diff options
Diffstat (limited to 'gn2/wqflask/static/new/javascript/get_traits_from_collection.js')
| -rw-r--r-- | gn2/wqflask/static/new/javascript/get_traits_from_collection.js | 414 |
1 files changed, 414 insertions, 0 deletions
diff --git a/gn2/wqflask/static/new/javascript/get_traits_from_collection.js b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js new file mode 100644 index 00000000..c115f3b0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js @@ -0,0 +1,414 @@ +// Generated by CoffeeScript 1.8.0 +var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + +this_trait_data = null; + +selected_traits = {}; + +$('#collections_list').attr("style", "width: 100%;"); +$('#trait_table').dataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + }, + "columns": [ + { "type": "natural", "width": "3%" }, + { "type": "natural", "width": "8%" }, + { "type": "natural", "width": "20%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "15%" } + ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true +} ); + +if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { + $('#collection_table').dataTable( { + "createdRow": function ( row, data, index ) { + if ($('td', row).eq(2).text().length > 40) { + $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40)); + $('td', row).eq(2).text($('td', row).eq(2).text() + '...') + } + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + }, + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "ZRtr", + "iDisplayLength": -1, + "autoWidth": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); +} + +collection_click = function() { + var this_collection_url; + + this_collection_url = $(this).find('.collection_name').prop("href"); + this_collection_url += "&json"; + collection_list = $("#collections_holder").html(); + return $.ajax({ + dataType: "json", + url: this_collection_url, + success: process_traits + }); +}; + +submit_click = function() { + var all_vals, sample, samples, scatter_matrix, this_trait_vals, trait, trait_names, trait_vals_csv, traits, _i, _j, _len, _len1, _ref; + selected_traits = {}; + traits = []; + $('#collections_holder').find('input[type=checkbox]:checked').each(function() { + var this_dataset, this_trait, this_trait_url; + this_trait = $(this).parents('tr').find('.trait').text(); + this_dataset = $(this).parents('tr').find('.dataset').text(); + this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset; + return $.ajax({ + dataType: "json", + url: this_trait_url, + async: false, + success: add_trait_data + }); + }); + trait_names = []; + samples = $('input[name=allsamples]').val().split(" "); + all_vals = []; + this_trait_vals = get_this_trait_vals(samples); + all_vals.push(this_trait_vals); + _ref = Object.keys(selected_traits); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + trait = _ref[_i]; + trait_names.push(trait); + this_trait_vals = []; + for (_j = 0, _len1 = samples.length; _j < _len1; _j++) { + sample = samples[_j]; + if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) { + this_trait_vals.push(parseFloat(selected_traits[trait][sample])); + } else { + this_trait_vals.push(null); + } + } + all_vals.push(this_trait_vals); + } + trait_vals_csv = create_trait_data_csv(selected_traits); + scatter_matrix = new ScatterMatrix(trait_vals_csv); + scatter_matrix.render(); + return $.colorbox.close(); +}; + +create_trait_data_csv = function(selected_traits) { + var all_vals, index, sample, sample_vals, samples, this_trait_vals, trait, trait_names, trait_vals_csv, _i, _j, _k, _l, _len, _len1, _len2, _len3, _ref; + trait_names = []; + trait_names.push($('input[name=trait_id]').val()); + samples = $('input[name=allsamples]').val().split(" "); + all_vals = []; + this_trait_vals = get_this_trait_vals(samples); + all_vals.push(this_trait_vals); + _ref = Object.keys(selected_traits); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + trait = _ref[_i]; + trait_names.push(trait); + this_trait_vals = []; + for (_j = 0, _len1 = samples.length; _j < _len1; _j++) { + sample = samples[_j]; + if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) { + this_trait_vals.push(parseFloat(selected_traits[trait][sample])); + } else { + this_trait_vals.push(null); + } + } + all_vals.push(this_trait_vals); + } + + trait_vals_csv = trait_names.join(","); + trait_vals_csv += "\n"; + for (index = _k = 0, _len2 = samples.length; _k < _len2; index = ++_k) { + sample = samples[index]; + if (all_vals[0][index] === null) { + continue; + } + sample_vals = []; + for (_l = 0, _len3 = all_vals.length; _l < _len3; _l++) { + trait = all_vals[_l]; + sample_vals.push(trait[index]); + } + trait_vals_csv += sample_vals.join(","); + trait_vals_csv += "\n"; + } + return trait_vals_csv; +}; + +trait_click = function() { + var dataset, this_trait_url, trait; + + trait = $(this).parent().find('.trait').text(); + dataset = $(this).parent().find('.dataset').text(); + this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset; + $.ajax({ + dataType: "json", + url: this_trait_url, + success: get_trait_data + }); + return $.colorbox.close(); +}; + +trait_row_click = function() { + var dataset, this_trait_url, trait; + trait = $(this).find('.trait').text(); + dataset = $(this).find('.dataset').data("dataset"); + this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset; + $.ajax({ + dataType: "json", + url: this_trait_url, + success: get_trait_data + }); + return $.colorbox.close(); +}; + +add_trait_data = function(trait_data, textStatus, jqXHR) { + var trait_name, trait_sample_data; + trait_name = trait_data[0]; + trait_sample_data = trait_data[1]; + selected_traits[trait_name] = trait_sample_data; + return console.log("selected_traits:", selected_traits); +}; + +populate_cofactor_info = function(trait_info) { + if ($('input[name=selecting_which_cofactor]').val() == "1"){ + $('#cofactor1_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor1').text("Change Cofactor 1"); + $('#cofactor1_info_container').css("display", "inline"); + $('#cofactor2_button').css("display", "inline-block"); + } else if ($('input[name=selecting_which_cofactor]').val() == "2"){ + $('#cofactor2_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor2').text("Change Cofactor 2"); + $('#cofactor2_info_container').css("display", "inline"); + $('#cofactor3_button').css("display", "inline-block"); + } else { + $('#cofactor3_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor3_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor3').text("Change Cofactor 3"); + $('#cofactor3_info_container').css("display", "inline"); + } +} + +get_trait_data = function(trait_data, textStatus, jqXHR) { + var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len; + trait_sample_data = trait_data[1]; + if ( $('input[name=allsamples]').length ) { + samples = $('input[name=allsamples]').val().split(" "); + } else { + samples = js_data.indIDs + } + sample_vals = []; + vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + if (sample in trait_sample_data) { + sample_vals.push(sample + ":" + parseFloat(trait_sample_data[sample])) + vals.push(parseFloat(trait_sample_data[sample])) + } else { + sample_vals.push(null) + vals.push(null) + } + } + if ( $('input[name=allsamples]').length ) { + if ($('input[name=samples]').length < 1) { + $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />'); + } + $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />'); + this_trait_vals = get_this_trait_vals(samples); + return color_by_trait(trait_sample_data); + } else{ + sorted = vals.slice().sort(function(a,b){return a-b}) + ranks = vals.slice().map(function(v){ return sorted.indexOf(v)+1 }); + sample_ranks = [] + for (_i = 0; _i < samples.length; _i++){ + if (samples[_i] in trait_sample_data){ + sample_ranks.push(samples[_i] + ":" + ranks[_i]) + } else { + sample_ranks.push(null) + } + } + + if ($('input[name=selecting_which_cofactor]').val() == "1"){ + if ($('#cofactor1_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor1_vals]').val(sample_vals) + $('input[name=ranked_cofactor1_vals]').val(sample_ranks) + } else if ($('input[name=selecting_which_cofactor]').val() == "2"){ + if ($('#cofactor2_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor2_vals]').val(sample_vals) + $('input[name=ranked_cofactor2_vals]').val(sample_ranks) + } else{ + if ($('#cofactor3_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor3_vals]').val(sample_vals) + $('input[name=ranked_cofactor3_vals]').val(sample_ranks) + } + populate_cofactor_info(trait_data[0]) + chartupdatedata(); + return false + } +}; + +get_this_trait_vals = function(samples) { + var sample, this_trait_vals, this_val, this_vals_json, _i, _len; + this_trait_vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + this_val = parseFloat($("input[name='value:" + sample + "']").val()); + if (!isNaN(this_val)) { + this_trait_vals.push(this_val); + } else { + this_trait_vals.push(null); + } + } + this_vals_json = '[' + this_trait_vals.toString() + ']'; + return this_trait_vals; +}; + +assemble_into_json = function(this_trait_vals) { + var json_data, json_ids, num_traits, samples; + num_traits = $('input[name=vals]').length; + samples = $('input[name=samples]').val(); + json_ids = samples; + json_data = '[' + this_trait_vals; + $('input[name=vals]').each((function(_this) { + return function(index, element) { + return json_data += ',' + $(element).val(); + }; + })(this)); + json_data += ']'; + return [json_ids, json_data]; +}; + +color_by_trait = function(trait_sample_data, textStatus, jqXHR) { + return root.bar_chart.color_by_trait(trait_sample_data); +}; + +process_traits = function(trait_data, textStatus, jqXHR) { + var the_html, trait, _i, _len; + the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; + the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; + the_html += " <button id='submit_cofactors' class='btn btn-primary btn-small submit'> Submit </button>"; + the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; + the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; + the_html += "<tbody>"; + for (_i = 0, _len = trait_data.length; _i < _len; _i++) { + trait = trait_data[_i]; + the_html += "<tr class='trait_line'>"; + the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>"; + if ("abbreviation" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>"; + } else if ("symbol" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>"; + } else { + the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>"; + } + the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>"; + the_html += "<td class='description'>" + trait.description + "</td>"; + } + the_html += "</tbody>"; + the_html += "</table>"; + the_html += "<script type='text/javascript' src='/static/new/javascript/get_traits_from_collection.js'></script>" + $("#collections_holder").html(the_html); + return $('#collections_holder').colorbox.resize(); +}; + +back_to_collections = function() { + $("#collections_holder").html(collection_list); + $(document).on("click", ".collection_line", collection_click); + return $('#collections_holder').colorbox.resize(); +}; + +$(".collection_line").on("click", collection_click); +$("#submit_cofactors").on("click", submit_click); +if ($('#scatterplot2').length){ + $(".trait_line").on("click", trait_row_click); +} else { + $(".trait").on("click", trait_click); +} +$("#back_to_collections").on("click", back_to_collections); |