validation_download_url
  14 $trait_abbr
  15 $trait_name
  16
  17 $stocks_no
  18 $markers_no
  19 $traits_no =>''
  20 $trait_id
  21 $model_pheno_means_descriptive_stat
  22 $model_pheno_raw_descriptive_stat =>''
  23 $selection_prediction_download =>''
  24 $selection_pop_id => ''
  25 $selection_pop_name => ''
  26 $list_of_prediction_pops=> ''
  27 $training_pop_analyzed_traits => ''
  28 $owner=>''
  29 $protocol_url => ''
  30 $combo_pops_id => ''
  31 $genotyping_protocol_id => ''
  32 $training_pop_url
  33 </%args>
  34
  35 <%perl>
  36
  37 </%perl>
  38
  39
  40 <& /util/import_javascript.mas, classes => ["d3.d3Min", "solGS.histogram", "statistics/simple_statistics"] &>
  41
  42
  43 <& /util/import_css.mas, paths => ['/static/css/solgs/solgs.css'] &>
  44
  45 <& /page/page_title.mas,
  46    title => "Genomic selection model for $trait_name ($trait_abbr) in $training_pop_name"
  47 &>
  48
  49 <&| /page/info_section.mas,
  50   collapsible => 1,
  51   collapsed   => 0,
  52   title       => "Training population summary",
  53   &>
  54
  55  <& summary.mas,
  56     training_pop_id   => $training_pop_id,
  57         training_pop_name => $training_pop_name,
  58     training_pop_desc => $training_pop_desc,
  59         training_pop_url    => $training_pop_url,
  60     stocks_no    => $stocks_no,
  61     markers_no   => $markers_no,
  62     traits_no    => $traits_no,
  63     owner        => $owner,
  64     protocol_url => $protocol_url,
  65  &>
  66
  67    <& /solgs/population/hidden_input.mas,
  68       training_pop_id  => $training_pop_id,
  69      training_pop_name => $training_pop_name,
  70      training_pop_desc => $training_pop_desc,
  71      trait_id => $trait_id,
  72      combo_pops_id => $combo_pops_id,
  73      genotyping_protocol_id => $genotyping_protocol_id,
  74
  75      &>
  76 </&>
  77
  78 <&| /page/info_section.mas,
  79     collapsible => 1,
  80     collapsed   => 0,
  81   title       => "Trait phenotype data"
  82 &>
  83
  84 <& /solgs/model/phenotype/trait_phenotype_data.mas,
  85    model_pheno_means_descriptive_stat => $model_pheno_means_descriptive_stat,
  86    model_pheno_raw_descriptive_stat => $model_pheno_raw_descriptive_stat
  87  &>
  88
  89 </&>
  90
  91 <& /solgs/tools/pca/analysis.mas &>
  92 <& /solgs/tools/cluster/analysis.mas &>
  93
  94 % if ($show_data)
  95 %{
  96
  97 <& /solgs/model/model_parameters.mas,
  98    model_parameters => $model_parameters,
  99 &>
 100
 101 <& /solgs/model/accuracy.mas,
 102    accuracy_report        => $accuracy_report,
 103   validation_download_url => $validation_download_url
 104 &>
 105
 106 <& /solgs/model/gebvs.mas,
 107    top_blups          => $top_blups,
 108    blups_download_url => $blups_download_url,
 109    pop_id             => $training_pop_id,
 110   trait_id            => $trait_id
 111   &>
 112
 113   <& /solgs/population/gebv_pheno_regression.mas,
 114         pop_id       => $training_pop_id,
 115        trait_id      => $trait_id,
 116        combo_pops_id => $combo_pops_id,
 117 &>
 118
 119
 120 <& /solgs/tools/kinship/analysis.mas,
 121    pop_id  => $training_pop_id,
 122   &>
 123
 124 <& /solgs/model/marker_effects.mas,
 125    top_marker_effects          => $top_marker_effects,
 126    marker_effects_download_url => $marker_effects_download_url
 127 &>
 128
 129 <& selection_populations.mas,
 130    selection_prediction_download     => $selection_prediction_download,
 131    training_pop_analyzed_traits         => $training_pop_analyzed_traits,
 132    training_pop_id        => $training_pop_id,
 133    training_pop_name   => $training_pop_name,
 134    selection_pop_id       => $selection_pop_id,
 135    selection_pop_name     => $selection_pop_name,
 136     list_of_prediction_pops => $list_of_prediction_pops,
 137 &>
 138
 139 %}
 140 % else
 141 %{
 142 <&| /page/info_section.mas,
 143   collapsible => 1,
 144   collapsed   => 0,
 145   title       => "Data Accessibility",
 146   &>
 147 <p>This is private data.</p>
 148 </&>
 149 %}