js/anova.js

   1 /**
   2 * ANOVA analysis
   3 * Isaak Y Tecle <iyt2@cornell.edu>
   4 *
   5 */
   6
   7
   8 jQuery(document).ready( function() {
   9
  10     var url = document.URL;
  11
  12     if (url.match(/\/breeders_toolbox\/trial|breeders\/trial|\/solgs\/population\//)) {
  13             allowAnova();
  14         }
  15
  16 });
  17
  18
  19 function allowAnova () {
  20
  21     checkDesign();
  22
  23 }
  24
  25
  26 function checkDesign () {
  27
  28     var trialId = getTrialId();
  29
  30     jQuery.ajax({
  31         type: 'POST',
  32         dataType: 'json',
  33         data: {'trial_id': trialId},
  34         url: '/anova/check/design/',
  35         success: function(response) {
  36
  37             if (response.Error) {
  38                 showMessage(response.Error);
  39                 jQuery("#run_anova").hide();
  40             } else {
  41
  42                 listAnovaTraits();
  43             }
  44         },
  45         error: function(response) {
  46             showMessage("Error occured running the ANOVA.");
  47             jQuery("#run_anova").show();
  48         }
  49     });
  50
  51 }
  52
  53
  54 jQuery(document).ready(function () {
  55     jQuery(document).on("click", "#run_anova", function() {
  56
  57         var traitId    =  jQuery("#anova_selected_trait_id").val();
  58
  59         if (traitId) {
  60
  61             queryPhenoData(traitId);
  62
  63             jQuery("#run_anova").hide();
  64
  65             showMessage("Running anova analysis...");
  66         } else {
  67             var msg = 'You need to select a trait first.'
  68             anovaAlert(msg);
  69         }
  70
  71     });
  72
  73 });
  74
  75
  76 function anovaAlert(msg) {
  77
  78         jQuery('<div />')
  79         .html(msg)
  80             .dialog({
  81                 modal  : true,
  82                 title  : 'Alert',
  83                 buttons: {
  84                     OK: {
  85                         click: function () {
  86                             jQuery(this).dialog('close');
  87                         },
  88                         class: 'btn btn-success',
  89                         text : 'OK',
  90                     },
  91                 }
  92             });
  93
  94
  95 }
  96
  97 function queryPhenoData(traitId) {
  98
  99     var trialId = getTrialId();
 100
 101     jQuery.ajax({
 102         type: 'POST',
 103         dataType: 'json',
 104         data: {'trial_id': trialId, 'traits_ids': [traitId]},
 105         url: '/anova/phenotype/data/',
 106         success: function(response) {
 107
 108             if (response.Error) {
 109                 showMessage(response.Error);
 110                 jQuery("#run_anova").show();
 111             } else {
 112                 var traitsAbbrs = response.traits_abbrs;
 113                 runAnovaAnalysis(traitsAbbrs);
 114             }
 115         },
 116         error: function(response) {
 117             showMessage("Error occured running the ANOVA.");
 118             jQuery("#run_anova").show();
 119         }
 120     });
 121 }
 122
 123
 124 function showMessage (msg) {
 125      jQuery("#anova_message")
 126         .css({"padding-left": '0px'})
 127         .html(msg);
 128
 129 }
 130
 131
 132 function runAnovaAnalysis(traits) {
 133
 134     var trialId = getTrialId();
 135
 136     var captions       = jQuery('#anova_table table').find('caption').text();
 137     var analyzedTraits = captions.replace(/ANOVA result:/g, ' ');
 138
 139     for (var i = 0; i < traits.length; i++) {
 140         var traitAbbr = traits[i].trait_abbr;
 141
 142         if (analyzedTraits.match(traitAbbr) == null) {
 143             var anovaTraits = JSON.stringify(traits);
 144
 145             jQuery.ajax({
 146                 type: 'POST',
 147                 dataType: 'json',
 148                 data: {'trial_id': trialId, 'traits': [anovaTraits]},
 149                 url: '/anova/analysis/',
 150                 success: function(response) {
 151
 152                     if (response) {
 153                         var anovaTable = response.anova_html_table;
 154
 155                         jQuery("#anova_table").append('<div style="margin-top: 20px">' + anovaTable + '</div>').show();
 156
 157                         var anovaFile = response.anova_table_file;
 158                         var modelFile = response.anova_model_file;
 159                         var meansFile = response.adj_means_file;
 160                         var diagnosticsFile = response.anova_diagnostics_file;
 161
 162                         var fileNameAnova = anovaFile.split('/').pop();
 163                         var fileNameModel = modelFile.split('/').pop();
 164                         var fileNameMeans = meansFile.split('/').pop();
 165                         var fileNameDiagnostics = diagnosticsFile.split('/').pop()
 166
 167                         anovaFile = "<a href=\"" + anovaFile +  "\" download=" + fileNameAnova + ">[Anova table]</a>";
 168                         modelFile = "<a href=\"" + modelFile +  "\" download=" + fileNameModel + ">[Model Summary]</a>";
 169                         meansFile = "<a href=\"" + meansFile +  "\" download=" + fileNameMeans + ">[Adjusted Means]</a>";
 170
 171                         diagnosticsFile = "<a href=\"" + diagnosticsFile
 172                             +  "\" download=" + fileNameDiagnostics + ">[Model Diagnostics]</a>";
 173
 174                         jQuery("#anova_table")
 175                             .append('<br /> <strong>Download:</strong> '
 176                                     + anovaFile + ' | '
 177                                     + modelFile + ' | '
 178                                     + meansFile + ' | '
 179                                     + diagnosticsFile)
 180                             .show();
 181
 182                         jQuery("#anova_message").empty();
 183
 184                         jQuery("#run_anova").show();
 185                     } else {
 186                         showMessage("There is no anova output for this dataset.");
 187                         jQuery("#run_anova").show();
 188                     }
 189
 190                     clearTraitSelection();
 191                 },
 192                 error: function(response) {
 193                     showMessage("Error occured running the anova analysis.");
 194                     jQuery("#run_anova").show();
 195                     clearTraitSelection();
 196                 }
 197             });
 198         } else {
 199             jQuery("#anova_message").empty();
 200             jQuery("#run_anova").show();
 201             clearTraitSelection();
 202         }
 203     }
 204
 205 }
 206
 207
 208 function listAnovaTraits ()  {
 209
 210     var trialId = getTrialId();
 211
 212      jQuery.ajax({
 213         type: 'POST',
 214         dataType: 'json',
 215         data: {'trial_id': trialId},
 216         url: '/anova/traits/list/',
 217          success: function(response) {
 218              var traits = response.anova_traits;
 219
 220              if (traits.length) {
 221                  formatAnovaTraits(traits);
 222                  jQuery("#run_anova").show();
 223              } else {
 224                  showMessage('This trial has no phenotyped traits.');
 225                  jQuery("#run_anova").hide();
 226              }
 227         },
 228         error: function(response) {
 229             showMessage("Error occured listing anova traits.");
 230             jQuery("#run_anova").hide();
 231         }
 232     });
 233
 234
 235 }
 236
 237 function formatAnovaTraits(traits) {
 238
 239     var traitsList = '';
 240
 241     for (var i = 0; i < traits.length; i++) {
 242         var traitName = traits[i].trait_name;
 243
 244         var idName = JSON.stringify(traits[i]);
 245         traitsList +='<li>'
 246         + '<a href="#">' + traitName + '<span class=value>' + idName + '</span></a>'
 247         + '</li>';
 248     }
 249
 250     var  traitsList =  '<dl id="anova_selected_trait" class="anova_dropdown">'
 251         + '<dt> <a href="#"><span>Select a trait</span></a></dt>'
 252         + '<dd>'
 253         + '<ul>'
 254         + traitsList
 255         + '</ul></dd></dl>';
 256
 257     jQuery("#anova_select_a_trait_div").empty().append(traitsList).show();
 258
 259     jQuery(".anova_dropdown dt a").click(function() {
 260         jQuery(".anova_dropdown dd ul").toggle();
 261     });
 262
 263     jQuery(".anova_dropdown dd ul li a").click(function() {
 264
 265         var text = jQuery(this).html();
 266
 267         jQuery(".anova_dropdown dt a span").html(text);
 268         jQuery(".anova_dropdown dd ul").hide();
 269
 270         var traitIdName = jQuery("#anova_selected_trait").find("dt a span.value").html();
 271         traitIdName     = JSON.parse(traitIdName);
 272
 273         var traitId   = traitIdName.trait_id;
 274         var traitName = traitIdName.trait_name;
 275
 276         console.log('id ' + traitId + ' name ' + traitName)
 277
 278         jQuery("#anova_selected_trait_name").val(traitName);
 279         jQuery("#anova_selected_trait_id").val(traitId);
 280
 281     });
 282
 283     jQuery(".anova_dropdown").bind('click', function(e) {
 284         var clicked = jQuery(e.target);
 285
 286         if (!clicked.parents().hasClass("anova_dropdown"))
 287             jQuery(".anova_dropdown dd ul").hide();
 288
 289         e.preventDefault();
 290
 291
 292     });
 293
 294 }
 295
 296
 297 function clearTraitSelection () {
 298
 299     jQuery("#anova_selected_trait_name").val('');
 300     jQuery("#anova_selected_trait_id").val('');
 301
 302 }
 303
 304
 305 function getTrialId () {
 306
 307     var trialId    =  jQuery("#trial_id").val();
 308
 309     if (!trialId) {
 310
 311         trialId = jQuery("#population_id").val();
 312     }
 313
 314     return trialId;
 315
 316 }