From 606718eef5bcc24baac69c24a65c4fdec984ef25 Mon Sep 17 00:00:00 2001 From: zsloan Date: Wed, 27 Jul 2022 21:48:48 +0000 Subject: Change most variables in show_trait.js to camelCase --- .../wqflask/static/new/javascript/show_trait.js | 584 ++++++++++----------- 1 file changed, 292 insertions(+), 292 deletions(-) diff --git a/wqflask/wqflask/static/new/javascript/show_trait.js b/wqflask/wqflask/static/new/javascript/show_trait.js index 6b81b47e..1b79e261 100644 --- a/wqflask/wqflask/static/new/javascript/show_trait.js +++ b/wqflask/wqflask/static/new/javascript/show_trait.js @@ -1,12 +1,12 @@ -var Stat_Table_Rows, is_number, +var statTableRows, isNumber, __hasProp = {}.hasOwnProperty, __slice = [].slice; -is_number = function(o) { +isNumber = function(o) { return !isNaN((o - 0) && o !== null); }; -Stat_Table_Rows = [ +statTableRows = [ { vn: "n_of_samples", pretty: "N of Samples", @@ -40,27 +40,27 @@ Stat_Table_Rows = [ if (js_data.dataset_type == "ProbeSet"){ if (js_data.data_scale == "linear_positive" || js_data.data_scale == "log2") { - Stat_Table_Rows.push({ + statTableRows.push({ vn: "range", pretty: "Range (log2)", digits: 3 }) } else { - Stat_Table_Rows.push({ + statTableRows.push({ vn: "range", pretty: "Range", digits: 3 }) } } else { - Stat_Table_Rows.push({ + statTableRows.push({ vn: "range", pretty: "Range", digits: 3 }) } -Stat_Table_Rows.push( +statTableRows.push( { vn: "range_fold", pretty: "Range (fold)", @@ -83,7 +83,7 @@ Stat_Table_Rows.push( } ); -var add, block_by_attribute_value, block_by_index, block_outliers, change_stats_value, create_value_dropdown, edit_data_change, export_sample_table_data, get_sample_table_data, hide_no_value, hide_tabs, make_table, on_corr_method_change, open_trait_selection, populate_sample_attributes_values_dropdown, process_id, update_bar_chart, update_histogram, update_prob_plot, reset_samples_table, sample_group_types, sample_lists, show_hide_outliers, stats_mdp_change, update_stat_values; +var add, blockByAttributeValue, blockByIndex, blockOutliers, changeStatsValue, createValueDropdown, editDataChange, exportSampleTableData, getSampleTableData, hideNoValue, hideTabs, makeTable, onCorrMethodChange, openTraitSelection, populateSampleAttributesValuesDropdown, processId, updateBarChart, updateHistogram, updateProbPlot, resetSamplesTable, sampleGroupTypes, sampleLists, showHideOutliers, statsMdpChange, updateStatValues; add = function() { var trait; trait = $("input[name=trait_hmac]").val(); @@ -92,11 +92,11 @@ add = function() { }); }; $('#add_to_collection').click(add); -sample_lists = js_data.sample_lists; -sample_group_types = js_data.sample_group_types; +sampleLists = js_data.sample_lists; +sampleGroupTypes = js_data.sample_group_types; $(".select_covariates").click(function () { - open_covariate_selection(); + openCovariateSelection(); }); $(".remove_covariates").click(function () { @@ -146,7 +146,7 @@ $(".remove_all_covariates").click(function() { $("input[name=covariates]").val(""); }) -open_trait_selection = function() { +openTraitSelection = function() { return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { return function() { $.colorbox({ @@ -160,7 +160,7 @@ open_trait_selection = function() { }; })(this)); }; -open_covariate_selection = function() { +openCovariateSelection = function() { return $('#collections_holder').load('/collections/list #collections_list', (function(_this) { return function() { $.colorbox({ @@ -176,7 +176,7 @@ open_covariate_selection = function() { }; })(this)); }; -hide_tabs = function(start) { +hideTabs = function(start) { var x, _i, _results; _results = []; for (x = _i = start; start <= 10 ? _i <= 10 : _i >= 10; x = start <= 10 ? ++_i : --_i) { @@ -184,15 +184,15 @@ hide_tabs = function(start) { } return _results; }; -stats_mdp_change = function() { +statsMdpChange = function() { var selected; selected = $(this).val(); - hide_tabs(0); + hideTabs(0); return $("#stats_tabs" + selected).show(); }; -change_stats_value = function(sample_sets, category, value_type, decimal_places, effects) { +changeStatsValue = function(sample_sets, category, value_type, decimal_places, effects) { var current_value, id, in_box, the_value, title_value; - id = "#" + process_id(category, value_type); + id = "#" + processId(category, value_type); in_box = $(id).html; current_value = parseFloat($(in_box)).toFixed(decimal_places); the_value = sample_sets[category][value_type](); @@ -213,7 +213,7 @@ change_stats_value = function(sample_sets, category, value_type, decimal_places, return $(id).attr('title', title_value); } }; -update_stat_values = function(sample_sets) { +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']; @@ -223,9 +223,9 @@ update_stat_values = function(sample_sets) { _results.push((function() { var _j, _len1, _results1; _results1 = []; - for (_j = 0, _len1 = Stat_Table_Rows.length; _j < _len1; _j++) { - row = Stat_Table_Rows[_j]; - _results1.push(change_stats_value(sample_sets, category, row.vn, row.digits, show_effects)); + 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; })()); @@ -233,7 +233,7 @@ update_stat_values = function(sample_sets) { return _results; }; -update_histogram_width = function() { +updateHistogram_width = function() { num_bins = $('#histogram').find('g.trace.bars').find('g.point').length if (num_bins < 10) { @@ -245,7 +245,7 @@ update_histogram_width = function() { } } -update_histogram = function() { +updateHistogram = function() { var x; var _i, _len, _ref, data; _ref = _.values(root.selected_samples[root.stats_group]); @@ -263,10 +263,10 @@ update_histogram = function() { } Plotly.newPlot('histogram', root.histogram_data, root.histogram_layout, root.modebar_options); - update_histogram_width() + updateHistogram_width() }; -update_bar_chart = function() { +updateBarChart = function() { var x; var _i, _len, _ref, data; _ref = _.values(root.selected_samples[root.stats_group]); @@ -302,7 +302,7 @@ update_bar_chart = function() { } } - new_chart_range = get_bar_range(trait_vals, trait_vars) + new_chart_range = getBarRange(trait_vals, trait_vars) root.bar_layout['yaxis']['range'] = new_chart_range @@ -327,7 +327,7 @@ update_bar_chart = function() { update_box_plot = function() { var y_value_list = [] - if (sample_lists.length > 1) { + if (sampleLists.length > 1) { i = 0; for (var sample_group in root.selected_samples){ var trait_sample_data = _.values(root.selected_samples[sample_group]) @@ -358,9 +358,9 @@ update_box_plot = function() { Plotly.newPlot('box_plot', root.box_data, root.box_layout, root.modebar_options) } -update_violin_plot = function() { +updateViolinPlot = function() { var y_value_list = [] - if (sample_lists.length > 1) { + if (sampleLists.length > 1) { i = 0; for (var sample_group in root.selected_samples){ var trait_sample_data = _.values(root.selected_samples[sample_group]) @@ -392,11 +392,11 @@ update_violin_plot = function() { } -update_prob_plot = function() { +updateProbPlot = function() { return root.redraw_prob_plot_impl(root.selected_samples, root.prob_plot_group); }; -make_table = function() { +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 = "Trait " + js_data.trait_id + " - " + js_data.trait_symbol + "Statistic"; @@ -409,7 +409,7 @@ make_table = function() { for (key in _ref) { if (!__hasProp.call(_ref, key)) continue; value = _ref[key]; - the_id = process_id("column", key); + the_id = processId("column", key); if (Object.keys(_ref).length > 1) { header += "" + value + ""; } else { @@ -419,8 +419,8 @@ make_table = function() { header += ""; the_rows = ""; - for (_i = 0, _len = Stat_Table_Rows.length; _i < _len; _i++) { - row = Stat_Table_Rows[_i]; + for (_i = 0, _len = statTableRows.length; _i < _len; _i++) { + row = statTableRows[_i]; if ((row.vn == "range_fold") && js_data.dataset_type == "Publish"){ continue; } @@ -434,7 +434,7 @@ make_table = function() { for (key in _ref1) { if (!__hasProp.call(_ref1, key)) continue; value = _ref1[key]; - the_id = process_id(key, row.vn); + the_id = processId(key, row.vn); row_line += "N/A"; } row_line += ""; @@ -444,7 +444,7 @@ make_table = function() { table = header + the_rows; return $("#stats_table").append(table); }; -process_id = function() { +processId = function() { var processed, value, values, _i, _len; values = 1 <= arguments.length ? __slice.call(arguments, 0) : []; @@ -461,14 +461,14 @@ process_id = function() { return processed; }; -fetch_sample_values = function() { +fetchSampleValues = function() { // This is meant to fetch all sample values using DataTables API, since they can't all be submitted with the form when using Scroller (and this should also be faster) sample_val_dict = {}; table = 'samples_primary'; if ($('#' + table).length){ - table_api = $('#' + table).DataTable(); - val_nodes = table_api.column(3).nodes().to$(); + 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 @@ -479,7 +479,7 @@ fetch_sample_values = function() { return sample_val_dict; } -edit_data_change = function() { +editDataChange = function() { var already_seen, checkbox, name, real_dict, real_value, real_variance, row, rows, sample_sets, table, tables, _i, _j, _len, _len1; already_seen = {}; sample_sets = { @@ -497,20 +497,20 @@ edit_data_change = function() { for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; if ($('#' + table).length){ - table_api = $('#' + table).DataTable(); + tableApi = $('#' + table).DataTable(); sample_vals = []; - name_nodes = table_api.column(2).nodes().to$(); - val_nodes = table_api.column(3).nodes().to$(); - var_nodes = table_api.column(5).nodes().to$(); + 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 = $.trim(name_nodes[_j].childNodes[0].textContent) - if (is_number(sample_val) && sample_val !== "") { + if (isNumber(sample_val) && sample_val !== "") { sample_val = parseFloat(sample_val); sample_sets[table].add_value(sample_val); try { sample_var = var_nodes[_j].childNodes[0].value - if (is_number(sample_var)) { + if (isNumber(sample_var)) { sample_var = parseFloat(sample_var) } else { sample_var = null; @@ -534,37 +534,37 @@ edit_data_change = function() { } - update_stat_values(sample_sets); + updateStatValues(sample_sets); if ($('#histogram').hasClass('js-plotly-plot')){ - update_histogram(); + updateHistogram(); } if ($('#bar_chart').hasClass('js-plotly-plot')){ - update_bar_chart(); + updateBarChart(); } if ($('#box_plot').hasClass('js-plotly-plot')){ update_box_plot(); } if ($('#violin_plot').hasClass('js-plotly-plot')){ - update_violin_plot(); + updateViolinPlot(); } if ($('#prob_plot_div').hasClass('js-plotly-plot')){ - return update_prob_plot(); + return updateProbPlot(); } }; -show_hide_outliers = function() { +showHideOutliers = function() { var label; - label = $('#show_hide_outliers').val(); + label = $('#showHideOutliers').val(); if (label === "Hide Outliers") { - return $('#show_hide_outliers').val("Show Outliers"); + return $('#showHideOutliers').val("Show Outliers"); } else if (label === "Show Outliers") { - $('#show_hide_outliers').val("Hide Outliers"); + $('#showHideOutliers').val("Hide Outliers"); return console.log("Should be now Hide Outliers"); } }; -on_corr_method_change = function() { +onCorrMethodChange = function() { var corr_method; corr_method = $('select[name=corr_type]').val(); $('.correlation_desc').hide(); @@ -575,7 +575,7 @@ on_corr_method_change = function() { return $("#corr_sample_method").show(); } }; -$('select[name=corr_type]').change(on_corr_method_change); +$('select[name=corr_type]').change(onCorrMethodChange); on_dataset_change = function() { let dataset_type = $('select[name=corr_dataset] option:selected').data('type'); @@ -601,38 +601,38 @@ $('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(fetch_sample_values())) + $("input[name=sample_vals]").val(JSON.stringify(fetchSampleValues())) $("#trait_data_form").attr("action", url); $("#trait_data_form").submit(); }; -get_table_contents_for_form_submit = function(form_id) { - // Borrowed code from - https://stackoverflow.com/questions/31418047/how-to-post-data-for-the-whole-table-using-jquery-datatables - let this_form = $("#" + form_id); - var params = primary_table.$('input').serializeArray(); - - $.each(params, function(){ - // If element doesn't exist in DOM - if(!$.contains(document, this_form[this.name])){ - // Create a hidden element - this_form.append( - $('') - .attr('type', 'hidden') - .attr('name', this.name) - .val(this.value) - ); - } - }); -} - -var corr_input_list = ['sample_vals', 'corr_type', 'primary_samples', 'trait_id', 'dataset', 'group', 'tool_used', 'form_url', 'corr_sample_method', 'corr_samples_group', 'corr_dataset', 'min_expr', +// getTableContentsForFormSubmit = function(form_id) { +// // Borrowed code from - https://stackoverflow.com/questions/31418047/how-to-post-data-for-the-whole-table-using-jquery-datatables +// let this_form = $("#" + form_id); +// var params = primary_table.$('input').serializeArray(); + +// $.each(params, function(){ +// // If element doesn't exist in DOM +// if(!$.contains(document, this_form[this.name])){ +// // Create a hidden element +// this_form.append( +// $('') +// .attr('type', 'hidden') +// .attr('name', this.name) +// .val(this.value) +// ); +// } +// }); +// } + +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'] $(".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(corr_input_list.join(",")); + $('input[name=wanted_inputs]').val(corrInputList.join(",")); url = "/loading"; return submit_special(url); }; @@ -642,17 +642,17 @@ $(".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(corr_input_list.join(",")); + $('input[name=wanted_inputs]').val(corrInputList.join(",")); url = "/loading"; return submit_special(url); }; })(this)); -create_value_dropdown = function(value) { +createValueDropdown = function(value) { return ""; }; -populate_sample_attributes_values_dropdown = function() { +populateSampleAttributesValuesDropdown = function() { var attribute_info, key, sample_attributes, selected_attribute, value, _i, _len, _ref, _ref1, _results; $('#attribute_values').empty(); sample_attributes = []; @@ -682,33 +682,33 @@ populate_sample_attributes_values_dropdown = function() { for (_i = 0, _len = _ref1.length; _i < _len; _i++) { value = _ref1[_i]; if (value != ""){ - _results.push($(create_value_dropdown(value)).appendTo($('#attribute_values'))); + _results.push($(createValueDropdown(value)).appendTo($('#attribute_values'))); } } return _results; }; if (js_data.categorical_attr_exists == "true"){ - populate_sample_attributes_values_dropdown(); + populateSampleAttributesValuesDropdown(); } -$('#exclude_column').change(populate_sample_attributes_values_dropdown); -block_by_attribute_value = function() { +$('#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 table_api = $('#samples_other').DataTable(); + var tableApi = $('#samples_other').DataTable(); } else { - var table_api = $('#samples_primary').DataTable(); + var tableApi = $('#samples_primary').DataTable(); } exclude_by_value = $('#attribute_values').val(); - let val_nodes = table_api.column(3).nodes().to$(); - let exclude_val_nodes = table_api.column(attribute_start_pos + parseInt(exclude_column)).nodes().to$(); + let val_nodes = tableApi.column(3).nodes().to$(); + let exclude_val_nodes = tableApi.column(attributeStartPos + parseInt(exclude_column)).nodes().to$(); for (i = 0; i < exclude_val_nodes.length; i++) { if (exclude_val_nodes[i].hasChildNodes()) { @@ -721,11 +721,11 @@ block_by_attribute_value = function() { } } - edit_data_change(); + editDataChange(); }; -$('#exclude_by_attr').click(block_by_attribute_value); +$('#exclude_by_attr').click(blockByAttributeValue); -block_by_index = function() { +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 = []; @@ -751,11 +751,11 @@ block_by_index = function() { let block_group = $('#block_group').val(); if (block_group === "other") { - table_api = $('#samples_other').DataTable(); + tableApi = $('#samples_other').DataTable(); } else { - table_api = $('#samples_primary').DataTable(); + tableApi = $('#samples_primary').DataTable(); } - val_nodes = table_api.column(3).nodes().to$(); + val_nodes = tableApi.column(3).nodes().to$(); for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) { index = index_list[_k]; val_nodes[index - 1].childNodes[0].value = "x"; @@ -771,14 +771,14 @@ filter_by_study = function() { if ($('#filter_study_group').length){ let block_group = $('#filter_study_group').val(); if (block_group === "other") { - table_api = $('#samples_other').DataTable(); + tableApi = $('#samples_other').DataTable(); } else { - table_api = $('#samples_primary').DataTable(); + tableApi = $('#samples_primary').DataTable(); } } - let sample_nodes = table_api.column(2).nodes().to$(); - let val_nodes = table_api.column(3).nodes().to$(); + let sample_nodes = tableApi.column(2).nodes().to$(); + 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)){ @@ -794,20 +794,20 @@ filter_by_value = function() { let block_group = $('#filter_group').val(); if (block_group === "other") { - var table_api = $('#samples_other').DataTable(); + var tableApi = $('#samples_other').DataTable(); } else { - var table_api = $('#samples_primary').DataTable(); + var tableApi = $('#samples_primary').DataTable(); } - let val_nodes = table_api.column(3).nodes().to$(); + let val_nodes = tableApi.column(3).nodes().to$(); if (filter_column == "value"){ - var filter_val_nodes = table_api.column(3).nodes().to$(); + var filter_val_nodes = tableApi.column(3).nodes().to$(); } else if (filter_column == "stderr"){ - var filter_val_nodes = table_api.column(5).nodes().to$(); + var filter_val_nodes = tableApi.column(5).nodes().to$(); } else if (!isNaN(filter_column)){ - var filter_val_nodes = table_api.column(attribute_start_pos + parseInt(filter_column)).nodes().to$(); + var filter_val_nodes = tableApi.column(attributeStartPos + parseInt(filter_column)).nodes().to$(); } else { return false @@ -850,8 +850,8 @@ filter_by_value = function() { } }; -hide_no_value_filter = function( settings, data, dataIndex ) { - this_value = table_api.column(3).nodes().to$()[dataIndex].childNodes[0].value; +hideNoValue_filter = function( settings, data, dataIndex ) { + this_value = tableApi.column(3).nodes().to$()[dataIndex].childNodes[0].value; if (this_value == "x"){ return false } else { @@ -859,77 +859,77 @@ hide_no_value_filter = function( settings, data, dataIndex ) { } } -hide_no_value = function() { +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) { - table_api = $('#' + table).DataTable(); + tableApi = $('#' + table).DataTable(); if (filter_active == "true"){ $(this).val("Hide No Value") - table_api.draw(); + tableApi.draw(); $(this).data("active", "false"); } else { $(this).val("Show No Value") - $.fn.dataTable.ext.search.push(hide_no_value_filter); - table_api.search(); - table_api.draw(); - $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hide_no_value_filter, 1)); + $.fn.dataTable.ext.search.push(hideNoValue_filter); + tableApi.search(); + tableApi.draw(); + $.fn.dataTable.ext.search.splice($.fn.dataTable.ext.search.indexOf(hideNoValue_filter, 1)); $(this).data("active", "true"); } } } }; -$('#hide_no_value').click(hide_no_value); +$('#hideNoValue').click(hideNoValue); -block_outliers = function() { +blockOutliers = function() { return $('.outlier').each((function(_this) { return function(_index, element) { return $(element).find('.trait-value-input').val('x'); }; })(this)); }; -$('#block_outliers').click(block_outliers); +$('#blockOutliers').click(blockOutliers); -reset_samples_table = function() { +resetSamplesTable = function() { $('input[name="transform"]').val(""); $('span[name="transform_text"]').text("") - $('#hide_no_value').val("Hide No Value") + $('#hideNoValue').val("Hide No Value") tables = ['samples_primary', 'samples_other']; for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; if ($('#' + table).length) { - table_api = $('#' + table).DataTable(); - val_nodes = table_api.column(3).nodes().to$(); + 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 = table_api.column(5).nodes().to$(); + se_nodes = tableApi.column(5).nodes().to$(); for (i = 0; i < val_nodes.length; i++) { this_node = val_nodes[i].childNodes[0]; this_node.value = this_node.attributes["data-value"].value; } } - table_api.draw(); + tableApi.draw(); } } }; $('.reset').click(function() { - reset_samples_table(); + resetSamplesTable(); $('input[name="transform"]').val(""); - edit_data_change(); + editDataChange(); }); -check_for_zero_to_one_vals = function() { +checkForZeroToOneVals = function() { tables = ['samples_primary', 'samples_other']; for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; if ($('#' + table).length) { - table_api = $('#' + table).DataTable(); - val_nodes = table_api.column(3).nodes().to$(); + 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)) { @@ -943,47 +943,47 @@ check_for_zero_to_one_vals = function() { return false } -log2_data = function(this_node) { +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 (zero_to_one_vals_exist){ + if (zeroToOneValsExist){ original_value = parseFloat(original_value) + 1; } this_node.value = Math.log2(original_value).toFixed(3); } }; -log10_data = function() { +log10Data = function() { current_value = this_node.value; original_value = this_node.attributes['data-value'].value; if(!isNaN(current_value) && !isNaN(original_value)) { - if (zero_to_one_vals_exist){ + if (zeroToOneValsExist){ original_value = parseFloat(original_value) + 1; } this_node.value = Math.log10(original_value).toFixed(3); } }; -sqrt_data = function() { +sqrtData = function() { current_value = this_node.value; original_value = this_node.attributes['data-value'].value; if(!isNaN(current_value) && !isNaN(original_value)) { - if (zero_to_one_vals_exist){ + if (zeroToOneValsExist){ original_value = parseFloat(original_value) + 1; } this_node.value = Math.sqrt(original_value).toFixed(3); } }; -invert_data = function() { +invertData = function() { current_value = this_node.value; if(!isNaN(current_value)) { this_node.value = parseFloat(-(current_value)).toFixed(3); } }; -qnorm_data = function() { +qnormData = function() { current_value = this_node.value; qnorm_value = this_node.attributes['data-qnorm'].value; if(!isNaN(current_value)) { @@ -991,7 +991,7 @@ qnorm_data = function() { } }; -zscore_data = function() { +zScoreData = function() { current_value = this_node.value; zscore_value = this_node.attributes['data-zscore'].value; if(!isNaN(current_value)) { @@ -999,47 +999,47 @@ zscore_data = function() { } }; -do_transform = function(transform_type) { +doTransform = function(transform_type) { tables = ['samples_primary', 'samples_other']; for (_i = 0, _len = tables.length; _i < _len; _i++) { table = tables[_i]; if ($('#' + table).length) { - table_api = $('#' + table).DataTable(); - val_nodes = table_api.column(3).nodes().to$(); + 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"){ - log2_data(this_node) + log2Data(this_node) } if (transform_type == "log10"){ - log10_data(this_node) + log10Data(this_node) } if (transform_type == "sqrt"){ - sqrt_data(this_node) + sqrtData(this_node) } if (transform_type == "invert"){ - invert_data(this_node) + invertData(this_node) } if (transform_type == "qnorm"){ - qnorm_data(this_node) + qnormData(this_node) } if (transform_type == "zscore"){ - zscore_data(this_node) + zScoreData(this_node) } } } } } -normalize_data = function() { +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') { - do_transform("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'){ - do_transform("log10") + doTransform("log10") $('input[name="transform"]').val("log10") $('span[name="transform_text"]').text(" - log10 Transformed") } @@ -1047,13 +1047,13 @@ normalize_data = function() { } else if ($('#norm_method option:selected').val() == 'sqrt'){ if ($('input[name="transform"]').val() != "sqrt") { - do_transform("sqrt") + doTransform("sqrt") $('input[name="transform"]').val("sqrt") $('span[name="transform_text"]').text(" - Square Root Transformed") } } else if ($('#norm_method option:selected').val() == 'invert'){ - do_transform("invert") + doTransform("invert") $('input[name="transform"]').val("inverted") if ($('span[name="transform_text"]:eq(0)').text() != ""){ current_text = $('span[name="transform_text"]:eq(0)').text(); @@ -1064,26 +1064,26 @@ normalize_data = function() { } else if ($('#norm_method option:selected').val() == 'qnorm'){ if ($('input[name="transform"]').val() != "qnorm") { - do_transform("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") { - do_transform("zscore") + doTransform("zscore") $('input[name="transform"]').val("zscore") $('span[name="transform_text"]').text(" - Z-Scores") } } } -zero_to_one_vals_exist = check_for_zero_to_one_vals(); +zeroToOneValsExist = checkForZeroToOneVals(); -show_transform_warning = function() { +showTransformWarning = function() { transform_type = $('#norm_method option:selected').val() if (transform_type == "log2" || transform_type == "log10"){ - if (zero_to_one_vals_exist){ + if (zeroToOneValsExist){ $('#transform_alert').css("display", "block") } } else { @@ -1092,15 +1092,15 @@ show_transform_warning = function() { } $('#norm_method').change(function(){ - show_transform_warning() + showTransformWarning() }); $('#normalize').hover(function(){ - show_transform_warning() + showTransformWarning() }); -$('#normalize').click(normalize_data) +$('#normalize').click(normalizeData) -switch_qnorm_data = function() { +switchQNormData = function() { return $('.trait-value-input').each((function(_this) { return function(_index, element) { transform_val = $(element).data('transform') @@ -1111,9 +1111,9 @@ switch_qnorm_data = function() { }; })(this)); }; -$('#qnorm').click(switch_qnorm_data); +$('#qnorm').click(switchQNormData); -get_sample_table_data = function(table_name) { +getSampleTableData = function(table_name) { var samples; samples = []; @@ -1121,32 +1121,32 @@ get_sample_table_data = function(table_name) { var n_exists = false; if ($('#' + table_name).length){ - table_api = $('#' + table_name).DataTable(); + tableApi = $('#' + table_name).DataTable(); sample_vals = []; - name_nodes = table_api.column(2).nodes().to$(); - val_nodes = table_api.column(3).nodes().to$(); + name_nodes = tableApi.column(2).nodes().to$(); + val_nodes = tableApi.column(3).nodes().to$(); if (js_data.se_exists){ - var_nodes = table_api.column(5).nodes().to$(); + var_nodes = tableApi.column(5).nodes().to$(); if (js_data.has_num_cases) { - n_nodes = table_api.column(6).nodes().to$(); + n_nodes = tableApi.column(6).nodes().to$(); } } else { if (js_data.has_num_cases){ - n_nodes = table_api.column(4).nodes().to$(); + n_nodes = tableApi.column(4).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 (is_number(sample_val) && sample_val !== "") { + if (isNumber(sample_val) && sample_val !== "") { sample_val = parseFloat(sample_val); if (typeof var_nodes == 'undefined'){ sample_var = null; } else { sample_var = var_nodes[_j].childNodes[0].value; - if (is_number(sample_var)) { + if (isNumber(sample_var)) { sample_var = parseFloat(sample_var); se_exists = true; } else { @@ -1157,7 +1157,7 @@ get_sample_table_data = function(table_name) { sample_n = null; } else { sample_n = n_nodes[_j].childNodes[0].value; - if (is_number(sample_n)) { + if (isNumber(sample_n)) { n_exists = true; sample_n = parseInt(sample_n); } else { @@ -1177,11 +1177,11 @@ get_sample_table_data = function(table_name) { return samples; }; -export_sample_table_data = function() { +exportSampleTableData = function() { var format, json_sample_data, sample_data; sample_data = {}; - sample_data.primary_samples = get_sample_table_data('samples_primary'); - sample_data.other_samples = get_sample_table_data('samples_other'); + sample_data.primary_samples = getSampleTableData('samples_primary'); + sample_data.other_samples = getSampleTableData('samples_other'); json_sample_data = JSON.stringify(sample_data); $('input[name=export_data]').val(json_sample_data); format = $('input[name=export_format]').val(); @@ -1203,11 +1203,11 @@ $('.export_format').change(function() { $('.export_format').val( this.value ); }); -$('.export').click(export_sample_table_data); -$('#block_outliers').click(block_outliers); +$('.export').click(exportSampleTableData); +$('#blockOutliers').click(blockOutliers); _.mixin(_.str.exports()); -get_sample_vals = function(sample_list) { +getSampleVals = function(sample_list) { var sample; return this.sample_vals = (function() { var i, len, results; @@ -1222,7 +1222,7 @@ get_sample_vals = function(sample_list) { })(); }; -get_sample_errors = function(sample_list) { +getSampleErrors = function(sample_list) { var sample; return this.sample_vals = (function() { var i, len, results; @@ -1239,9 +1239,9 @@ get_sample_errors = function(sample_list) { })(); }; -get_sample_names = function(sample_list) { +getSampleNames = function(sample_list) { var sample; - return this.sample_names = (function() { + return this.sampleNames = (function() { var i, len, results; results = []; for (i = 0, len = sample_list.length; i < len; i++) { @@ -1254,31 +1254,31 @@ get_sample_names = function(sample_list) { })(); }; -get_bar_bottom_margin = function(sample_list){ - bottom_margin = 80 - max_length = 0 - sample_names = get_sample_names(sample_list) - for (i=0; i < sample_names.length; i++){ - if (sample_names[i].length > max_length) { - max_length = sample_names[i].length +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 (max_length > 6){ - bottom_margin += 11*(max_length - 6) + if (maxLength > 6){ + bottomMargin += 11*(maxLength - 6) } - return bottom_margin; + return bottomMargin; } root.stats_group = 'samples_primary'; if (Object.keys(js_data.sample_group_types).length > 1) { - full_sample_lists = [sample_lists[0], sample_lists[1], sample_lists[0].concat(sample_lists[1])] - sample_group_list = [js_data.sample_group_types['samples_primary'], js_data.sample_group_types['samples_other'], js_data.sample_group_types['samples_all']] + 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 { - full_sample_lists = [sample_lists[0]] - sample_group_list = [js_data.sample_group_types['samples_primary']] + fullSampleLists = [sampleLists[0]] + sampleGroupList = [js_data.sample_group_types['samples_primary']] } // Define Plotly Options (for the options bar at the top of each figure) @@ -1307,76 +1307,76 @@ root.modebar_options = { // Bar Chart -root.errors_exist = get_sample_errors(sample_lists[0])[1] -var bar_trace = { - x: get_sample_names(sample_lists[0]), - y: get_sample_vals(sample_lists[0]), +root.errors_exist = getSampleErrors(sampleLists[0])[1] +var barTrace = { + x: getSampleNames(sampleLists[0]), + y: getSampleVals(sampleLists[0]), error_y: { type: 'data', - array: get_sample_errors(sample_lists[0])[0], + array: getSampleErrors(sampleLists[0])[0], visible: root.errors_exist }, type: 'bar' } -root.bar_data = [bar_trace] +root.bar_data = [barTrace] -get_bar_range = function(sample_vals, sample_errors = null){ - positive_error_vals = [] - negative_error_vals = [] +getBarRange = function(sample_vals, sampleErrors = null){ + positiveErrorVals = [] + negativeErrorVals = [] for (i = 0;i < sample_vals.length; i++){ - if (sample_errors[i] != undefined) { - positive_error_vals.push(sample_vals[i] + sample_errors[i]) - negative_error_vals.push(sample_vals[i] - sample_errors[i]) + if (sampleErrors[i] != undefined) { + positiveErrorVals.push(sample_vals[i] + sampleErrors[i]) + negativeErrorVals.push(sample_vals[i] - sampleErrors[i]) } else { - positive_error_vals.push(sample_vals[i]) - negative_error_vals.push(sample_vals[i]) + positiveErrorVals.push(sample_vals[i]) + negativeErrorVals.push(sample_vals[i]) } } - min_y_val = Math.min(...negative_error_vals) - max_y_val = Math.max(...positive_error_vals) + minYVal = Math.min(...negativeErrorVals) + maxYVal = Math.max(...positiveErrorVals) - if (min_y_val == 0) { - range_top = max_y_val + Math.abs(max_y_val)*0.1 - range_bottom = 0; + if (minYVal == 0) { + rangeTop = maxYVal + Math.abs(maxYVal)*0.1 + rangeBottom = 0; } else { - range_top = max_y_val + Math.abs(max_y_val)*0.1 - range_bottom = min_y_val - Math.abs(min_y_val)*0.1 - if (min_y_val > 0) { - range_bottom = min_y_val - 0.1*Math.abs(min_y_val) - } else if (min_y_val < 0) { - range_bottom = min_y_val + 0.1*min_y_val + 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 { - range_bottom = 0 + rangeBottom = 0 } } - return [range_bottom, range_top] + return [rangeBottom, rangeTop] } -root.chart_range = get_bar_range(get_sample_vals(sample_lists[0]), get_sample_errors(sample_lists[0])[0]) -val_range = root.chart_range[1] - root.chart_range[0] - -if (val_range < 0.05){ - tick_digits = '.3f' - left_margin = 80 -} else if (val_range < 0.5) { - tick_digits = '.2f' - left_margin = 70 -} else if (val_range < 5){ - tick_digits = '.1f' - left_margin = 60 +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 { - tick_digits = 'f' - left_margin = 55 + tickDigits = 'f' + leftMargin = 55 } if (js_data.num_values < 256) { - bar_chart_width = 25 * get_sample_vals(sample_lists[0]).length + barChartWidth = 25 * getSampleVals(sampleLists[0]).length //ZS: Set bottom margin dependent on longest sample name length, since those can get long - bottom_margin = get_bar_bottom_margin(sample_lists[0]) + bottomMargin = getBarBottomMargin(sampleLists[0]) root.bar_layout = { title: "Trait " + js_data.trait_id + ": " + js_data.short_description + "", @@ -1402,32 +1402,32 @@ if (js_data.num_values < 256) { tickfont: { size: 16 }, - tickformat: tick_digits, + tickformat: tickDigits, fixedrange: true }, - width: bar_chart_width, + width: barChartWidth, height: 600, margin: { - l: left_margin, + l: leftMargin, r: 30, t: 100, - b: bottom_margin + b: bottomMargin } }; $('.bar_chart_tab').click(function() { - update_bar_chart(); + updateBarChart(); }); } total_sample_count = 0 -for (i = 0, i < sample_lists.length; i++;) { - total_sample_count += get_sample_vals(sample_lists[i]).length +for (i = 0, i < sampleLists.length; i++;) { + total_sample_count += getSampleVals(sampleLists[i]).length } // Histogram var hist_trace = { - x: get_sample_vals(sample_lists[0]), + x: getSampleVals(sampleLists[0]), type: 'histogram' }; root.histogram_data = [hist_trace]; @@ -1472,14 +1472,14 @@ root.histogram_layout = { }; $('.histogram_tab').click(function() { - update_histogram(); - update_histogram_width(); + updateHistogram(); + updateHistogram_width(); }); $('.histogram_samples_group').val(root.stats_group); $('.histogram_samples_group').change(function() { root.stats_group = $(this).val(); - return update_histogram(); + return updateHistogram(); }); root.box_layout = { @@ -1505,7 +1505,7 @@ root.box_layout = { tickfont: { size: 16 }, - tickformat: tick_digits, + tickformat: tickDigits, zeroline: false, automargin: true }, @@ -1516,13 +1516,13 @@ root.box_layout = { b: 80 } }; -if (full_sample_lists.length > 1) { +if (fullSampleLists.length > 1) { root.box_layout['width'] = 600; root.box_layout['height'] = 500; var trace1 = { - y: get_sample_vals(full_sample_lists[0]), + y: getSampleVals(fullSampleLists[0]), type: 'box', - name: sample_group_list[0], + name: sampleGroupList[0], boxpoints: 'Outliers', jitter: 0.5, whiskerwidth: 0.2, @@ -1537,9 +1537,9 @@ if (full_sample_lists.length > 1) { } } var trace2 = { - y: get_sample_vals(full_sample_lists[1]), + y: getSampleVals(fullSampleLists[1]), type: 'box', - name: sample_group_list[1], + name: sampleGroupList[1], boxpoints: 'Outliers', jitter: 0.5, whiskerwidth: 0.2, @@ -1554,9 +1554,9 @@ if (full_sample_lists.length > 1) { } } var trace3 = { - y: get_sample_vals(full_sample_lists[2]), + y: getSampleVals(fullSampleLists[2]), type: 'box', - name: sample_group_list[2], + name: sampleGroupList[2], boxpoints: 'Outliers', jitter: 0.5, whiskerwidth: 0.2, @@ -1577,7 +1577,7 @@ if (full_sample_lists.length > 1) { root.box_data = [ { type: 'box', - y: get_sample_vals(full_sample_lists[0]), + y: getSampleVals(fullSampleLists[0]), name: "Trait " + js_data.trait_id + "", boxpoints: 'Outliers', jitter: 0.5, @@ -1628,7 +1628,7 @@ root.violin_layout = { tickfont: { size: 16 }, - tickformat: tick_digits, + tickformat: tickDigits, zeroline: false, automargin: true }, @@ -1640,11 +1640,11 @@ root.violin_layout = { } }; -if (full_sample_lists.length > 1) { +if (fullSampleLists.length > 1) { root.violin_layout['width'] = 600; root.violin_layout['height'] = 500; var trace1 = { - y: get_sample_vals(full_sample_lists[2]), + y: getSampleVals(fullSampleLists[2]), type: 'violin', points: 'none', box: { @@ -1656,11 +1656,11 @@ if (full_sample_lists.length > 1) { meanline: { visible: true }, - name: sample_group_list[2], - x0: sample_group_list[2] + name: sampleGroupList[2], + x0: sampleGroupList[2] } var trace2 = { - y: get_sample_vals(full_sample_lists[1]), + y: getSampleVals(fullSampleLists[1]), type: 'violin', points: 'none', box: { @@ -1672,11 +1672,11 @@ if (full_sample_lists.length > 1) { meanline: { visible: true }, - name: sample_group_list[1], - x0: sample_group_list[1] + name: sampleGroupList[1], + x0: sampleGroupList[1] } var trace3 = { - y: get_sample_vals(full_sample_lists[0]), + y: getSampleVals(fullSampleLists[0]), type: 'violin', points: 'none', box: { @@ -1688,8 +1688,8 @@ if (full_sample_lists.length > 1) { meanline: { visible: true }, - name: sample_group_list[0], - x0: sample_group_list[0] + name: sampleGroupList[0], + x0: sampleGroupList[0] } root.violin_data = [trace1, trace2, trace3] } else { @@ -1697,7 +1697,7 @@ if (full_sample_lists.length > 1) { root.violin_layout['height'] = 400; root.violin_data = [ { - y: get_sample_vals(full_sample_lists[0]), + y: getSampleVals(fullSampleLists[0]), type: 'violin', points: 'none', box: { @@ -1713,33 +1713,33 @@ if (full_sample_lists.length > 1) { } $('.violin_plot_tab').click(function() { - update_violin_plot(); + updateViolinPlot(); }); -if (get_sample_vals(sample_lists[0]).length < 256) { +if (getSampleVals(sampleLists[0]).length < 256) { $('.bar_chart_samples_group').change(function() { root.stats_group = $(this).val(); - return update_bar_chart(); + return updateBarChart(); }); root.bar_sort = "name" } $('.sort_by_name').click(function() { root.bar_sort = "name" - return update_bar_chart(); + return updateBarChart(); }); $('.sort_by_value').click(function() { root.bar_sort = "value" - return update_bar_chart(); + return updateBarChart(); }); root.prob_plot_group = 'samples_primary'; $('.prob_plot_samples_group').val(root.prob_plot_group); $('.prob_plot_tab').click(function() { - return update_prob_plot(); + return updateProbPlot(); }); $('.prob_plot_samples_group').change(function() { root.prob_plot_group = $(this).val(); - return update_prob_plot(); + return updateProbPlot(); }); function isEmpty( el ){ @@ -1748,37 +1748,37 @@ function isEmpty( el ){ $('.stats_panel').click(function() { if (isEmpty($('#stats_table'))){ - make_table(); - edit_data_change(); + makeTable(); + editDataChange(); } else { - edit_data_change(); + editDataChange(); } }); -$('#block_by_index').click(function(){ - block_by_index(); - edit_data_change(); +$('#blockByIndex').click(function(){ + blockByIndex(); + editDataChange(); }); $('#filter_by_study').click(function(){ filter_by_study(); - edit_data_change(); + editDataChange(); }) $('#filter_by_value').click(function(){ filter_by_value(); - edit_data_change(); + editDataChange(); }) $('.edit_sample_value').change(function() { - edit_data_change(); + editDataChange(); }); -$('#exclude_group').click(edit_data_change); -$('#block_outliers').click(edit_data_change); -$('#reset').click(edit_data_change); -$('#qnorm').click(edit_data_change); -$('#normalize').click(edit_data_change); +$('#exclude_group').click(editDataChange); +$('#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; -- cgit v1.2.3