diff options
Diffstat (limited to 'gn2/wqflask/static/new/javascript/show_trait.js')
| -rw-r--r-- | gn2/wqflask/static/new/javascript/show_trait.js | 1677 |
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 new file mode 100644 index 00000000..c5214947 --- /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; +} |