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-rw-r--r--gn2/wqflask/static/new/javascript/show_trait.js1677
1 files changed, 1677 insertions, 0 deletions
diff --git a/gn2/wqflask/static/new/javascript/show_trait.js b/gn2/wqflask/static/new/javascript/show_trait.js
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--- /dev/null
+++ b/gn2/wqflask/static/new/javascript/show_trait.js
@@ -0,0 +1,1677 @@
+var statTableRows, isNumber,
+ __hasProp = {}.hasOwnProperty,
+ __slice = [].slice;
+
+isNumber = function(o) {
+ return !isNaN((o - 0) && o !== null);
+};
+
+statTableRows = [
+ {
+ vn: "n_of_samples",
+ pretty: "N of Samples",
+ digits: 0
+ }, {
+ vn: "mean",
+ pretty: "Mean",
+ digits: 3
+ }, {
+ vn: "median",
+ pretty: "Median",
+ digits: 3
+ }, {
+ vn: "std_error",
+ pretty: "Standard Error (SE)",
+ digits: 3
+ }, {
+ vn: "std_dev",
+ pretty: "Standard Deviation (SD)",
+ digits: 3
+ }, {
+ vn: "min",
+ pretty: "Minimum",
+ digits: 3
+ }, {
+ vn: "max",
+ pretty: "Maximum",
+ digits: 3
+ }
+]
+
+if (js_data.dataset_type == "ProbeSet"){
+ if (js_data.data_scale == "linear_positive" || js_data.data_scale == "log2") {
+ statTableRows.push({
+ vn: "range",
+ pretty: "Range (log2)",
+ digits: 3
+ })
+ } else {
+ statTableRows.push({
+ vn: "range",
+ pretty: "Range",
+ digits: 3
+ })
+ }
+} else {
+ statTableRows.push({
+ vn: "range",
+ pretty: "Range",
+ digits: 3
+ })
+}
+
+statTableRows.push(
+ {
+ vn: "range_fold",
+ pretty: "Range (fold)",
+ digits: 3
+ }, {
+ vn: "interquartile",
+ pretty: "<font color='black'>Interquartile Range</font>",
+ url: "http://www.genenetwork.org/glossary.html#Interquartile",
+ digits: 3
+ }, {
+ vn: "skewness",
+ pretty: "Skewness",
+ url: "https://en.wikipedia.org/wiki/Skewness",
+ digits: 3
+ }, {
+ vn: "kurtosis",
+ pretty: "Excess Kurtosis",
+ url: "https://en.wikipedia.org/wiki/Kurtosis",
+ digits: 3
+ }
+);
+
+toggleDescription = function() {
+ if ($('.truncDesc').is(':visible')) {
+ $('.truncDesc').hide();
+ $('.fullDesc').show();
+ } else {
+ $('.truncDesc').show();
+ $('.fullDesc').hide();
+ }
+}
+
+add = function() {
+ var trait;
+ trait = $("input[name=trait_hmac]").val();
+ return $.colorbox({
+ href: "/collections/add",
+ data: {
+ "traits": trait
+ }
+ });
+};
+$('#add_to_collection').click(add);
+
+sampleLists = js_data.sample_lists;
+sampleGroupTypes = js_data.sample_group_types;
+
+$(".select_covariates").click(function () {
+ openCovariateSelection();
+});
+
+$(".remove_covariates").click(function () {
+ $(".selected-covariates option:selected").each(function() {
+ this_val = $(this).val();
+ $(".selected-covariates option").each(function(){
+ if ($(this).val() == this_val){
+ $(this).remove();
+ }
+ })
+ cofactor_count = $(".selected-covariates:first option").length
+ if (cofactor_count > 2 && cofactor_count < 11){
+ $(".selected-covariates").each(function() {
+ $(this).attr("size", $(".selected-covariates:first option").length)
+ });
+ } else if (cofactor_count > 10) {
+ $(".selected-covariates").each(function() {
+ $(this).attr("size", 10)
+ });
+ } else {
+ $(".selected-covariates").each(function() {
+ $(this).attr("size", 2)
+ });
+ }
+ if (cofactor_count == 0){
+ $(".selected-covariates").each(function() {
+ $(this).append($("<option/>", {
+ value: "",
+ text: "No covariates selected"
+ }))
+ })
+ }
+ });
+
+ covariates_list = [];
+ $(".selected-covariates:first option").each(function() {
+ covariates_list.push($(this).val());
+ })
+ $("input[name=covariates]").val(covariates_list.join(","))
+});
+
+$(".remove_all_covariates").click(function() {
+ $(".selected-covariates option").each(function() {
+ $(this).remove();
+ });
+ $(".selected-covariates").attr("size", 2)
+ $("input[name=covariates]").val("");
+})
+
+openTraitSelection = function() {
+ return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) {
+ return function() {
+ $.colorbox({
+ inline: true,
+ href: "#collections_holder",
+ onComplete: function(){
+ $.getScript("/static/new/javascript/get_traits_from_collection.js");
+ }
+ });
+ return $('a.collection_name').attr('onClick', 'return false');
+ };
+ })(this));
+};
+openCovariateSelection = function() {
+ return $('#collections_holder').load('/collections/list #collections_list', (function(_this) {
+ return function() {
+ $.colorbox({
+ inline: true,
+ href: "#collections_holder",
+ width: "1000px",
+ height: "700px",
+ onComplete: function(){
+ $.getScript("/static/new/javascript/get_covariates_from_collection.js");
+ }
+ });
+ return $('a.collection_name').attr('onClick', 'return false');
+ };
+ })(this));
+};
+hideTabs = function(start) {
+ var x, _i, _results;
+ _results = [];
+ for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) {
+ _results.push($("#stats_tabs" + x).hide());
+ }
+ return _results;
+};
+statsMdpChange = function() {
+ var selected;
+ selected = $(this).val();
+ hideTabs(0);
+ return $("#stats_tabs" + selected).show();
+};
+changeStatsValue = function(sample_sets, category, value_type, decimal_places, effects) {
+ var current_value, id, in_box, the_value, title_value;
+ id = "#" + processId(category, value_type);
+ in_box = $(id).html;
+ current_value = parseFloat($(in_box)).toFixed(decimal_places);
+ the_value = sample_sets[category][value_type]();
+ if (decimal_places > 0) {
+ title_value = the_value.toFixed(decimal_places * 2);
+ the_value = the_value.toFixed(decimal_places);
+ } else {
+ title_value = null;
+ }
+ if (the_value !== current_value) {
+ if (effects) {
+ $(id).html(the_value).effect("highlight");
+ } else {
+ $(id).html(the_value);
+ }
+ }
+ if (title_value) {
+ return $(id).attr('title', title_value);
+ }
+};
+updateStatValues = function(sample_sets) {
+ var category, row, show_effects, _i, _len, _ref, _results;
+ show_effects = $(".tab-pane.active").attr("id") === "stats_tab";
+ _ref = ['samples_primary', 'samples_other', 'samples_all'];
+ _results = [];
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ category = _ref[_i];
+ _results.push((function() {
+ var _j, _len1, _results1;
+ _results1 = [];
+ for (_j = 0, _len1 = statTableRows.length; _j < _len1; _j++) {
+ row = statTableRows[_j];
+ _results1.push(changeStatsValue(sample_sets, category, row.vn, row.digits, show_effects));
+ }
+ return _results1;
+ })());
+ }
+ return _results;
+};
+
+updateHistogram_width = function() {
+ num_bins = $('#histogram').find('g.trace.bars').find('g.point').length
+
+ if (num_bins < 10) {
+ width_update = {
+ width: 400
+ }
+
+ Plotly.relayout('histogram', width_update)
+ }
+}
+
+updateHistogram = function() {
+ var x;
+ var _i, _len, _ref, data;
+ _ref = _.values(root.selected_samples[root.stats_group]);
+ var trait_vals = [];
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ x = _ref[_i];
+ trait_vals.push(x.value);
+ }
+ root.histogram_data[0]['x'] = trait_vals
+
+ if ($('input[name="transform"]').val() != ""){
+ root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.histogram_layout['xaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
+ }
+
+ Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options);
+ updateHistogram_width()
+};
+
+updateBarChart = function() {
+ var x;
+ var _i, _len, _ref, data;
+ _ref = _.values(root.selected_samples[root.stats_group]);
+ names_and_values = []
+ for (i = 0; i < _ref.length; i++){
+ _ref[i]["name"] = Object.keys(root.selected_samples[root.stats_group])[i]
+ }
+ trait_vals = [];
+ trait_vars = [];
+ trait_samples = [];
+
+ function sortFunction(a, b) {
+ if (a.value === b.value) {
+ return 0;
+ }
+ else {
+ return (a.value < b.value) ? -1 : 1;
+ }
+ }
+
+ if (root.bar_sort == "value") {
+ _ref.sort(sortFunction)
+ }
+
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ x = _ref[_i];
+ trait_samples.push(x.name)
+ trait_vals.push(x.value);
+ if (x["variance"] != undefined) {
+ trait_vars.push(x.variance);
+ } else{
+ trait_vars.push(null)
+ }
+ }
+
+ new_chart_range = getBarRange(trait_vals, trait_vars)
+
+ root.bar_layout['yaxis']['range'] = new_chart_range
+
+ if ($('input[name="transform"]').val() != ""){
+ root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.bar_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
+ }
+
+ root.bar_data[0]['y'] = trait_vals
+ root.bar_data[0]['error_y'] = {
+ type: 'data',
+ array: trait_vars,
+ visible: root.errors_exist
+ }
+ root.bar_data[0]['x'] = trait_samples
+
+ if (trait_vals.length < 256) {
+ Plotly.newPlot('bar_chart', root.bar_data, root.bar_layout, root.modebar_options);
+ }
+};
+
+updateViolinPlot = function() {
+ var y_value_list = []
+ if (sampleLists.length > 1) {
+ i = 0;
+ for (var sample_group in root.selected_samples){
+ var trait_sample_data = _.values(root.selected_samples[sample_group])
+ var trait_vals = [];
+ for (j = 0, len = trait_sample_data.length; j < len; j++) {
+ this_sample_data = trait_sample_data[j];
+ trait_vals.push(this_sample_data.value);
+ }
+ root.violin_data[i]['y'] = trait_vals
+ i++;
+ }
+ } else {
+ var trait_sample_data = _.values(root.selected_samples['samples_all'])
+ var trait_vals = [];
+ for (j = 0, len = trait_sample_data.length; j < len; j++) {
+ this_sample_data = trait_sample_data[j];
+ trait_vals.push(this_sample_data.value);
+ }
+ root.violin_data[0]['y'] = trait_vals
+ }
+
+ if ($('input[name="transform"]').val() != ""){
+ root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + " (" + $('input[name="transform"]').val() + ")</b>"
+ } else {
+ root.violin_layout['yaxis']['title'] = "<b>" + js_data.unit_type + "</b>"
+ }
+
+ Plotly.newPlot('violin_plot', root.violin_data, root.violin_layout, root.modebar_options)
+}
+
+
+updateProbPlot = function() {
+ return root.redraw_prob_plot_impl(root.selected_samples, root.prob_plot_group);
+};
+
+makeTable = function() {
+ var header, key, row, row_line, table, the_id, the_rows, value, _i, _len, _ref, _ref1;
+ if (js_data.trait_symbol != null) {
+ header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+ } else if (js_data.dataset_type == "Geno"){
+ header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Marker " + js_data.trait_id + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+ } else {
+ header = "<thead><tr><th style=\"color: white; background-color: #369; text-align: center;\" colspan=\"100%\">Trait " + js_data.trait_id + ": " + js_data.short_description + "</th></tr><tr><th style=\"text-align: right; padding-left: 5px;\">Statistic</th>";
+ }
+ _ref = js_data.sample_group_types;
+ for (key in _ref) {
+ if (!__hasProp.call(_ref, key)) continue;
+ value = _ref[key];
+ the_id = processId("column", key);
+ if (Object.keys(_ref).length > 1) {
+ header += "<th id=\"" + the_id + "\" style=\"text-align: right; padding-left: 5px;\">" + value + "</th>";
+ } else {
+ header += "<th id=\"" + the_id + "\" style=\"text-align: right; padding-left: 5px;\">Value</th>";
+ }
+ }
+
+ header += "</thead>";
+ the_rows = "<tbody>";
+ for (_i = 0, _len = statTableRows.length; _i < _len; _i++) {
+ row = statTableRows[_i];
+ if ((row.vn == "range_fold") && js_data.dataset_type == "Publish"){
+ continue;
+ }
+ row_line = "<tr>";
+ if (row.url != null) {
+ row_line += "<td id=\"" + row.vn + "\" align=\"right\"><a href=\"" + row.url + "\" style=\"color: #0000EE;\">" + row.pretty + "</a></td>";
+ } else {
+ row_line += "<td id=\"" + row.vn + "\" align=\"right\">" + row.pretty + "</td>";
+ }
+ _ref1 = js_data.sample_group_types;
+ for (key in _ref1) {
+ if (!__hasProp.call(_ref1, key)) continue;
+ value = _ref1[key];
+ the_id = processId(key, row.vn);
+ row_line += "<td id=\"" + the_id + "\" align=\"right\">N/A</td>";
+ }
+ row_line += "</tr>";
+ the_rows += row_line;
+ }
+ the_rows += "</tbody>";
+ table = header + the_rows;
+ return $("#stats_table").append(table);
+};
+processId = function() {
+ var processed, value, values, _i, _len;
+ values = 1 <= arguments.length ? __slice.call(arguments, 0) : [];
+
+ /* Make an id or a class valid javascript by, for example, eliminating spaces */
+ processed = "";
+ for (_i = 0, _len = values.length; _i < _len; _i++) {
+ value = values[_i];
+ value = value.replace(" ", "_");
+ if (processed.length) {
+ processed += "-";
+ }
+ processed += value;
+ }
+ return processed;
+};
+
+fetchSampleValues = function() {
+ // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster)
+ sample_val_dict = {};
+
+ table = 'samples_primary';
+ if ($('#' + table).length){
+ tableApi = $('#' + table).DataTable();
+ val_nodes = tableApi.column(3).nodes().to$();
+ for (_j = 0; _j < val_nodes.length; _j++){
+ sample_name = val_nodes[_j].childNodes[0].name.split(":")[1]
+ sample_val = val_nodes[_j].childNodes[0].value
+ sample_val_dict[sample_name] = sample_val
+ }
+ }
+
+ return sample_val_dict;
+}
+
+editDataChange = function() {
+ var already_seen, sample_sets, table, tables, _i, _j, _len;
+ already_seen = {};
+ sample_sets = {
+ samples_primary: new Stats([]),
+ samples_other: new Stats([]),
+ samples_all: new Stats([])
+ };
+ root.selected_samples = {
+ samples_primary: {},
+ samples_other: {},
+ samples_all: {}
+ };
+
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length){
+ tableApi = $('#' + table).DataTable();
+ sample_vals = [];
+ name_nodes = tableApi.column(2).nodes().to$();
+ val_nodes = tableApi.column(3).nodes().to$();
+ var_nodes = tableApi.column(5).nodes().to$();
+ for (_j = 0; _j < val_nodes.length; _j++){
+ sample_val = val_nodes[_j].childNodes[0].value
+ sample_name = $.trim(name_nodes[_j].childNodes[0].textContent)
+ if (isNumber(sample_val) && sample_val !== "") {
+ sample_val = parseFloat(sample_val);
+ sample_sets[table].add_value(sample_val);
+ try {
+ sample_var = var_nodes[_j].childNodes[0].value
+ if (isNumber(sample_var)) {
+ sample_var = parseFloat(sample_var)
+ } else {
+ sample_var = null;
+ }
+ } catch {
+ sample_var = null;
+ }
+ sample_dict = {
+ value: sample_val,
+ variance: sample_var
+ }
+ root.selected_samples[table][sample_name] = sample_dict;
+ if (!(sample_name in already_seen)) {
+ sample_sets['samples_all'].add_value(sample_val);
+ root.selected_samples['samples_all'][sample_name] = sample_dict;
+ already_seen[sample_name] = true;
+ }
+ }
+ }
+ }
+
+ }
+
+ updateStatValues(sample_sets);
+
+ if ($('#histogram').hasClass('js-plotly-plot')){
+ updateHistogram();
+ }
+ if ($('#bar_chart').hasClass('js-plotly-plot')){
+ updateBarChart();
+ }
+ if ($('#violin_plot').hasClass('js-plotly-plot')){
+ updateViolinPlot();
+ }
+ if ($('#prob_plot_div').hasClass('js-plotly-plot')){
+ return updateProbPlot();
+ }
+};
+
+showHideOutliers = function() {
+ var label;
+ label = $('#showHideOutliers').val();
+ if (label === "Hide Outliers") {
+ return $('#showHideOutliers').val("Show Outliers");
+ } else if (label === "Show Outliers") {
+ $('#showHideOutliers').val("Hide Outliers");
+ return console.log("Should be now Hide Outliers");
+ }
+};
+
+onCorrMethodChange = function() {
+ var corr_method;
+ corr_method = $('select[name=corr_type]').val();
+ $('.correlation_desc').hide();
+ $('#' + corr_method + "_r_desc").show().effect("highlight");
+ if (corr_method === "lit") {
+ return $("#corr_sample_method").hide();
+ } else {
+ return $("#corr_sample_method").show();
+ }
+};
+$('select[name=corr_type]').change(onCorrMethodChange);
+
+on_dataset_change = function() {
+ let dataset_type = $('select[name=corr_dataset] option:selected').data('type');
+ let location_type = $('select[name=location_type] option:selected').val();
+
+ if (dataset_type == "mrna_assay"){
+ $('#min_expr_filter').show();
+ $('select[name=location_type] option:disabled').prop('disabled', false)
+ }
+ else if (dataset_type == "pheno"){
+ $('#min_expr_filter').show();
+ $('select[name=location_type]>option:eq(0)').prop('disabled', true).attr('selected', false);
+ $('select[name=location_type]>option:eq(1)').prop('disabled', false).attr('selected', true);
+ }
+ else {
+ $('#min_expr_filter').hide();
+ $('select[name=location_type]>option:eq(0)').prop('disabled', false).attr('selected', true);
+ $('select[name=location_type]>option:eq(1)').prop('disabled', true).attr('selected', false);
+ }
+}
+
+$('select[name=corr_dataset]').change(on_dataset_change);
+$('select[name=location_type]').change(on_dataset_change);
+
+submit_special = function(url) {
+ $("input[name=sample_vals]").val(JSON.stringify(fetchSampleValues()))
+ $("#trait_data_form").attr("action", url);
+
+ $("#trait_data_form").submit();
+};
+
+var corrInputList = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr',
+ 'corr_return_results', 'location_type', 'loc_chr', 'min_loc_mb', 'max_loc_mb', 'p_range_lower', 'p_range_upper',"use_cache"]
+
+$(".test_corr_compute").on("click", (function(_this) {
+ return function() {
+ $('input[name=tool_used]').val("Correlation");
+ $('input[name=form_url]').val("/test_corr_compute");
+ $('input[name=wanted_inputs]').val(corrInputList.join(","));
+
+
+ url = "/loading";
+ return submit_special(url);
+ };
+})(this));
+
+$(".corr_compute").on("click", (function(_this) {
+
+ return function() {
+
+
+ $('input[name=tool_used]').val("Correlation");
+ $('input[name=form_url]').val("/corr_compute");
+ $('input[name=wanted_inputs]').val(corrInputList.join(","));
+
+
+ $('input[name=use_cache]').val($('#use_cache').is(":checked") ? "true": "false");
+
+ url = "/loading";
+ return submit_special(url);
+ };
+})(this));
+
+createValueDropdown = function(value) {
+ return "<option val=" + value + ">" + value + "</option>";
+};
+
+populateSampleAttributesValuesDropdown = function() {
+ var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results;
+ $('#attribute_values').empty();
+ sample_attributes = [];
+
+ var attributesAsList = Object.keys(js_data.attributes).map(function(key) {
+ return [key, js_data.attributes[key].id];
+ });
+
+ attributesAsList.sort(function(first, second) {
+ if (second[1] > first[1]){
+ return -1
+ }
+ if (first[1] > second[1]){
+ return 1
+ }
+ return 0
+ });
+
+ for (i=0; i < attributesAsList.length; i++) {
+ attribute_info = js_data.attributes[attributesAsList[i][1]]
+ sample_attributes.push(attribute_info.distinct_values);
+ }
+
+ selected_attribute = $('#exclude_column').val()
+ _ref1 = sample_attributes[selected_attribute - 1];
+ _results = [];
+ for (_i = 0, _len = _ref1.length; _i < _len; _i++) {
+ value = _ref1[_i];
+ if (value != ""){
+ _results.push($(createValueDropdown(value)).appendTo($('#attribute_values')));
+ }
+ }
+ return _results;
+};
+
+if (js_data.categorical_attr_exists == "true"){
+ populateSampleAttributesValuesDropdown();
+}
+
+$('#exclude_column').change(populateSampleAttributesValuesDropdown);
+blockByAttributeValue = function() {
+ var attribute_name, cell_class, exclude_by_value;
+
+ let exclude_group = $('#exclude_by_attr_group').val();
+ let exclude_column = $('#exclude_column').val();
+
+ if (exclude_group === "other") {
+ var tableApi = $('#samples_other').DataTable();
+ } else {
+ var tableApi = $('#samples_primary').DataTable();
+ }
+
+ exclude_by_value = $('#attribute_values').val();
+
+ let val_nodes = tableApi.column(3).nodes().to$();
+ let exclude_val_nodes = tableApi.column(attributeStartPos + parseInt(exclude_column)).nodes().to$();
+
+ for (i = 0; i < exclude_val_nodes.length; i++) {
+ if (exclude_val_nodes[i].hasChildNodes()) {
+ let this_col_value = exclude_val_nodes[i].childNodes[0].data;
+ let this_val_node = val_nodes[i].childNodes[0];
+
+ if (this_col_value == exclude_by_value){
+ this_val_node.value = "x";
+ }
+ }
+ }
+
+ editDataChange();
+};
+$('#exclude_by_attr').click(blockByAttributeValue);
+
+blockByIndex = function() {
+ var end_index, error, index, index_list, index_set, index_string, start_index, _i, _j, _k, _len, _len1, _ref;
+ index_string = $('#remove_samples_field').val();
+ index_list = [];
+ _ref = index_string.split(",");
+ for (_i = 0, _len = _ref.length; _i < _len; _i++) {
+ index_set = _ref[_i];
+ if (index_set.indexOf('-') !== -1) {
+ try {
+ start_index = parseInt(index_set.split("-")[0]);
+ end_index = parseInt(index_set.split("-")[1]);
+ for (index = _j = start_index; start_index <= end_index ? _j <= end_index : _j >= end_index; index = start_index <= end_index ? ++_j : --_j) {
+ index_list.push(index);
+ }
+ } catch (_error) {
+ error = _error;
+ alert("Syntax error");
+ }
+ } else {
+ index = parseInt(index_set);
+ index_list.push(index);
+ }
+ }
+
+ let block_group = $('#block_group').val();
+ if (block_group === "other") {
+ tableApi = $('#samples_other').DataTable();
+ } else {
+ tableApi = $('#samples_primary').DataTable();
+ }
+ val_nodes = tableApi.column(3).nodes().to$();
+ for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
+ index = index_list[_k];
+ val_nodes[index - 1].childNodes[0].value = "x";
+ }
+};
+
+filter_by_study = function() {
+ let this_study = $('#filter_study').val();
+
+ let study_sample_data = JSON.parse($('input[name=study_samplelists]').val())
+ let filter_samples = study_sample_data[parseInt(this_study)]['samples']
+
+ if ($('#filter_study_group').length){
+ let block_group = $('#filter_study_group').val();
+ if (block_group === "other") {
+ tableApi = $('#samples_other').DataTable();
+ } else {
+ tableApi = $('#samples_primary').DataTable();
+ }
+ }
+
+ let sample_nodes = tableApi.column(2).nodes().to$();
+ let val_nodes = tableApi.column(3).nodes().to$();
+ for (i = 0; i < sample_nodes.length; i++) {
+ this_sample = sample_nodes[i].childNodes[0].innerText;
+ if (!filter_samples.includes(this_sample)){
+ val_nodes[i].childNodes[0].value = "x";
+ }
+ }
+}
+
+filter_by_value = function() {
+ let filter_logic = $('#filter_logic').val();
+ let filter_column = $('#filter_column').val();
+ let filter_value = $('#filter_value').val();
+ let block_group = $('#filter_group').val();
+
+ if (block_group === "other") {
+ var tableApi = $('#samples_other').DataTable();
+ } else {
+ var tableApi = $('#samples_primary').DataTable();
+ }
+
+ let val_nodes = tableApi.column(3).nodes().to$();
+ if (filter_column == "value"){
+ var filter_val_nodes = tableApi.column(3).nodes().to$();
+ }
+ else if (filter_column == "stderr"){
+ var filter_val_nodes = tableApi.column(5).nodes().to$();
+ }
+ else if (!isNaN(filter_column)){
+ var filter_val_nodes = tableApi.column(attributeStartPos + parseInt(filter_column)).nodes().to$();
+ }
+ else {
+ return false
+ }
+
+ for (i = 0; i < filter_val_nodes.length; i++) {
+ if (filter_column == "value" || filter_column == "stderr"){
+ var this_col_value = filter_val_nodes[i].childNodes[0].value;
+ } else {
+ if (filter_val_nodes[i].childNodes[0] !== undefined){
+ var this_col_value = filter_val_nodes[i].innerText;
+ } else {
+ continue
+ }
+ }
+ let this_val_node = val_nodes[i].childNodes[0];
+
+ if(!isNaN(this_col_value) && !isNaN(filter_value)) {
+ if (filter_logic == "greater_than"){
+ if (parseFloat(this_col_value) <= parseFloat(filter_value)){
+ this_val_node.value = "x";
+ }
+ }
+ else if (filter_logic == "less_than"){
+ if (parseFloat(this_col_value) >= parseFloat(filter_value)){
+ this_val_node.value = "x";
+ }
+ }
+ else if (filter_logic == "greater_or_equal"){
+ if (parseFloat(this_col_value) < parseFloat(filter_value)){
+ this_val_node.value = "x";
+ }
+ }
+ else if (filter_logic == "less_or_equal"){
+ if (parseFloat(this_col_value) > parseFloat(filter_value)){
+ this_val_node.value = "x";
+ }
+ }
+ }
+ }
+};
+
+hideNoValue_filter = function( settings, data, dataIndex ) {
+ this_value = tableApi.column(3).nodes().to$()[dataIndex].childNodes[0].value;
+ if (this_value == "x"){
+ return false
+ } else {
+ return true
+ }
+}
+
+hideNoValue = function() {
+ tables = ['samples_primary', 'samples_other'];
+ filter_active = $(this).data("active");
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ tableApi = $('#' + table).DataTable();
+ if (filter_active == "true"){
+ $(this).val("Hide No Value")
+ tableApi.draw();
+ $(this).data("active", "false");
+ } else {
+ $(this).val("Show No Value")
+ $.fn.dataTable.ext.search.push(hideNoValue_filter);
+ tableApi.search();
+ tableApi.draw();
+ $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hideNoValue_filter, 1));
+ $(this).data("active", "true");
+ }
+ }
+ }
+};
+$('#hideNoValue').click(hideNoValue);
+
+blockOutliers = function() {
+ return $('.outlier').each((function(_this) {
+ return function(_index, element) {
+ return $(element).find('.trait-value-input').val('x');
+ };
+ })(this));
+};
+$('#blockOutliers').click(blockOutliers);
+
+resetSamplesTable = function() {
+ $('input[name="transform"]').val("");
+ $('span[name="transform_text"]').text("")
+ $('#hideNoValue').val("Hide No Value")
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ tableApi = $('#' + table).DataTable();
+ val_nodes = tableApi.column(3).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0];
+ this_node.value = this_node.attributes["data-value"].value;
+ }
+ if (js_data.se_exists){
+ se_nodes = tableApi.column(5).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0];
+ this_node.value = this_node.attributes["data-value"].value;
+ }
+ }
+ tableApi.draw();
+ }
+ }
+};
+$('.reset').click(function() {
+ $('.selected').each(function() {
+ $(this).removeClass('selected');
+ $(this).find('.edit_sample_checkbox').prop("checked", false);
+ })
+ resetSamplesTable();
+ $('input[name="transform"]').val("");
+ editDataChange();
+});
+
+checkForZeroToOneVals = function() {
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ tableApi = $('#' + table).DataTable();
+ val_nodes = tableApi.column(3).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0];
+ if(!isNaN(this_node.value)) {
+ if (0 <= this_node.value && this_node.value < 1){
+ return true
+ }
+ }
+ }
+ }
+ }
+ return false
+}
+
+log2Data = function(this_node) {
+ current_value = this_node.value;
+ original_value = this_node.attributes['data-value'].value;
+ if(!isNaN(current_value) && !isNaN(original_value)) {
+ if (zeroToOneValsExist){
+ original_value = parseFloat(original_value) + 1;
+ }
+ this_node.value = Math.log2(original_value).toFixed(3);
+ }
+};
+
+log10Data = function() {
+ current_value = this_node.value;
+ original_value = this_node.attributes['data-value'].value;
+ if(!isNaN(current_value) && !isNaN(original_value)) {
+ if (zeroToOneValsExist){
+ original_value = parseFloat(original_value) + 1;
+ }
+ this_node.value = Math.log10(original_value).toFixed(3);
+ }
+};
+
+sqrtData = function() {
+ current_value = this_node.value;
+ original_value = this_node.attributes['data-value'].value;
+ if(!isNaN(current_value) && !isNaN(original_value)) {
+ if (zeroToOneValsExist){
+ original_value = parseFloat(original_value) + 1;
+ }
+ this_node.value = Math.sqrt(original_value).toFixed(3);
+ }
+};
+
+invertData = function() {
+ current_value = this_node.value;
+ if(!isNaN(current_value)) {
+ this_node.value = parseFloat(-(current_value)).toFixed(3);
+ }
+};
+
+qnormData = function() {
+ current_value = this_node.value;
+ qnorm_value = this_node.attributes['data-qnorm'].value;
+ if(!isNaN(current_value)) {
+ this_node.value = qnorm_value;
+ }
+};
+
+zScoreData = function() {
+ current_value = this_node.value;
+ zscore_value = this_node.attributes['data-zscore'].value;
+ if(!isNaN(current_value)) {
+ this_node.value = zscore_value;
+ }
+};
+
+doTransform = function(transform_type) {
+ tables = ['samples_primary', 'samples_other'];
+ for (_i = 0, _len = tables.length; _i < _len; _i++) {
+ table = tables[_i];
+ if ($('#' + table).length) {
+ tableApi = $('#' + table).DataTable();
+ val_nodes = tableApi.column(3).nodes().to$();
+ for (i = 0; i < val_nodes.length; i++) {
+ this_node = val_nodes[i].childNodes[0]
+ if (transform_type == "log2"){
+ log2Data(this_node)
+ }
+ if (transform_type == "log10"){
+ log10Data(this_node)
+ }
+ if (transform_type == "sqrt"){
+ sqrtData(this_node)
+ }
+ if (transform_type == "invert"){
+ invertData(this_node)
+ }
+ if (transform_type == "qnorm"){
+ qnormData(this_node)
+ }
+ if (transform_type == "zscore"){
+ zScoreData(this_node)
+ }
+ }
+ }
+ }
+}
+
+normalizeData = function() {
+ if ($('#norm_method option:selected').val() == 'log2' || $('#norm_method option:selected').val() == 'log10'){
+ if ($('input[name="transform"]').val() != "log2" && $('#norm_method option:selected').val() == 'log2') {
+ doTransform("log2")
+ $('input[name="transform"]').val("log2")
+ $('span[name="transform_text"]').text(" - log2 Transformed")
+ } else {
+ if ($('input[name="transform"]').val() != "log10" && $('#norm_method option:selected').val() == 'log10'){
+ doTransform("log10")
+ $('input[name="transform"]').val("log10")
+ $('span[name="transform_text"]').text(" - log10 Transformed")
+ }
+ }
+ }
+ else if ($('#norm_method option:selected').val() == 'sqrt'){
+ if ($('input[name="transform"]').val() != "sqrt") {
+ doTransform("sqrt")
+ $('input[name="transform"]').val("sqrt")
+ $('span[name="transform_text"]').text(" - Square Root Transformed")
+ }
+ }
+ else if ($('#norm_method option:selected').val() == 'invert'){
+ doTransform("invert")
+ $('input[name="transform"]').val("inverted")
+ if ($('span[name="transform_text"]:eq(0)').text() != ""){
+ current_text = $('span[name="transform_text"]:eq(0)').text();
+ $('span[name="transform_text"]').text(current_text + " and Inverted");
+ } else {
+ $('span[name="transform_text"]').text(" - Inverted")
+ }
+ }
+ else if ($('#norm_method option:selected').val() == 'qnorm'){
+ if ($('input[name="transform"]').val() != "qnorm") {
+ doTransform("qnorm")
+ $('input[name="transform"]').val("qnorm")
+ $('span[name="transform_text"]').text(" - Quantile Normalized")
+ }
+ }
+ else if ($('#norm_method option:selected').val() == 'zscore'){
+ if ($('input[name="transform"]').val() != "zscore") {
+ doTransform("zscore")
+ $('input[name="transform"]').val("zscore")
+ $('span[name="transform_text"]').text(" - Z-Scores")
+ }
+ }
+}
+
+zeroToOneValsExist = checkForZeroToOneVals();
+
+showTransformWarning = function() {
+ transform_type = $('#norm_method option:selected').val()
+ if (transform_type == "log2" || transform_type == "log10"){
+ if (zeroToOneValsExist){
+ $('#transform_alert').css("display", "block")
+ }
+ } else {
+ $('#transform_alert').css("display", "none")
+ }
+}
+
+$('#norm_method').change(function(){
+ showTransformWarning()
+});
+$('#normalize').hover(function(){
+ showTransformWarning()
+});
+
+$('#normalize').click(normalizeData)
+
+switchQNormData = function() {
+ return $('.trait-value-input').each((function(_this) {
+ return function(_index, element) {
+ transform_val = $(element).data('transform')
+ if (transform_val != "") {
+ $(element).val(transform_val.toFixed(3));
+ }
+ return transform_val
+ };
+ })(this));
+};
+$('#qnorm').click(switchQNormData);
+
+getSampleTableData = function(tableName, attributesAsList, includeNAs=false) {
+ var samples = [];
+
+ if ($('#' + tableName).length){
+ tableApi = $('#' + tableName).DataTable();
+ attrCol = 4
+
+ nameNodes = tableApi.column(2).nodes().to$();
+ valNodes = tableApi.column(3).nodes().to$();
+ if (js_data.se_exists){
+ varNodes = tableApi.column(5).nodes().to$();
+ attrCol = 6
+ if (js_data.has_num_cases) {
+ nNodes = tableApi.column(6).nodes().to$();
+ attrCol = 7
+ }
+ } else {
+ if (js_data.has_num_cases){
+ nNodes = tableApi.column(4).nodes().to$();
+ attrCol = 5
+ }
+ }
+
+ attributeNodes = []
+ for (_i = 0; _i < attributesAsList.length; _i++){
+ attributeNodes.push(tableApi.column(attrCol + _i).nodes().to$())
+ }
+
+ checkedRows = getCheckedRows(tableName)
+
+ for (_j = 0; _j < valNodes.length; _j++){
+ if (!checkedRows.includes(_j) && checkedRows.length > 0) {
+ continue
+ }
+ sampleVal = valNodes[_j].childNodes[0].value
+ sampleName = $.trim(nameNodes[_j].childNodes[0].textContent)
+ if (isNumber(sampleVal) && sampleVal !== "") {
+ sampleVal = parseFloat(sampleVal);
+ } else {
+ sampleVal = 'x'
+ }
+ if (typeof varNodes == 'undefined'){
+ sampleVar = null;
+ } else {
+ sampleVar = varNodes[_j].childNodes[0].value;
+ if (isNumber(sampleVar)) {
+ sampleVar = parseFloat(sampleVar);
+ } else {
+ sampleVar = 'x';
+ }
+ }
+ if (typeof nNodes == 'undefined'){
+ sampleN = null;
+ } else {
+ sampleN = nNodes[_j].childNodes[0].value;
+ if (isNumber(sampleN)) {
+ sampleN = parseInt(sampleN);
+ } else {
+ sampleN = 'x';
+ }
+ }
+
+ rowDict = {
+ name: sampleName,
+ value: sampleVal,
+ se: sampleVar,
+ num_cases: sampleN
+ }
+
+ for (_k = 0; _k < attributeNodes.length; _k++){
+ rowDict[attributesAsList[_k]] = attributeNodes[_k][_j].textContent;
+ }
+ if (includeNAs || sampleVal != 'x') {
+ samples.push(rowDict)
+ }
+ }
+ }
+
+ return samples;
+};
+exportSampleTableData = function() {
+ var format, json_sample_data, sample_data;
+
+ var attributesAsList = Object.keys(js_data.attributes).map(function(key) {
+ return js_data.attributes[key].name;
+ });
+
+ sample_data = {};
+ sample_data.primary_samples = getSampleTableData('samples_primary', attributesAsList, true);
+ sample_data.other_samples = getSampleTableData('samples_other', attributesAsList, true);
+ sample_data.attributes = attributesAsList;
+ json_sample_data = JSON.stringify(sample_data);
+ $('input[name=export_data]').val(json_sample_data);
+ format = $('input[name=export_format]').val();
+ if (format === "excel") {
+ $('#trait_data_form').attr('action', '/export_trait_excel');
+ } else {
+ $('#trait_data_form').attr('action', '/export_trait_csv');
+ }
+ return $('#trait_data_form').submit();
+};
+
+$('.export_format').change(function() {
+ if (this.value == "csv"){
+ $('#export_code').css("display", "block")
+ } else{
+ $('#export_code').css("display", "none")
+ }
+ $('input[name=export_format]').val( this.value );
+ $('.export_format').val( this.value );
+});
+
+$('.export').click(exportSampleTableData);
+$('#blockOutliers').click(blockOutliers);
+_.mixin(_.str.exports());
+
+getSampleVals = function(sample_list) {
+ var sample;
+ return this.sample_vals = (function() {
+ var i, len, results;
+ results = [];
+ for (i = 0, len = sample_list.length; i < len; i++) {
+ sample = sample_list[i];
+ if (sample.value !== null) {
+ results.push(sample.value);
+ }
+ }
+ return results;
+ })();
+};
+
+getSampleErrors = function(sample_list) {
+ var sample;
+ return this.sample_vals = (function() {
+ var i, len, results;
+ variance_exists = false;
+ results = [];
+ for (i = 0, len = sample_list.length; i < len; i++) {
+ sample = sample_list[i];
+ if (sample.variance !== null) {
+ results.push(sample.variance);
+ variance_exists = true;
+ }
+ }
+ return [results, variance_exists];
+ })();
+};
+
+getSampleNames = function(sample_list) {
+ var sample;
+ return this.sampleNames = (function() {
+ var i, len, results;
+ results = [];
+ for (i = 0, len = sample_list.length; i < len; i++) {
+ sample = sample_list[i];
+ if (sample.value !== null) {
+ results.push(sample.name);
+ }
+ }
+ return results;
+ })();
+};
+
+getBarBottomMargin = function(sample_list){
+ bottomMargin = 80
+ maxLength = 0
+ sampleNames = getSampleNames(sample_list)
+ for (i=0; i < sampleNames.length; i++){
+ if (sampleNames[i].length > maxLength) {
+ maxLength = sampleNames[i].length
+ }
+ }
+
+ if (maxLength > 6){
+ bottomMargin += 11*(maxLength - 6)
+ }
+
+ return bottomMargin;
+}
+
+root.stats_group = 'samples_primary';
+
+if (Object.keys(js_data.sample_group_types).length > 1) {
+ fullSampleLists = [sampleLists[0], sampleLists[1], sampleLists[0].concat(sampleLists[1])]
+ sampleGroupList = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']]
+} else {
+ fullSampleLists = [sampleLists[0]]
+ sampleGroupList = [js_data.sample_group_types['samples_primary']]
+}
+
+// Define Plotly Options (for the options bar at the top of each figure)
+
+root.modebar_options = {
+ displayModeBar: true,
+ modeBarButtonsToAdd:[{
+ name: 'Export as SVG',
+ icon: Plotly.Icons.disk,
+ click: function(gd) {
+ Plotly.downloadImage(gd, {format: 'svg'})
+ }
+ },
+ {
+ name: 'Export as JPEG',
+ icon: Plotly.Icons.camera,
+ click: function(gd) {
+ Plotly.downloadImage(gd, {format: 'jpeg'})
+ }
+ }],
+ showEditInChartStudio: true,
+ plotlyServerURL: "https://chart-studio.plotly.com",
+ modeBarButtonsToRemove:['zoom2d', 'pan2d', 'toImage', 'hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines', 'resetScale2d'],
+ displaylogo: false
+ //modeBarButtons:['toImage2', 'zoom2d', 'pan2d', 'select2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d'],
+}
+
+// Bar Chart
+
+root.errors_exist = getSampleErrors(sampleLists[0])[1]
+var barTrace = {
+ x: getSampleNames(sampleLists[0]),
+ y: getSampleVals(sampleLists[0]),
+ error_y: {
+ type: 'data',
+ array: getSampleErrors(sampleLists[0])[0],
+ visible: root.errors_exist
+ },
+ type: 'bar'
+}
+
+root.bar_data = [barTrace]
+
+getBarRange = function(sample_vals, sampleErrors = null){
+ positiveErrorVals = []
+ negativeErrorVals = []
+ for (i = 0;i < sample_vals.length; i++){
+ if (sampleErrors[i] != undefined) {
+ positiveErrorVals.push(sample_vals[i] + sampleErrors[i])
+ negativeErrorVals.push(sample_vals[i] - sampleErrors[i])
+ } else {
+ positiveErrorVals.push(sample_vals[i])
+ negativeErrorVals.push(sample_vals[i])
+ }
+ }
+
+ minYVal = Math.min(...negativeErrorVals)
+ maxYVal = Math.max(...positiveErrorVals)
+
+ if (minYVal == 0) {
+ rangeTop = maxYVal + Math.abs(maxYVal)*0.1
+ rangeBottom = 0;
+ } else {
+ rangeTop = maxYVal + Math.abs(maxYVal)*0.1
+ rangeBottom = minYVal - Math.abs(minYVal)*0.1
+ if (minYVal > 0) {
+ rangeBottom = minYVal - 0.1*Math.abs(minYVal)
+ } else if (minYVal < 0) {
+ rangeBottom = minYVal + 0.1*minYVal
+ } else {
+ rangeBottom = 0
+ }
+ }
+
+ return [rangeBottom, rangeTop]
+}
+
+root.chart_range = getBarRange(getSampleVals(sampleLists[0]), getSampleErrors(sampleLists[0])[0])
+valRange = root.chart_range[1] - root.chart_range[0]
+
+if (valRange < 0.05){
+ tickDigits = '.3f'
+ leftMargin = 80
+} else if (valRange < 0.5) {
+ tickDigits = '.2f'
+ leftMargin = 70
+} else if (valRange < 5){
+ tickDigits = '.1f'
+ leftMargin = 60
+} else {
+ tickDigits = 'f'
+ leftMargin = 55
+}
+
+if (js_data.num_values < 256) {
+ barChartWidth = 25 * getSampleVals(sampleLists[0]).length
+
+ // Set bottom margin dependent on longest sample name length, since those can get long
+ bottomMargin = getBarBottomMargin(sampleLists[0])
+
+ root.bar_layout = {
+ title: {
+ x: 0,
+ y: 10,
+ xanchor: 'left',
+ text: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
+ },
+ xaxis: {
+ type: 'category',
+ titlefont: {
+ size: 16
+ },
+ showline: true,
+ ticklen: 4,
+ tickfont: {
+ size: 16
+ },
+ },
+ yaxis: {
+ title: "<b>" + js_data.unit_type + "</b>",
+ range: root.chart_range,
+ titlefont: {
+ size: 16
+ },
+ showline: true,
+ ticklen: 4,
+ tickfont: {
+ size: 16
+ },
+ tickformat: tickDigits,
+ fixedrange: true
+ },
+ width: barChartWidth,
+ height: 600,
+ margin: {
+ l: leftMargin,
+ r: 30,
+ t: 100,
+ b: bottomMargin
+ },
+ dragmode: false
+ };
+
+ $('.bar_chart_tab').click(function() {
+ updateBarChart();
+ });
+}
+
+total_sample_count = 0
+for (i = 0, i < sampleLists.length; i++;) {
+ total_sample_count += getSampleVals(sampleLists[i]).length
+}
+
+// Histogram
+var hist_trace = {
+ x: getSampleVals(sampleLists[0]),
+ type: 'histogram'
+};
+root.histogram_data = [hist_trace];
+root.histogram_layout = {
+ bargap: 0.05,
+ title: {
+ x: 0,
+ y: 10,
+ xanchor: 'left',
+ text: "<b> Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
+ },
+ xaxis: {
+ autorange: true,
+ title: js_data.unit_type,
+ titlefont: {
+ family: "arial",
+ size: 16
+ },
+ ticklen: 4,
+ tickfont: {
+ size: 16
+ }
+ },
+ yaxis: {
+ autorange: true,
+ title: "<b>count</b>",
+ titlefont: {
+ family: "arial",
+ size: 16
+ },
+ showline: true,
+ ticklen: 4,
+ tickfont: {
+ size: 16
+ },
+ automargin: true,
+ fixedrange: true
+ },
+ width: 500,
+ height: 600,
+ margin: {
+ l: 100,
+ r: 30,
+ t: 100,
+ b: 50
+ }
+};
+
+$('.histogram_tab').click(function() {
+ updateHistogram();
+ updateHistogram_width();
+});
+
+$('.histogram_samples_group').val(root.stats_group);
+$('.histogram_samples_group').change(function() {
+ root.stats_group = $(this).val();
+ return updateHistogram();
+});
+
+// Violin Plot
+
+root.violin_layout = {
+ title: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>",
+ xaxis: {
+ showline: true,
+ titlefont: {
+ family: "arial",
+ size: 16
+ },
+ tickfont: {
+ family: "arial",
+ size: 16
+ }
+ },
+ yaxis: {
+ title: {
+ text: "<b>"+js_data.unit_type+"</b>"
+ },
+ titlefont: {
+ family: "arial",
+ size: 16
+ },
+ autorange: true,
+ showline: true,
+ ticklen: 4,
+ tickfont: {
+ size: 16
+ },
+ tickformat: tickDigits,
+ zeroline: false,
+ automargin: true
+ },
+ margin: {
+ l: 100,
+ r: 30,
+ t: 100,
+ b: 80
+ },
+ dragmode: false,
+ showlegend: false
+};
+
+if (fullSampleLists.length > 1) {
+ root.violin_layout['width'] = 600;
+ root.violin_layout['height'] = 500;
+ var trace1 = {
+ y: getSampleVals(fullSampleLists[2]),
+ type: 'violin',
+ points: 'none',
+ box: {
+ visible: true
+ },
+ line: {
+ color: 'blue',
+ },
+ meanline: {
+ visible: true
+ },
+ name: "<b>" + sampleGroupList[2] + "</b>",
+ x0: "<b>" + sampleGroupList[2] + "</b>"
+ }
+ var trace2 = {
+ y: getSampleVals(fullSampleLists[1]),
+ type: 'violin',
+ points: 'none',
+ box: {
+ visible: true
+ },
+ line: {
+ color: 'red',
+ },
+ meanline: {
+ visible: true
+ },
+ name: "<b>" + sampleGroupList[1] + "</b>",
+ x0: "<b>" + sampleGroupList[1] + "</b>"
+ }
+ var trace3 = {
+ y: getSampleVals(fullSampleLists[0]),
+ type: 'violin',
+ points: 'none',
+ box: {
+ visible: true
+ },
+ line: {
+ color: 'green',
+ },
+ meanline: {
+ visible: true
+ },
+ name: "<b>" + sampleGroupList[0] + "</b>",
+ x0: "<b>" + sampleGroupList[0] + "</b>"
+ }
+ root.violin_data = [trace1, trace2, trace3]
+} else {
+ root.violin_layout['width'] = 320;
+ root.violin_layout['height'] = 400;
+ root.violin_data = [
+ {
+ y: getSampleVals(fullSampleLists[0]),
+ type: 'violin',
+ points: 'none',
+ box: {
+ visible: true
+ },
+ meanline: {
+ visible: true
+ },
+ name: "<b>Trait " + js_data.trait_id + "</b>",
+ x0: "<b>density</b>"
+ }
+ ]
+}
+
+$('.violin_plot_tab').click(function() {
+ updateViolinPlot();
+});
+
+if (getSampleVals(sampleLists[0]).length < 256) {
+ $('.bar_chart_samples_group').change(function() {
+ root.stats_group = $(this).val();
+ return updateBarChart();
+ });
+ root.bar_sort = "name"
+}
+$('.sort_by_name').click(function() {
+ root.bar_sort = "name"
+ return updateBarChart();
+});
+$('.sort_by_value').click(function() {
+ root.bar_sort = "value"
+ return updateBarChart();
+});
+
+root.prob_plot_group = 'samples_primary';
+$('.prob_plot_samples_group').val(root.prob_plot_group);
+$('.prob_plot_tab').click(function() {
+ return updateProbPlot();
+});
+$('.prob_plot_samples_group').change(function() {
+ root.prob_plot_group = $(this).val();
+ return updateProbPlot();
+});
+
+function isEmpty( el ){
+ return !$.trim(el.html())
+}
+
+$('.stats_panel').click(function() {
+ if (isEmpty($('#stats_table'))){
+ makeTable();
+ editDataChange();
+ } else {
+ editDataChange();
+ }
+});
+
+$('#block_by_index').click(function(){
+ blockByIndex();
+ editDataChange();
+});
+
+$('#filter_by_study').click(function(){
+ filter_by_study();
+ editDataChange();
+})
+
+$('#filter_by_value').click(function(){
+ filter_by_value();
+ editDataChange();
+})
+
+$('.edit_sample_value').change(function() {
+ editDataChange();
+});
+
+$('#exclude_group').click(editDataChange);
+$('#blockOutliers').click(editDataChange);
+$('#reset').click(editDataChange);
+$('#qnorm').click(editDataChange);
+$('#normalize').click(editDataChange);
+
+Number.prototype.countDecimals = function () {
+ if(Math.floor(this.valueOf()) === this.valueOf()) return 0;
+ return this.toString().split(".")[1].length || 0;
+}
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-18 19:33:57 +0000