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: "{{ url_for('gn_docs_blueprint.glossary') }}#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(block=true) {
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 (block) {
if (this_col_value == exclude_by_value){
this_val_node.value = "x";
}
} else {
if (this_col_value != exclude_by_value){
this_val_node.value = "x";
}
}
}
}
editDataChange();
};
$('#exclude_by_attr').click(blockByAttributeValue);
$('#select_by_attr').click(function() {
blockByAttributeValue(block=false);
});
blockByIndex = function(block=true) {
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 = $('#samples_primary').DataTable();
}
val_nodes = tableApi.column(3).nodes().to$();
if (block) {
for (_k = 0, _len1 = index_list.length; _k < _len1; _k++) {
index = index_list[_k];
val_nodes[index - 1].childNodes[0].value = "x";
}
} else {
for (_k = 0, _len1 = val_nodes.length; _k < _len1; _k++) {
if (!index_list.includes(_k + 1)) {
val_nodes[_k].childNodes[0].value = "x";
}
}
}
editDataChange();
};
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();
});
$('#select_by_index').click(function(){
blockByIndex(block=false);
});
$('#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;
}
