diff options
Diffstat (limited to 'gn2/wqflask/static/new/javascript')
53 files changed, 12109 insertions, 0 deletions
diff --git a/gn2/wqflask/static/new/javascript/auth/search.js b/gn2/wqflask/static/new/javascript/auth/search.js new file mode 100644 index 00000000..d094cebf --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search.js @@ -0,0 +1,172 @@ +class InvalidCSSIDSelector extends Error { + constructor(message) { + super(message); + this.name = "InvalidCSSIDSelector"; + } +} + +class InvalidDataAttributeName extends Error { + constructor(message) { + super(message); + this.name = "InvalidDataAttributeName"; + } +} + +/** + * CSSIDSelector: A CSS ID Selector + * @param {String} A CSS selector of the form '#...' + */ +class CSSIDSelector { + constructor(selector) { + if(!selector.startsWith("#")) { + throw new InvalidCSSIDSelector( + "Expected the CSS selector to begin with a `#` character."); + } + let id_str = selector.slice(1, selector.length); + if(document.getElementById(id_str) == null) { + throw new InvalidCSSIDSelector( + "Element with ID '" + id_str + "' does not exist."); + } + this.selector = selector; + } +} + +/** + * TableDataSource: A type to represent a table's data source + * @param {String} A CSS selector for an ID + * @param {String} A `data-*` attribute name + */ +class TableDataSource { + constructor(table_id, data_attribute_name, checkbox_creation_function) { + this.table_id = new CSSIDSelector(table_id); + let data = document.querySelector( + table_id).getAttribute(data_attribute_name); + if(data == null) { + throw new InvalidDataAttributeName( + "data-* attribute '" + data_attribute_name + "' does not exist " + + "for table with ID '" + table_id.slice(1, table_id.length) + + "'."); + } else { + this.data_attribute_name = data_attribute_name; + } + this.checkbox_creation_function = checkbox_creation_function; + } +} + +/** + * Render the table + * @param {String} The selector for the table's ID + * @param {String} The name of the data-* attribute holding the table's data + * @param {Function} The function to call to generate the appropriate checkbox + */ +function render_table(table_data_source) { + table_id = table_data_source.table_id.selector; + data_attr_name = table_data_source.data_attribute_name; + $(table_id + " tbody tr").remove(); + table_data = JSON.parse($(table_id).attr(data_attr_name)).sort((d1, d2) => { + return (d1.dataset_name > d2.dataset_name ? 1 : ( + d1.dataset_name < d2.dataset_name ? -1 : 0)) + }); + if(table_data.length < 1) { + row = $("<tr>") + cell = $('<td colspan="100%" align="center">'); + cell.append( + $('<span class="glyphicon glyphicon-info-sign text-info">')); + cell.append(" "); + cell.append("No genotype datasets remaining."); + row.append(cell); + $(table_id + " tbody").append(row); + } + table_data.forEach(function(dataset) { + row = $("<tr>") + row.append(table_data_source.checkbox_creation_function(dataset)); + row.append(table_cell(dataset.InbredSetName)); + row.append(table_cell(dataset.dataset_name)); + row.append(table_cell(dataset.dataset_fullname)); + row.append(table_cell(dataset.dataset_shortname)); + $(table_id + " tbody").append(row); + }); +} + +function in_array(items, filter_fn) { + return items.filter(filter_fn).length > 0; +} + +function remove_from_table_data(dataset, table_data_source, filter_fn) { + let table_id = table_data_source.table_id.selector; + let data_attr_name = table_data_source.data_attribute_name; + without_dataset = JSON.parse($(table_id).attr(data_attr_name)).filter( + filter_fn); + $(table_id).attr(data_attr_name, JSON.stringify(without_dataset)); +} + +function add_to_table_data(dataset, table_data_source, filter_fn) { + let table_id = table_data_source.table_id.selector; + let data_attr_name = table_data_source.data_attribute_name; + table_data = JSON.parse($(table_id).attr(data_attr_name)); + if(!in_array(table_data, filter_fn)) { + table_data.push(dataset); + } + $(table_id).attr(data_attr_name, JSON.stringify(Array.from(table_data))); +} + +/** + * Switch the dataset/trait from search table to selection table and vice versa + * @param {Object} A dataset/trait object + * @param {TableDataSource} The source table for the dataset/trait + * @param {TableDataSource} The destination table for the dataset/trait + */ +function select_deselect(item, source, destination, filter_fn, render_fn=render_table) { + dest_selector = destination.table_id.selector + dest_data = JSON.parse( + $(dest_selector).attr(destination.data_attribute_name)); + add_to_table_data(item, destination, filter_fn); // Add to destination table + remove_from_table_data(item, source, (arg) => {return !filter_fn(arg)}); // Remove from source table + /***** BEGIN: Re-render tables *****/ + render_fn(destination); + render_fn(source); + /***** END: Re-render tables *****/ +} + +function debounce(func, delay=500) { + var timeout; + return function search(event) { + clearTimeout(timeout); + timeout = setTimeout(func, delay); + }; +} + +/** + * Build a checkbox + * @param {Dataset Object} A JSON.stringify-able object + * @param {String} The name to assign the checkbox + */ +function build_checkbox(data_object, checkbox_name, checkbox_aux_classes="", checked=false) { + cell = $("<td>"); + check = $( + '<input type="checkbox" class="checkbox" ' + + 'name="' + checkbox_name + '">'); + check.val(JSON.stringify(data_object)); + check.prop("checked", checked); + auxilliary_classes = checkbox_aux_classes.trim(); + if(Boolean(auxilliary_classes)) { + check.attr("class", + check.attr("class") + " " + auxilliary_classes.trim()); + } + cell.append(check); + return cell; +} + +function link_checkbox(dataset) { + return build_checkbox(dataset, "selected", "checkbox-selected", true); +} + +function search_checkbox(dataset) { + return build_checkbox(dataset, "search_datasets", "checkbox-search"); +} + +function table_cell(value) { + cell = $("<td>"); + cell.html(value); + return cell; +} diff --git a/gn2/wqflask/static/new/javascript/auth/search_genotypes.js b/gn2/wqflask/static/new/javascript/auth/search_genotypes.js new file mode 100644 index 00000000..d1b8ed9e --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search_genotypes.js @@ -0,0 +1,95 @@ +function toggle_link_button() { + num_groups = $("#frm-link-genotypes select option").length - 1; + num_selected = JSON.parse( + $("#tbl-link-genotypes").attr("data-selected-datasets")).length; + if(num_groups > 0 && num_selected > 0) { + $("#frm-link-genotypes input[type='submit']").prop("disabled", false); + } else { + $("#frm-link-genotypes input[type='submit']").prop("disabled", true); + } +} + +function search_genotypes() { + query = document.getElementById("txt-query").value; + selected = JSON.parse(document.getElementById( + "tbl-link-genotypes").getAttribute("data-selected-datasets")); + species_name = document.getElementById("txt-species-name").value + search_endpoint = "/auth/data/genotype/search" + search_table = new TableDataSource( + "#tbl-genotypes", "data-datasets", search_checkbox); + $.ajax( + search_endpoint, + { + "method": "POST", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "data": JSON.stringify({ + "query": query, + "selected": selected, + "dataset_type": "genotype", + "species_name": species_name}), + "error": function(jqXHR, textStatus, errorThrown) { + data = jqXHR.responseJSON + elt = document.getElementById("search-error").setAttribute( + "style", "display: block;"); + document.getElementById("search-error-text").innerHTML = ( + data.error + " (" + data.status_code + "): " + + data.error_description); + document.getElementById("tbl-genotypes").setAttribute( + "data-datasets", JSON.stringify([])); + render_table(search_table); + }, + "success": function(data, textStatus, jqXHR) { + document.getElementById("search-error").setAttribute( + "style", "display: none;"); + document.getElementById("tbl-genotypes").setAttribute( + "data-datasets", JSON.stringify(data)); + render_table(search_table); + } + }); +} + +/** + * Return function to check whether `dataset` is in array of `datasets`. + * @param {GenotypeDataset} A genotype dataset. + * @param {Array} An array of genotype datasets. + */ +function make_filter(trait) { + return (dst) => { + return (dst.SpeciesId == dataset.SpeciesId && + dst.InbredSetId == dataset.InbredSetId && + dst.GenoFreezeId == dataset.GenoFreezeId); + }; +} + +$(document).ready(function() { + let search_table = new TableDataSource( + "#tbl-genotypes", "data-datasets", search_checkbox); + let link_table = new TableDataSource( + "#tbl-link-genotypes", "data-selected-datasets", link_checkbox); + + $("#frm-search-traits").submit(function(event) { + event.preventDefault(); + return false; + }); + + $("#txt-query").keyup(debounce(search_genotypes)); + + $("#tbl-genotypes").on("change", ".checkbox-search", function(event) { + if(this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, search_table, link_table, make_filter(dataset)); + toggle_link_button(); + } + }); + + $("#tbl-link-genotypes").on("change", ".checkbox-selected", function(event) { + if(!this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, link_table, search_table, make_filter(dataset)); + toggle_link_button(); + } + }); +}); diff --git a/gn2/wqflask/static/new/javascript/auth/search_mrna.js b/gn2/wqflask/static/new/javascript/auth/search_mrna.js new file mode 100644 index 00000000..3eca4ed2 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search_mrna.js @@ -0,0 +1,97 @@ +function toggle_link_button() { + num_groups = $("#frm-link select option").length - 1; + num_selected = JSON.parse( + $("#tbl-link").attr("data-datasets")).length; + if(num_groups > 0 && num_selected > 0) { + $("#frm-link input[type='submit']").prop("disabled", false); + } else { + $("#frm-link input[type='submit']").prop("disabled", true); + } +} + +function search_mrna() { + query = document.getElementById("txt-query").value; + selected = JSON.parse(document.getElementById( + "tbl-link").getAttribute("data-datasets")); + species_name = document.getElementById("txt-species-name").value + search_endpoint = "/auth/data/mrna/search" + search_table = new TableDataSource( + "#tbl-search", "data-datasets", search_checkbox); + $.ajax( + search_endpoint, + { + "method": "POST", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "data": JSON.stringify({ + "query": query, + "selected": selected, + "dataset_type": "mrna", + "species_name": species_name}), + "error": function(jqXHR, textStatus, errorThrown) { + error_data = jqXHR.responseJSON + console.debug("ERROR_DATA:", error_data); + elt = document.getElementById("search-error").setAttribute( + "style", "display: block;"); + document.getElementById("search-error-text").innerHTML = ( + error_data.error + " (" + error_data.status_code + "): " + + error_data.error_description); + document.getElementById("tbl-search").setAttribute( + "data-datasets", JSON.stringify([])); + render_table(search_table); + }, + "success": function(data, textStatus, jqXHR) { + document.getElementById("search-error").setAttribute( + "style", "display: none;"); + document.getElementById("tbl-search").setAttribute( + "data-datasets", JSON.stringify(data)); + render_table(search_table); + } + }); +} + +/** + * Make function to check whether `dataset` is in array of `datasets`. + * @param {mRNADataset} A mrna dataset. + * @param {Array} An array of mrna datasets. + */ +function make_filter(dataset) { + return (dst) => { + return (dst.SpeciesId == dataset.SpeciesId && + dst.InbredSetId == dataset.InbredSetId && + dst.ProbeFreezeId == dataset.ProbeFreezeId && + dst.ProbeSetFreezeId == dataset.ProbeSetFreezeId); + }; +} + +$(document).ready(function() { + let search_table = new TableDataSource( + "#tbl-search", "data-datasets", search_checkbox); + let link_table = new TableDataSource( + "#tbl-link", "data-datasets", link_checkbox); + + $("#frm-search").submit(function(event) { + event.preventDefault(); + return false; + }); + + $("#txt-query").keyup(debounce(search_mrna)); + + $("#tbl-search").on("change", ".checkbox-search", function(event) { + if(this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, search_table, link_table, make_filter(dataset)); + toggle_link_button(); + } + }); + + $("#tbl-link").on("change", ".checkbox-selected", function(event) { + if(!this.checked) { + dataset = JSON.parse(this.value); + select_deselect( + dataset, link_table, search_table, make_filter(dataset)); + toggle_link_button(); + } + }); +}); diff --git a/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js new file mode 100644 index 00000000..99ecb16e --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auth/search_phenotypes.js @@ -0,0 +1,188 @@ +/** + * Global variables: Bad idea - figure out how to pass them down a call stack. + */ +search_table = new TableDataSource( + "#tbl-phenotypes", "data-traits", (trait) => { + return build_checkbox(trait, "search_traits", "checkbox-search"); + }); +link_table = new TableDataSource( + "#tbl-link-phenotypes", "data-traits", (trait) => { + return build_checkbox( + trait, "selected", "checkbox-selected", checked=true); + }); + +/** + * Toggle the state for the "Link Traits" button + */ +function toggle_link_button() { + num_groups = $("#frm-link-phenotypes select option").length - 1; + num_selected = JSON.parse( + $("#tbl-link-phenotypes").attr("data-traits")).length; + if(num_groups > 0 && num_selected > 0) { + $("#frm-link-phenotypes input[type='submit']").prop("disabled", false); + } else { + $("#frm-link-phenotypes input[type='submit']").prop("disabled", true); + } +} + +/** + * Default error function: print out debug messages + */ +function default_error_fn(jqXHR, textStatus, errorThrown) { + console.debug("XHR:", jqXHR); + console.debug("STATUS:", textStatus); + console.debug("ERROR:", errorThrown); +} + +/** + * Render the table(s) for the phenotype traits + * @param {TableDataSource} The table to render + */ +function render_pheno_table(table_data_source) { + table_id = table_data_source.table_id.selector; + data_attr_name = table_data_source.data_attribute_name; + $(table_id + " tbody tr").remove(); + table_data = JSON.parse($(table_id).attr(data_attr_name)).sort((t1, t2) => { + return (t1.name > t2.name ? 1 : (t1.name < t2.name ? -1 : 0)) + }); + if(table_data.length < 1) { + row = $("<tr>") + cell = $('<td colspan="100%" align="center">'); + cell.append( + $('<span class="glyphicon glyphicon-info-sign text-info">')); + cell.append(" "); + cell.append("No phenotype traits to select from."); + row.append(cell); + $(table_id + " tbody").append(row); + } + table_data.forEach(function(trait) { + row = $("<tr>") + row.append(table_data_source.checkbox_creation_function(trait)); + row.append(table_cell(trait.name)); + row.append(table_cell(trait.group)); + row.append(table_cell(trait.dataset)); + row.append(table_cell(trait.dataset_fullname)); + row.append(table_cell(trait.description)); + row.append(table_cell(trait.authors.join(", "))); + row.append(table_cell( + '<a href="' + trait.pubmed_link + + '" title="Pubmed link for trait ' + trait.name + '.">' + + trait.year + "</a>")); + row.append(table_cell("Chr:" + trait.geno_chr + "@" + trait.geno_mb)); + row.append(table_cell(trait.lrs)); + row.append(table_cell(trait.additive)); + $(table_id + " tbody").append(row); + }); +} + +function display_search_results(data, textStatus, jqXHR) { + if(data.status == "queued" || data.status == "started") { + setTimeout(() => { + fetch_search_results(data.job_id, display_search_results); + }, 250); + return; + } + if(data.status == "completed") { + $("#tbl-phenotypes").attr( + "data-traits", JSON.stringify(data.search_results)); + // Remove this reference to global variable + render_pheno_table(search_table); + } + $("#txt-search").prop("disabled", false); +} + +/** + * Fetch the search results + * @param {UUID}: The job id to fetch data for + */ +function fetch_search_results(job_id, success, error=default_error_fn) { + host = $("#frm-search-traits").attr("data-gn-server-url"); + endpoint = host + "auth/data/search/phenotype/" + job_id + $("#txt-search").prop("disabled", true); + $.ajax( + endpoint, + { + "method": "GET", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "error": error, + "success": success + } + ); +} + +function search_phenotypes() { + query = document.getElementById("txt-query").value; + selected = JSON.parse(document.getElementById( + "tbl-link-phenotypes").getAttribute("data-traits")); + species_name = document.getElementById("txt-species-name").value + per_page = document.getElementById("txt-per-page").value + search_table = new TableDataSource( + "#tbl-phenotypes", "data-traits", search_checkbox); + endpoint = "/auth/data/phenotype/search" + $.ajax( + endpoint, + { + "method": "POST", + "contentType": "application/json; charset=utf-8", + "dataType": "json", + "data": JSON.stringify({ + "query": query, + "species_name": species_name, + "dataset_type": "phenotype", + "per_page": per_page, + "selected_traits": selected + }), + "error": default_error_fn, + "success": (data, textStatus, jqXHR) => { + fetch_search_results(data.job_id, display_search_results); + } + }); +} + +/** + * Return a function to check whether `trait` is in array of `traits`. + * @param {PhenotypeTrait} A phenotype trait. + * @param {Array} An array of phenotype traits. + */ +function make_filter(trait) { + return (trt) => { + return (trt.species == trait.species && + trt.group == trait.group && + trt.dataset == trait.dataset && + trt.name == trait.name); + }; +} + +$(document).ready(function() { + $("#frm-search-traits").submit(event => { + event.preventDefault(); + return false; + }); + + $("#txt-query").keyup(debounce(search_phenotypes)); + + $("#tbl-link-phenotypes").on("change", ".checkbox-selected", function(event) { + if(!this.checked) { + trait = JSON.parse(this.value); + select_deselect(trait, link_table, search_table, + make_filter(trait), render_pheno_table); + toggle_link_button(); + } + }); + + $("#tbl-phenotypes").on("change", ".checkbox-search", function(event) { + if(this.checked) { + trait = JSON.parse(this.value) + select_deselect(trait, search_table, link_table, + make_filter(trait), render_pheno_table); + toggle_link_button(); + } + }); + + setTimeout(() => { + fetch_search_results( + $("#tbl-phenotypes").attr("data-initial-job-id"), + display_search_results); + }, 500); +}); diff --git a/gn2/wqflask/static/new/javascript/auto_hide_column.js b/gn2/wqflask/static/new/javascript/auto_hide_column.js new file mode 100644 index 00000000..1a4dc039 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/auto_hide_column.js @@ -0,0 +1,21 @@ + function filterDatatable(datatable){ + let invalidColumns=[] + let columnCount=datatable.columns().header().length; + let numberOfRows=datatable.rows().count(); + for (let col=0; col<columnCount; col++){ + colObj = datatable.column(col).nodes().to$(); + allNAs = true; + for (let i=0;i<numberOfRows;i++){ + cellContent = colObj[i].childNodes[0].data + if (cellContent != "N/A" && cellContent != ""){ + allNAs = false; + break; + } + } + if (allNAs){ + invalidColumns.push(col) + } + } + return datatable.columns(invalidColumns).visible(false); + + }
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/bar_chart.js b/gn2/wqflask/static/new/javascript/bar_chart.js new file mode 100644 index 00000000..d8540580 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/bar_chart.js @@ -0,0 +1,498 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var Bar_Chart, root, + bind = function(fn, me){ return function(){ return fn.apply(me, arguments); }; }, + indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }, + hasProp = {}.hasOwnProperty; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + Bar_Chart = (function() { + function Bar_Chart(sample_lists) { + this.add_legend_discrete = bind(this.add_legend_discrete, this); + this.add_legend_continuous = bind(this.add_legend_continuous, this); + this.remove_legend = bind(this.remove_legend, this); + this.add_legend = bind(this.add_legend, this); + var key, l1, l1_names, l2, l3, longest_sample_name_len, s, sample, x; + this.sample_lists = {}; + l1 = this.sample_lists['samples_primary'] = sample_lists[0] || []; + l2 = this.sample_lists['samples_other'] = sample_lists[1] || []; + l1_names = (function() { + var j, len, results; + results = []; + for (j = 0, len = l1.length; j < len; j++) { + x = l1[j]; + results.push(x.name); + } + return results; + })(); + l3 = l1.concat((function() { + var j, len, ref, results; + results = []; + for (j = 0, len = l2.length; j < len; j++) { + x = l2[j]; + if (ref = x.name, indexOf.call(l1_names, ref) < 0) { + results.push(x); + } + } + return results; + })()); + this.sample_lists['samples_all'] = l3; + longest_sample_name_len = d3.max((function() { + var j, len, results; + results = []; + for (j = 0, len = l3.length; j < len; j++) { + sample = l3[j]; + results.push(sample.name.length); + } + return results; + })()); + this.margin = { + top: 20, + right: 20, + bottom: longest_sample_name_len * 6, + left: 40 + }; + this.attributes = (function() { + var results; + results = []; + for (key in sample_lists[0][0]["extra_attributes"]) { + results.push(key); + } + return results; + })(); + this.sample_attr_vals = (function() { + var j, len, ref, results; + ref = this.sample_lists['samples_all']; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + s = ref[j]; + if (s.value !== null) { + results.push(this.extra(s)); + } + } + return results; + }).call(this); + this.get_distinct_attr_vals(); + this.get_attr_color_dict(this.distinct_attr_vals); + this.attribute_name = "None"; + this.sort_by = "name"; + this.chart = null; + this.select_attribute_box = $("#color_attribute"); + d3.select("#color_attribute").on("change", (function(_this) { + return function() { + _this.attribute_name = _this.select_attribute_box.val(); + return _this.rebuild_bar_graph(); + }; + })(this)); + $(".sort_by_value").on("click", (function(_this) { + return function() { + console.log("sorting by value"); + _this.sort_by = "value"; + return _this.rebuild_bar_graph(); + }; + })(this)); + $(".sort_by_name").on("click", (function(_this) { + return function() { + console.log("sorting by name"); + _this.sort_by = "name"; + return _this.rebuild_bar_graph(); + }; + })(this)); + d3.select("#color_by_trait").on("click", (function(_this) { + return function() { + return _this.open_trait_selection(); + }; + })(this)); + } + + Bar_Chart.prototype.value = function(sample) { + return this.value_dict[sample.name].value; + }; + + Bar_Chart.prototype.variance = function(sample) { + return this.value_dict[sample.name].variance; + }; + + Bar_Chart.prototype.extra = function(sample) { + var attr_vals, attribute, j, len, ref; + attr_vals = {}; + ref = this.attributes; + for (j = 0, len = ref.length; j < len; j++) { + attribute = ref[j]; + attr_vals[attribute] = sample["extra_attributes"][attribute]; + } + return attr_vals; + }; + + Bar_Chart.prototype.redraw = function(samples_dict, selected_group) { + var x; + this.value_dict = samples_dict[selected_group]; + this.raw_data = (function() { + var j, len, ref, results; + ref = this.sample_lists[selected_group]; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + if (x.name in this.value_dict && this.value(x) !== null) { + results.push(x); + } + } + return results; + }).call(this); + return this.rebuild_bar_graph(); + }; + + Bar_Chart.prototype.rebuild_bar_graph = function() { + var container, h, raw_data; + raw_data = this.raw_data.slice(); + if (this.sort_by === 'value') { + raw_data = raw_data.sort((function(_this) { + return function(x, y) { + return _this.value(x) - _this.value(y); + }; + })(this)); + } + console.log("raw_data: ", raw_data); + h = 600; + container = $("#bar_chart_container"); + container.height(h + this.margin.top + this.margin.bottom); + if (this.chart === null) { + this.chart = nv.models.multiBarChart().height(h).errorBarColor((function(_this) { + return function() { + return 'red'; + }; + })(this)).reduceXTicks(false).staggerLabels(false).showControls(false).showLegend(false); + this.chart.multibar.dispatch.on('elementMouseover.tooltip', (function(_this) { + return function(evt) { + var k, ref, v; + evt.value = _this.chart.x()(evt.data); + evt['series'] = [ + { + key: 'Value', + value: evt.data.y, + color: evt.color + } + ]; + if (evt.data.yErr) { + evt['series'].push({ + key: 'SE', + value: evt.data.yErr + }); + } + if (evt.data.attr) { + ref = evt.data.attr; + for (k in ref) { + v = ref[k]; + evt['series'].push({ + key: k, + value: v + }); + } + } + return _this.chart.tooltip.data(evt).hidden(false); + }; + })(this)); + this.chart.tooltip.valueFormatter(function(d, i) { + return d; + }); + } + return nv.addGraph((function(_this) { + return function() { + var d, s, values; + _this.remove_legend(); + values = (function() { + var j, len, results; + results = []; + for (j = 0, len = raw_data.length; j < len; j++) { + s = raw_data[j]; + results.push({ + x: s.name, + y: this.value(s), + yErr: this.variance(s) || 0, + attr: s.extra_attributes + }); + } + return results; + }).call(_this); + if (_this.attribute_name !== "None") { + _this.color_dict = _this.attr_color_dict[_this.attribute_name]; + _this.chart.barColor(function(d) { + return _this.color_dict[d.attr[_this.attribute_name]]; + }); + _this.add_legend(); + } else if (typeof _this.trait_color_dict !== 'undefined') { + _this.color_dict = _this.trait_color_dict; + _this.chart.barColor(function(d) { + return _this.color_dict[d['x']]; + }); + } else { + _this.chart.barColor(function() { + return 'steelblue'; + }); + } + _this.chart.width(raw_data.length * 20); + //User should be able to change Y domain, but should still have good default + _this.chart.yDomain([ + 0.95 * _.min((function() { // ZS: Decreasing this constant decreases the min Y axis value + var j, len, results; + results = []; + for (j = 0, len = values.length; j < len; j++) { + d = values[j]; + results.push(d.y - 0.5 * d.yErr); //ZS: the 0.5 was originally 1.5 + } + return results; + })()), 1.05 * _.max((function() { // ZS: Decreasing this constant decreases the max Y axis value + var j, len, results; + results = []; + for (j = 0, len = values.length; j < len; j++) { + d = values[j]; + results.push(d.y + 0.5 * d.yErr); // //ZS: the 0.5 was originally 1.5 + } + return results; + })()) + ]); + console.log("values: ", values); + + decimal_exists = "False"; + for(i=0; i < values.length; i++){ + if (values[i]['y'] % 1 != 0){ + decimal_exists = "True"; + break; + } + } + if (decimal_exists == "False"){ + _this.chart.yAxis.tickFormat(d3.format('d')) + } + d3.select("#bar_chart_container svg").datum([ + { + values: values + } + ]).style('width', raw_data.length * 20 + 'px').transition().duration(1000).call(_this.chart); + d3.select("#bar_chart_container .nv-x").selectAll('.tick text').style("font-size", "12px").style("text-anchor", "end").attr("dx", "-.8em").attr("dy", "-.3em").attr("transform", function(d) { + return "rotate(-90)"; + }); + return _this.chart; + }; + })(this)); + }; + + Bar_Chart.prototype.get_attr_color_dict = function(vals) { + var color, color_range, discrete, distinct_vals, i, j, key, l, len, len1, results, this_color_dict, value; + this.attr_color_dict = {}; + this.is_discrete = {}; + this.minimum_values = {}; + this.maximum_values = {}; + console.log("vals:", vals); + results = []; + for (key in vals) { + if (!hasProp.call(vals, key)) continue; + distinct_vals = vals[key]; + this.min_val = d3.min(distinct_vals); + this.max_val = d3.max(distinct_vals); + this_color_dict = {}; + discrete = distinct_vals.length < 10; + if (discrete) { + color = d3.scale.category10(); + for (i = j = 0, len = distinct_vals.length; j < len; i = ++j) { + value = distinct_vals[i]; + this_color_dict[value] = color(i); + } + } else { + console.log("distinct_values:", distinct_vals); + if (_.every(distinct_vals, (function(_this) { + return function(d) { + if (isNaN(d)) { + return false; + } else { + return true; + } + }; + })(this))) { + color_range = d3.scale.linear().domain([this.min_val, this.max_val]).range([0, 255]); + for (i = l = 0, len1 = distinct_vals.length; l < len1; i = ++l) { + value = distinct_vals[i]; + console.log("color_range(value):", parseInt(color_range(value))); + this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0); + } + } + } + this.attr_color_dict[key] = this_color_dict; + this.is_discrete[key] = discrete; + this.minimum_values[key] = this.min_val; + results.push(this.maximum_values[key] = this.max_val); + } + return results; + }; + + Bar_Chart.prototype.get_distinct_attr_vals = function() { + var attribute, j, len, ref, results, sample; + this.distinct_attr_vals = {}; + ref = this.sample_attr_vals; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + sample = ref[j]; + results.push((function() { + var ref1, results1; + results1 = []; + for (attribute in sample) { + if (!this.distinct_attr_vals[attribute]) { + this.distinct_attr_vals[attribute] = []; + } + if (ref1 = sample[attribute], indexOf.call(this.distinct_attr_vals[attribute], ref1) < 0) { + results1.push(this.distinct_attr_vals[attribute].push(sample[attribute])); + } else { + results1.push(void 0); + } + } + return results1; + }).call(this)); + } + return results; + }; + + Bar_Chart.prototype.add_legend = function() { + if (this.is_discrete[this.attribute_name]) { + return this.add_legend_discrete(); + } else { + return this.add_legend_continuous(); + } + }; + + Bar_Chart.prototype.remove_legend = function() { + $(".legend").remove(); + return $("#legend-left,#legend-right,#legend-colors").empty(); + }; + + Bar_Chart.prototype.add_legend_continuous = function() { + var svg_html; + $('#legend-left').html(this.minimum_values[this.attribute_name]); + $('#legend-right').html(this.maximum_values[this.attribute_name]); + svg_html = '<svg height="15" width="120"> <rect x="0" width="20" height="15" style="fill: rgb(0, 0, 0);"></rect> <rect x="20" width="20" height="15" style="fill: rgb(50, 0, 0);"></rect> <rect x="40" width="20" height="15" style="fill: rgb(100, 0, 0);"></rect> <rect x="60" width="20" height="15" style="fill: rgb(150, 0, 0);"></rect> <rect x="80" width="20" height="15" style="fill: rgb(200, 0, 0);"></rect> <rect x="100" width="20" height="15" style="fill: rgb(255, 0, 0);"></rect> </svg>'; + console.log("svg_html:", svg_html); + return $('#legend-colors').html(svg_html); + }; + + Bar_Chart.prototype.add_legend_discrete = function() { + var legend_span; + legend_span = d3.select('#bar_chart_legend').append('div').style('word-wrap', 'break-word').attr('class', 'legend').selectAll('span').data(this.distinct_attr_vals[this.attribute_name]).enter().append('span').style({ + 'word-wrap': 'normal', + 'display': 'inline-block' + }); + legend_span.append('span').style("background-color", (function(_this) { + return function(d) { + return _this.attr_color_dict[_this.attribute_name][d]; + }; + })(this)).style({ + 'display': 'inline-block', + 'width': '15px', + 'height': '15px', + 'margin': '0px 5px 0px 15px' + }); + return legend_span.append('span').text((function(_this) { + return function(d) { + return d; + }; + })(this)).style('font-size', '20px'); + }; + + Bar_Chart.prototype.open_trait_selection = function() { + return $('#collections_holder').load('/collections/list?color_by_trait #collections_list', (function(_this) { + return function() { + $.colorbox({ + inline: true, + href: "#collections_holder" + }); + return $('a.collection_name').attr('onClick', 'return false'); + }; + })(this)); + }; + + Bar_Chart.prototype.color_by_trait = function(trait_sample_data) { + var distinct_values, trimmed_samples; + console.log("BXD1:", trait_sample_data["BXD1"]); + console.log("trait_sample_data:", trait_sample_data); + trimmed_samples = this.trim_values(trait_sample_data); + distinct_values = {}; + distinct_values["collection_trait"] = this.get_distinct_values(trimmed_samples); + this.trait_color_dict = this.get_trait_color_dict(trimmed_samples, distinct_values); + console.log("TRAIT_COLOR_DICT:", this.trait_color_dict); + return this.rebuild_bar_graph(); + //return console.log("SAMPLES:", this.samples); + }; + + Bar_Chart.prototype.trim_values = function(trait_sample_data) { + var j, len, ref, sample, trimmed_samples; + trimmed_samples = {}; + ref = this.sample_lists['samples_all']; + for (j = 0, len = ref.length; j < len; j++) { + sample = ref[j]['name']; + if (sample in trait_sample_data) { + trimmed_samples[sample] = trait_sample_data[sample]; + } + } + console.log("trimmed_samples:", trimmed_samples); + return trimmed_samples; + }; + + Bar_Chart.prototype.get_distinct_values = function(samples) { + var distinct_values; + distinct_values = _.uniq(_.values(samples)); + console.log("distinct_values:", distinct_values); + return distinct_values; + }; + + Bar_Chart.prototype.get_trait_color_dict = function(samples, vals) { + var color, color_range, distinct_vals, i, j, k, key, len, len1, results, sample, this_color_dict, value; + trait_color_dict = {}; + console.log("vals:", vals); + for (key in vals) { + if (!hasProp.call(vals, key)) continue; + distinct_vals = vals[key]; + this_color_dict = {}; + this.min_val = d3.min(distinct_vals); + this.max_val = d3.max(distinct_vals); + if (distinct_vals.length < 10) { + color = d3.scale.category10(); + for (i = j = 0, len = distinct_vals.length; j < len; i = ++j) { + value = distinct_vals[i]; + this_color_dict[value] = color(i); + } + } else { + console.log("distinct_values:", distinct_vals); + if (_.every(distinct_vals, (function(_this) { + return function(d) { + if (isNaN(d)) { + return false; + } else { + return true; + } + }; + })(this))) { + color_range = d3.scale.linear().domain([d3.min(distinct_vals), d3.max(distinct_vals)]).range([0, 255]); + for (i = k = 0, len1 = distinct_vals.length; k < len1; i = ++k) { + value = distinct_vals[i]; + //console.log("color_range(value):", parseInt(color_range(value))); + this_color_dict[value] = d3.rgb(parseInt(color_range(value)), 0, 0); + } + } + } + } + results = []; + console.log("SAMPLES:", samples) + for (sample in samples) { + if (!hasProp.call(samples, sample)) continue; + value = samples[sample]; + trait_color_dict[sample] = this_color_dict[value]; + //results.push(this.trait_color_dict[sample] = this_color_dict[value]); + } + return trait_color_dict; + }; + + return Bar_Chart; + + })(); + + root.Bar_Chart = Bar_Chart; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/box.js b/gn2/wqflask/static/new/javascript/box.js new file mode 100644 index 00000000..aae80f05 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/box.js @@ -0,0 +1,307 @@ +//Taken from http://bl.ocks.org/mbostock/4061502
+
+(function() {
+
+// Inspired by http://informationandvisualization.de/blog/box-plot
+d3.box = function() {
+ var width = 1,
+ height = 1,
+ duration = 0,
+ domain = null,
+ value = Number,
+ whiskers = boxWhiskers,
+ quartiles = boxQuartiles,
+ tickFormat = null;
+
+ // For each small multiple…
+ function box(g) {
+ g.each(function(d, i) {
+ console.log("d:", d)
+ console.log("domain:", domain)
+ d = d.map(value).sort(d3.ascending);
+ var g = d3.select(this),
+ n = d.length,
+ min = d[0],
+ max = d[n - 1];
+
+ // Compute quartiles. Must return exactly 3 elements.
+ var quartileData = d.quartiles = quartiles(d);
+
+ // Compute whiskers. Must return exactly 2 elements, or null.
+ var whiskerIndices = whiskers && whiskers.call(this, d, i),
+ whiskerData = whiskerIndices && whiskerIndices.map(function(i) { return d[i]; });
+
+ // Compute outliers. If no whiskers are specified, all data are "outliers".
+ // We compute the outliers as indices, so that we can join across transitions!
+ var outlierIndices = whiskerIndices
+ ? d3.range(0, whiskerIndices[0]).concat(d3.range(whiskerIndices[1] + 1, n))
+ : d3.range(n);
+
+ // Compute the new x-scale.
+ var x1 = d3.scale.linear()
+ .domain(domain && domain.call(this, d, i) || [min, max])
+ .range([height, 0]);
+
+ // Retrieve the old x-scale, if this is an update.
+ var x0 = this.__chart__ || d3.scale.linear()
+ .domain([0, Infinity])
+ .range(x1.range());
+
+ // Stash the new scale.
+ this.__chart__ = x1;
+
+ // Note: the box, median, and box tick elements are fixed in number,
+ // so we only have to handle enter and update. In contrast, the outliers
+ // and other elements are variable, so we need to exit them! Variable
+ // elements also fade in and out.
+
+ // Update center line: the vertical line spanning the whiskers.
+ var center = g.selectAll("line.center")
+ .data(whiskerData ? [whiskerData] : []);
+
+ center.enter().insert("line", "rect")
+ .attr("class", "center")
+ .attr("x1", width / 2)
+ .attr("y1", function(d) { return x0(d[0]); })
+ .attr("x2", width / 2)
+ .attr("y2", function(d) { return x0(d[1]); })
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .style("opacity", 1)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); });
+
+ center.transition()
+ .duration(duration)
+ .style("opacity", 1)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); });
+
+ center.exit().transition()
+ .duration(duration)
+ .style("opacity", 1e-6)
+ .attr("y1", function(d) { return x1(d[0]); })
+ .attr("y2", function(d) { return x1(d[1]); })
+ .remove();
+
+ // Update innerquartile box.
+ var box = g.selectAll("rect.box")
+ .data([quartileData]);
+
+ box.enter().append("rect")
+ .attr("class", "box")
+ .attr("x", 0)
+ .attr("y", function(d) { return x0(d[2]); })
+ .attr("width", width)
+ .attr("height", function(d) { return x0(d[0]) - x0(d[2]); })
+ .transition()
+ .duration(duration)
+ .attr("y", function(d) { return x1(d[2]); })
+ .attr("height", function(d) { return x1(d[0]) - x1(d[2]); });
+
+ box.transition()
+ .duration(duration)
+ .attr("y", function(d) { return x1(d[2]); })
+ .attr("height", function(d) { return x1(d[0]) - x1(d[2]); });
+
+ // Update median line.
+ var medianLine = g.selectAll("line.median")
+ .data([quartileData[1]]);
+
+ medianLine.enter().append("line")
+ .attr("class", "median")
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", width)
+ .attr("y2", x0)
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ medianLine.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1);
+
+ // Update whiskers.
+ var whisker = g.selectAll("line.whisker")
+ .data(whiskerData || []);
+
+ whisker.enter().insert("line", "circle, text")
+ .attr("class", "whisker")
+ .attr("x1", 0)
+ .attr("y1", x0)
+ .attr("x2", width)
+ .attr("y2", x0)
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1);
+
+ whisker.transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1);
+
+ whisker.exit().transition()
+ .duration(duration)
+ .attr("y1", x1)
+ .attr("y2", x1)
+ .style("opacity", 1e-6)
+ .remove();
+
+ // Update outliers.
+ var outlier = g.selectAll("circle.outlier")
+ .data(outlierIndices, Number);
+
+ outlier.enter().insert("circle", "text")
+ .attr("class", "outlier")
+ .attr("r", 5)
+ .attr("cx", width / 2)
+ .attr("cy", function(i) { return x0(d[i]); })
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1);
+
+ outlier.transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1);
+
+ outlier.exit().transition()
+ .duration(duration)
+ .attr("cy", function(i) { return x1(d[i]); })
+ .style("opacity", 1e-6)
+ .remove();
+
+ // Compute the tick format.
+ var format = tickFormat || x1.tickFormat(8);
+
+ // Update box ticks.
+ var boxTick = g.selectAll("text.box")
+ .data(quartileData);
+
+ console.log("quartileData:", quartileData);
+
+ boxTick.enter().append("text")
+ .attr("class", "box")
+ .attr("dy", ".3em")
+ .attr("dx", function(d, i) { return i & 1 ? 6 : -6 })
+ .attr("x", function(d, i) { return i & 1 ? width : 0 })
+ .attr("y", x0)
+ .attr("text-anchor", function(d, i) { return i & 1 ? "start" : "end"; })
+ .text(format)
+ .transition()
+ .duration(duration)
+ .attr("y", x1);
+
+ boxTick.transition()
+ .duration(duration)
+ .text(format)
+ .attr("y", x1);
+
+ // Update whisker ticks. These are handled separately from the box
+ // ticks because they may or may not exist, and we want don't want
+ // to join box ticks pre-transition with whisker ticks post-.
+ var whiskerTick = g.selectAll("text.whisker")
+ .data(whiskerData || []);
+
+ whiskerTick.enter().append("text")
+ .attr("class", "whisker")
+ .attr("dy", ".3em")
+ .attr("dx", 6)
+ .attr("x", width)
+ .attr("y", x0)
+ .text(format)
+ .style("opacity", 1e-6)
+ .transition()
+ .duration(duration)
+ .attr("y", x1)
+ .style("opacity", 1);
+
+ whiskerTick.transition()
+ .duration(duration)
+ .text(format)
+ .attr("y", x1)
+ .style("opacity", 1);
+
+ whiskerTick.exit().transition()
+ .duration(duration)
+ .attr("y", x1)
+ .style("opacity", 1e-6)
+ .remove();
+ });
+ d3.timer.flush();
+ }
+
+ box.width = function(x) {
+ if (!arguments.length) return width;
+ width = x;
+ return box;
+ };
+
+ box.height = function(x) {
+ if (!arguments.length) return height;
+ height = x;
+ return box;
+ };
+
+ box.tickFormat = function(x) {
+ if (!arguments.length) return tickFormat;
+ tickFormat = x;
+ return box;
+ };
+
+ box.duration = function(x) {
+ if (!arguments.length) return duration;
+ duration = x;
+ return box;
+ };
+
+ box.domain = function(x) {
+ if (!arguments.length) return domain;
+ domain = x == null ? x : d3.functor(x);
+ return box;
+ };
+
+ box.value = function(x) {
+ if (!arguments.length) return value;
+ value = x;
+ return box;
+ };
+
+ box.whiskers = function(x) {
+ if (!arguments.length) return whiskers;
+ whiskers = x;
+ return box;
+ };
+
+ box.quartiles = function(x) {
+ if (!arguments.length) return quartiles;
+ quartiles = x;
+ return box;
+ };
+
+ return box;
+};
+
+function boxWhiskers(d) {
+ return [0, d.length - 1];
+}
+
+function boxQuartiles(d) {
+ return [
+ d3.quantile(d, .25),
+ d3.quantile(d, .5),
+ d3.quantile(d, .75)
+ ];
+}
+
+})();
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/box_plot.js b/gn2/wqflask/static/new/javascript/box_plot.js new file mode 100644 index 00000000..566a8eb8 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/box_plot.js @@ -0,0 +1,80 @@ +// Generated by CoffeeScript 1.8.0 +var Box_Plot, root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +Box_Plot = (function() { + function Box_Plot(sample_list, sample_group) { + this.sample_list = sample_list; + this.sample_group = sample_group; + this.get_samples(); + this.margin = { + top: 10, + right: 50, + bottom: 20, + left: 50 + }; + this.plot_width = 200 - this.margin.left - this.margin.right; + this.plot_height = 500 - this.margin.top - this.margin.bottom; + this.min = d3.min(this.sample_vals); + this.max = d3.max(this.sample_vals); + this.svg = this.create_svg(); + this.enter_data(); + } + + Box_Plot.prototype.get_samples = function() { + var sample; + return this.sample_vals = (function() { + var _i, _len, _ref, _results; + _ref = this.sample_list; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + sample = _ref[_i]; + if (sample.value !== null) { + _results.push(sample.value); + } + } + return _results; + }).call(this); + }; + + Box_Plot.prototype.create_svg = function() { + var svg; + svg = d3.box().whiskers(this.inter_quartile_range(1.5)).width(this.plot_width - 30).height(this.plot_height - 30).domain([this.min, this.max]); + return svg; + }; + + Box_Plot.prototype.enter_data = function() { + return d3.select("#box_plot").selectAll("svg").data([this.sample_vals]).enter().append("svg:svg").attr("class", "box").attr("width", this.plot_width).attr("height", this.plot_height).append("svg:g").call(this.svg); + }; + + Box_Plot.prototype.inter_quartile_range = function(k) { + return (function(_this) { + return function(d, i) { + var inter_quartile_range, j, q1, q3; + console.log("iqr d:", d); + q1 = d.quartiles[0]; + q3 = d.quartiles[2]; + inter_quartile_range = (q3 - q1) * k; + console.log("iqr:", inter_quartile_range); + i = 0; + j = d.length; + console.log("d[-1]:", d[1]); + console.log("q1 - iqr:", q1 - inter_quartile_range); + while (d[i] < q1 - inter_quartile_range) { + i++; + } + while (d[j] > q3 + inter_quartile_range) { + j--; + } + console.log("[i, j]", [i, j]); + return [i, j]; + }; + })(this); + }; + + return Box_Plot; + +})(); + +root.Box_Plot = Box_Plot; diff --git a/gn2/wqflask/static/new/javascript/chr_lod_chart.js b/gn2/wqflask/static/new/javascript/chr_lod_chart.js new file mode 100644 index 00000000..c6cbd01b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/chr_lod_chart.js @@ -0,0 +1,297 @@ +// Generated by CoffeeScript 1.9.2 +var Chr_Lod_Chart; + +Chr_Lod_Chart = (function() { + function Chr_Lod_Chart(plot_height, plot_width, chr, manhattanPlot, mappingScale) { + this.plot_height = plot_height; + this.plot_width = plot_width; + this.chr = chr; + this.manhattanPlot = manhattanPlot; + this.mappingScale = mappingScale; + this.qtl_results = js_data.qtl_results; + console.log("qtl_results are:", this.qtl_results); + console.log("chr is:", this.chr); + this.get_max_chr(); + this.filter_qtl_results(); + console.log("filtered results:", this.these_results); + this.get_qtl_count(); + this.x_coords = []; + this.y_coords = []; + this.marker_names = []; + console.time('Create coordinates'); + this.create_coordinates(); + console.log("@x_coords: ", this.x_coords); + console.log("@y_coords: ", this.y_coords); + console.timeEnd('Create coordinates'); + this.x_buffer = this.plot_width / 30; + this.y_buffer = this.plot_height / 20; + this.x_max = d3.max(this.x_coords); + this.y_max = d3.max(this.y_coords) * 1.2; + this.y_threshold = this.get_lod_threshold(); + this.svg = this.create_svg(); + this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); + console.log("coordinates:", this.plot_coordinates); + this.plot_height -= this.y_buffer; + this.create_scales(); + console.time('Create graph'); + this.create_graph(); + console.timeEnd('Create graph'); + } + + Chr_Lod_Chart.prototype.get_max_chr = function() { + var key, results; + this.max_chr = 0; + results = []; + for (key in js_data.chromosomes) { + console.log("key is:", key); + if (parseInt(key) > this.max_chr) { + results.push(this.max_chr = parseInt(key)); + } else { + results.push(void 0); + } + } + return results; + }; + + Chr_Lod_Chart.prototype.filter_qtl_results = function() { + var i, len, ref, result, results, this_chr; + this.these_results = []; + this_chr = 100; + ref = this.qtl_results; + results = []; + for (i = 0, len = ref.length; i < len; i++) { + result = ref[i]; + if (result.chr === "X") { + this_chr = this.max_chr; + } else { + this_chr = result.chr; + } + if (this_chr > parseInt(this.chr[0])) { + break; + } + if (parseInt(this_chr) === parseInt(this.chr[0])) { + results.push(this.these_results.push(result)); + } else { + results.push(void 0); + } + } + return results; + }; + + Chr_Lod_Chart.prototype.get_qtl_count = function() { + var high_qtl_count, i, len, ref, result; + high_qtl_count = 0; + ref = this.these_results; + for (i = 0, len = ref.length; i < len; i++) { + result = ref[i]; + if (result.lod_score > 1) { + high_qtl_count += 1; + } + } + console.log("high_qtl_count:", high_qtl_count); + return this.y_axis_filter = 2; + }; + + Chr_Lod_Chart.prototype.create_coordinates = function() { + var i, len, ref, result, results; + ref = this.these_results; + console.log("THESE_RESULTS:", ref) + results = []; + for (i = 0, len = ref.length; i < len; i++) { + result = ref[i]; + this.x_coords.push(parseFloat(result.Mb)); + if (js_data.result_score_type == "LOD") { + this.y_coords.push(result.lod_score); + } + else { + console.log("LRS VALUE:", result['lrs_value']) + this.y_coords.push(result['lrs_value']); + } + results.push(this.marker_names.push(result.name)); + } + return results; + }; + + Chr_Lod_Chart.prototype.create_svg = function() { + var svg; + svg = d3.select("#topchart").append("svg").attr("class", "chr_manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g"); + return svg; + }; + + Chr_Lod_Chart.prototype.create_scales = function() { + if (this.mappingScale == "morgan") { + max_pos = 0 + for (i = 0, len = this.these_results.length; i < len; i++) { + marker = this.these_results[i] + if (parseFloat(marker['Mb']) > max_pos){ + max_pos = parseFloat(marker.Mb) + } + } + this.x_scale = d3.scale.linear().domain([0, max_pos]).range([this.x_buffer, this.plot_width]); + } + else { + this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); + } + return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); + }; + + Chr_Lod_Chart.prototype.get_lod_threshold = function() { + if (this.y_max / 2 > 2) { + return this.y_max / 2; + } else { + return 2; + } + }; + + Chr_Lod_Chart.prototype.create_graph = function() { + this.add_border(); + this.add_x_axis(); + this.add_y_axis(); + this.add_title(); + this.add_back_button(); + if (this.manhattanPlot) { + return this.add_plot_points(); + } else { + return this.add_path(); + } + }; + + Chr_Lod_Chart.prototype.add_border = function() { + var border_coords; + border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]]; + return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) { + return function(d) { + return d[0]; + }; + })(this)).attr("y2", (function(_this) { + return function(d) { + return d[1]; + }; + })(this)).attr("x1", (function(_this) { + return function(d) { + return d[2]; + }; + })(this)).attr("x2", (function(_this) { + return function(d) { + return d[3]; + }; + })(this)).style("stroke", "#000"); + }; + + Chr_Lod_Chart.prototype.add_x_axis = function() { + this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20); + this.xAxis.tickFormat((function(_this) { + return function(d) { + d3.format("d"); + return d; + }; + })(this)); + return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) { + return function(d) { + return "translate(-12,0) rotate(-90)"; + }; + })(this)); + }; + + Chr_Lod_Chart.prototype.add_y_axis = function() { + this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis); + }; + + Chr_Lod_Chart.prototype.add_title = function() { + return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) { + return function(d) { + return (_this.plot_width + _this.x_buffer) / 2; + }; + })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black"); + }; + + Chr_Lod_Chart.prototype.add_back_button = function() { + return $("#return_to_full_view").show().click((function(_this) { + return function() { + return _this.return_to_full_view(); + }; + })(this)); + }; + + Chr_Lod_Chart.prototype.add_path = function() { + var line_function, line_graph; + line_function = d3.svg.line().x((function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).y((function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).interpolate("linear"); + return line_graph = this.svg.append("path").attr("d", line_function(this.plot_coordinates)).attr("stroke", "blue").attr("stroke-width", 1).attr("fill", "none"); + }; + + Chr_Lod_Chart.prototype.add_plot_points = function() { + return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).attr("cy", (function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).attr("r", (function(_this) { + return function(d) { + return 2; + }; + })(this)).attr("fill", (function(_this) { + return function(d) { + return "black"; + }; + })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) { + return function(d) { + return "point_" + String(d[2]); + }; + })(this)).classed("circle", true).on("mouseover", (function(_this) { + return function(d) { + var this_id; + console.log("d3.event is:", d3.event); + console.log("d is:", d); + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); + }; + })(this)).on("mouseout", (function(_this) { + return function(d) { + var this_id; + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { + return 2; + }).attr("fill", function(d) { + return "black"; + }).attr("stroke", "black").attr("stroke-width", "1"); + }; + })(this)).append("svg:title").text((function(_this) { + return function(d) { + return d[2]; + }; + })(this)); + }; + + Chr_Lod_Chart.prototype.return_to_full_view = function() { + $("#return_to_full_view").hide(); + $('#topchart').remove(); + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + return create_lod_chart(); + }; + + Chr_Lod_Chart.prototype.show_marker_in_table = function(marker_info) { + var marker_name; + console.log("in show_marker_in_table"); + + /* Searches for the select marker in the results table below */ + if (marker_info) { + marker_name = marker_info[2]; + return $("#qtl_results_filter").find("input:first").val(marker_name).change(); + } + }; + + return Chr_Lod_Chart; + +})(); diff --git a/gn2/wqflask/static/new/javascript/chr_manhattan_plot.js b/gn2/wqflask/static/new/javascript/chr_manhattan_plot.js new file mode 100644 index 00000000..c661edc7 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/chr_manhattan_plot.js @@ -0,0 +1,273 @@ +// Generated by CoffeeScript 1.8.0 +var Chr_Manhattan_Plot; + +Chr_Manhattan_Plot = (function() { + function Chr_Manhattan_Plot(plot_height, plot_width, chr, manhattanPlot) { + this.plot_height = plot_height; + this.plot_width = plot_width; + this.chr = chr; + this.qtl_results = js_data.qtl_results; + console.log("qtl_results are:", this.qtl_results); + console.log("chr is:", this.chr); + this.get_max_chr(); + this.filter_qtl_results(); + console.log("filtered results:", this.these_results); + this.get_qtl_count(); + this.x_coords = []; + this.y_coords = []; + this.marker_names = []; + console.time('Create coordinates'); + this.create_coordinates(); + console.log("@x_coords: ", this.x_coords); + console.log("@y_coords: ", this.y_coords); + console.timeEnd('Create coordinates'); + this.x_buffer = this.plot_width / 30; + this.y_buffer = this.plot_height / 20; + this.x_max = d3.max(this.x_coords); + this.y_max = d3.max(this.y_coords) * 1.2; + this.y_threshold = this.get_lod_threshold(); + this.svg = this.create_svg(); + this.plot_coordinates = _.zip(this.x_coords, this.y_coords, this.marker_names); + console.log("coordinates:", this.plot_coordinates); + this.plot_height -= this.y_buffer; + this.create_scales(); + console.time('Create graph'); + this.create_graph(); + console.timeEnd('Create graph'); + } + + Chr_Manhattan_Plot.prototype.get_max_chr = function() { + var key, _results; + this.max_chr = 0; + _results = []; + for (key in js_data.chromosomes) { + console.log("key is:", key); + if (parseInt(key) > this.max_chr) { + _results.push(this.max_chr = parseInt(key)); + } else { + _results.push(void 0); + } + } + return _results; + }; + + Chr_Manhattan_Plot.prototype.filter_qtl_results = function() { + var result, this_chr, _i, _len, _ref, _results; + this.these_results = []; + this_chr = 100; + _ref = this.qtl_results; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + if (result.chr === "X") { + this_chr = this.max_chr; + } else { + this_chr = result.chr; + } + console.log("this_chr is:", this_chr); + console.log("@chr[0] is:", parseInt(this.chr[0])); + if (this_chr > parseInt(this.chr[0])) { + break; + } + if (parseInt(this_chr) === parseInt(this.chr[0])) { + _results.push(this.these_results.push(result)); + } else { + _results.push(void 0); + } + } + return _results; + }; + + Chr_Manhattan_Plot.prototype.get_qtl_count = function() { + var high_qtl_count, result, _i, _len, _ref; + high_qtl_count = 0; + _ref = this.these_results; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + if (result.lod_score > 1) { + high_qtl_count += 1; + } + } + console.log("high_qtl_count:", high_qtl_count); + return this.y_axis_filter = 2; + }; + + Chr_Manhattan_Plot.prototype.create_coordinates = function() { + var result, _i, _len, _ref, _results; + _ref = this.these_results; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + result = _ref[_i]; + this.x_coords.push(parseFloat(result.Mb)); + this.y_coords.push(result.lod_score); + _results.push(this.marker_names.push(result.name)); + } + return _results; + }; + + Chr_Manhattan_Plot.prototype.create_svg = function() { + var svg; + svg = d3.select("#topchart").append("svg").attr("class", "chr_manhattan_plot").attr("width", this.plot_width + this.x_buffer).attr("height", this.plot_height + this.y_buffer).append("g"); + return svg; + }; + + Chr_Manhattan_Plot.prototype.create_scales = function() { + this.x_scale = d3.scale.linear().domain([0, this.chr[1]]).range([this.x_buffer, this.plot_width]); + return this.y_scale = d3.scale.linear().domain([0, this.y_max]).range([this.plot_height, this.y_buffer]); + }; + + Chr_Manhattan_Plot.prototype.get_lod_threshold = function() { + if (this.y_max / 2 > 2) { + return this.y_max / 2; + } else { + return 2; + } + }; + + Chr_Manhattan_Plot.prototype.create_graph = function() { + this.add_border(); + this.add_x_axis(); + this.add_y_axis(); + this.add_title(); + this.add_back_button(); + if (manhattanPlot) { + return this.add_plot_points(); + } else { + return this.add_path(); + } + }; + + Chr_Manhattan_Plot.prototype.add_border = function() { + var border_coords; + border_coords = [[this.y_buffer, this.plot_height, this.x_buffer, this.x_buffer], [this.y_buffer, this.plot_height, this.plot_width, this.plot_width], [this.y_buffer, this.y_buffer, this.x_buffer, this.plot_width], [this.plot_height, this.plot_height, this.x_buffer, this.plot_width]]; + return this.svg.selectAll("line").data(border_coords).enter().append("line").attr("y1", (function(_this) { + return function(d) { + return d[0]; + }; + })(this)).attr("y2", (function(_this) { + return function(d) { + return d[1]; + }; + })(this)).attr("x1", (function(_this) { + return function(d) { + return d[2]; + }; + })(this)).attr("x2", (function(_this) { + return function(d) { + return d[3]; + }; + })(this)).style("stroke", "#000"); + }; + + Chr_Manhattan_Plot.prototype.add_x_axis = function() { + this.xAxis = d3.svg.axis().scale(this.x_scale).orient("bottom").ticks(20); + this.xAxis.tickFormat((function(_this) { + return function(d) { + d3.format("d"); + return d; + }; + })(this)); + return this.svg.append("g").attr("class", "x_axis").attr("transform", "translate(0," + this.plot_height + ")").call(this.xAxis).selectAll("text").attr("text-anchor", "right").attr("font-size", "12px").attr("dx", "-1.6em").attr("transform", (function(_this) { + return function(d) { + return "translate(-12,0) rotate(-90)"; + }; + })(this)); + }; + + Chr_Manhattan_Plot.prototype.add_y_axis = function() { + this.yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y_axis").attr("transform", "translate(" + this.x_buffer + ",0)").call(this.yAxis); + }; + + Chr_Manhattan_Plot.prototype.add_title = function() { + return this.svg.append("text").attr("class", "title").text("Chr " + this.chr[0]).attr("x", (function(_this) { + return function(d) { + return (_this.plot_width + _this.x_buffer) / 2; + }; + })(this)).attr("y", this.y_buffer + 20).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("fill", "black"); + }; + + Chr_Manhattan_Plot.prototype.add_back_button = function() { + return this.svg.append("text").attr("class", "back").text("Return to full view").attr("x", this.x_buffer * 2).attr("y", this.y_buffer / 2).attr("dx", "0em").attr("text-anchor", "middle").attr("font-family", "sans-serif").attr("font-size", "18px").attr("cursor", "pointer").attr("fill", "black").on("click", this.return_to_full_view); + }; + + Chr_Manhattan_Plot.prototype.add_path = function() { + var line_function, line_graph; + line_function = d3.svg.line().x((function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).y((function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).interpolate("linear"); + return line_graph = this.svg.append("path").attr("d", line_function(this.plot_coordinates)).attr("stroke", "blue").attr("stroke-width", 1).attr("fill", "none"); + }; + + Chr_Manhattan_Plot.prototype.add_plot_points = function() { + return this.plot_point = this.svg.selectAll("circle").data(this.plot_coordinates).enter().append("circle").attr("cx", (function(_this) { + return function(d) { + return _this.x_scale(d[0]); + }; + })(this)).attr("cy", (function(_this) { + return function(d) { + return _this.y_scale(d[1]); + }; + })(this)).attr("r", (function(_this) { + return function(d) { + return 2; + }; + })(this)).attr("fill", (function(_this) { + return function(d) { + return "black"; + }; + })(this)).attr("stroke", "black").attr("stroke-width", "1").attr("id", (function(_this) { + return function(d) { + return "point_" + String(d[2]); + }; + })(this)).classed("circle", true).on("mouseover", (function(_this) { + return function(d) { + var this_id; + console.log("d3.event is:", d3.event); + console.log("d is:", d); + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", true).attr("r", 5).attr("stroke", "none").attr("fill", "blue").call(_this.show_marker_in_table(d)); + }; + })(this)).on("mouseout", (function(_this) { + return function(d) { + var this_id; + this_id = "point_" + String(d[2]); + return d3.select("#" + this_id).classed("d3_highlight", false).attr("r", function(d) { + return 2; + }).attr("fill", function(d) { + return "black"; + }).attr("stroke", "black").attr("stroke-width", "1"); + }; + })(this)).append("svg:title").text((function(_this) { + return function(d) { + return d[2]; + }; + })(this)); + }; + + Chr_Manhattan_Plot.prototype.return_to_full_view = function() { + $('#topchart').remove(); + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + return create_manhattan_plot(); + }; + + Chr_Manhattan_Plot.prototype.show_marker_in_table = function(marker_info) { + var marker_name; + console.log("in show_marker_in_table"); + + /* Searches for the select marker in the results table below */ + if (marker_info) { + marker_name = marker_info[2]; + return $("#qtl_results_filter").find("input:first").val(marker_name).change(); + } + }; + + return Chr_Manhattan_Plot; + +})(); diff --git a/gn2/wqflask/static/new/javascript/colorbrewer.js b/gn2/wqflask/static/new/javascript/colorbrewer.js new file mode 100644 index 00000000..2efa9632 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/colorbrewer.js @@ -0,0 +1,302 @@ +// This product includes color specifications and designs developed by Cynthia Brewer (http://colorbrewer.org/).
+var colorbrewer = {YlGn: {
+3: ["#f7fcb9","#addd8e","#31a354"],
+4: ["#ffffcc","#c2e699","#78c679","#238443"],
+5: ["#ffffcc","#c2e699","#78c679","#31a354","#006837"],
+6: ["#ffffcc","#d9f0a3","#addd8e","#78c679","#31a354","#006837"],
+7: ["#ffffcc","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#005a32"],
+8: ["#ffffe5","#f7fcb9","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#005a32"],
+9: ["#ffffe5","#f7fcb9","#d9f0a3","#addd8e","#78c679","#41ab5d","#238443","#006837","#004529"]
+},YlGnBu: {
+3: ["#edf8b1","#7fcdbb","#2c7fb8"],
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+},Spectral: {
+3: ["#fc8d59","#ffffbf","#99d594"],
+4: ["#d7191c","#fdae61","#abdda4","#2b83ba"],
+5: ["#d7191c","#fdae61","#ffffbf","#abdda4","#2b83ba"],
+6: ["#d53e4f","#fc8d59","#fee08b","#e6f598","#99d594","#3288bd"],
+7: ["#d53e4f","#fc8d59","#fee08b","#ffffbf","#e6f598","#99d594","#3288bd"],
+8: ["#d53e4f","#f46d43","#fdae61","#fee08b","#e6f598","#abdda4","#66c2a5","#3288bd"],
+9: ["#d53e4f","#f46d43","#fdae61","#fee08b","#ffffbf","#e6f598","#abdda4","#66c2a5","#3288bd"],
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+11: ["#9e0142","#d53e4f","#f46d43","#fdae61","#fee08b","#ffffbf","#e6f598","#abdda4","#66c2a5","#3288bd","#5e4fa2"]
+},RdYlGn: {
+3: ["#fc8d59","#ffffbf","#91cf60"],
+4: ["#d7191c","#fdae61","#a6d96a","#1a9641"],
+5: ["#d7191c","#fdae61","#ffffbf","#a6d96a","#1a9641"],
+6: ["#d73027","#fc8d59","#fee08b","#d9ef8b","#91cf60","#1a9850"],
+7: ["#d73027","#fc8d59","#fee08b","#ffffbf","#d9ef8b","#91cf60","#1a9850"],
+8: ["#d73027","#f46d43","#fdae61","#fee08b","#d9ef8b","#a6d96a","#66bd63","#1a9850"],
+9: ["#d73027","#f46d43","#fdae61","#fee08b","#ffffbf","#d9ef8b","#a6d96a","#66bd63","#1a9850"],
+10: ["#a50026","#d73027","#f46d43","#fdae61","#fee08b","#d9ef8b","#a6d96a","#66bd63","#1a9850","#006837"],
+11: ["#a50026","#d73027","#f46d43","#fdae61","#fee08b","#ffffbf","#d9ef8b","#a6d96a","#66bd63","#1a9850","#006837"]
+},Accent: {
+3: ["#7fc97f","#beaed4","#fdc086"],
+4: ["#7fc97f","#beaed4","#fdc086","#ffff99"],
+5: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0"],
+6: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f"],
+7: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f","#bf5b17"],
+8: ["#7fc97f","#beaed4","#fdc086","#ffff99","#386cb0","#f0027f","#bf5b17","#666666"]
+},Dark2: {
+3: ["#1b9e77","#d95f02","#7570b3"],
+4: ["#1b9e77","#d95f02","#7570b3","#e7298a"],
+5: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e"],
+6: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02"],
+7: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02","#a6761d"],
+8: ["#1b9e77","#d95f02","#7570b3","#e7298a","#66a61e","#e6ab02","#a6761d","#666666"]
+},Paired: {
+3: ["#a6cee3","#1f78b4","#b2df8a"],
+4: ["#a6cee3","#1f78b4","#b2df8a","#33a02c"],
+5: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99"],
+6: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c"],
+7: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f"],
+8: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00"],
+9: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6"],
+10: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a"],
+11: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a","#ffff99"],
+12: ["#a6cee3","#1f78b4","#b2df8a","#33a02c","#fb9a99","#e31a1c","#fdbf6f","#ff7f00","#cab2d6","#6a3d9a","#ffff99","#b15928"]
+},Pastel1: {
+3: ["#fbb4ae","#b3cde3","#ccebc5"],
+4: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4"],
+5: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6"],
+6: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc"],
+7: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd"],
+8: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd","#fddaec"],
+9: ["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd","#fddaec","#f2f2f2"]
+},Pastel2: {
+3: ["#b3e2cd","#fdcdac","#cbd5e8"],
+4: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4"],
+5: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9"],
+6: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9","#fff2ae"],
+7: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9","#fff2ae","#f1e2cc"],
+8: ["#b3e2cd","#fdcdac","#cbd5e8","#f4cae4","#e6f5c9","#fff2ae","#f1e2cc","#cccccc"]
+},Set1: {
+3: ["#e41a1c","#377eb8","#4daf4a"],
+4: ["#e41a1c","#377eb8","#4daf4a","#984ea3"],
+5: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00"],
+6: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33"],
+7: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628"],
+8: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628","#f781bf"],
+9: ["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628","#f781bf","#999999"]
+},Set2: {
+3: ["#66c2a5","#fc8d62","#8da0cb"],
+4: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3"],
+5: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854"],
+6: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854","#ffd92f"],
+7: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854","#ffd92f","#e5c494"],
+8: ["#66c2a5","#fc8d62","#8da0cb","#e78ac3","#a6d854","#ffd92f","#e5c494","#b3b3b3"]
+},Set3: {
+3: ["#8dd3c7","#ffffb3","#bebada"],
+4: ["#8dd3c7","#ffffb3","#bebada","#fb8072"],
+5: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3"],
+6: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462"],
+7: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69"],
+8: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5"],
+9: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9"],
+10: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9","#bc80bd"],
+11: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9","#bc80bd","#ccebc5"],
+12: ["#8dd3c7","#ffffb3","#bebada","#fb8072","#80b1d3","#fdb462","#b3de69","#fccde5","#d9d9d9","#bc80bd","#ccebc5","#ffed6f"]
+}};
diff --git a/gn2/wqflask/static/new/javascript/compare_traits_scatterplot.js b/gn2/wqflask/static/new/javascript/compare_traits_scatterplot.js new file mode 100644 index 00000000..5c0ef16c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/compare_traits_scatterplot.js @@ -0,0 +1,121 @@ +// Generated by CoffeeScript 1.8.0 +var root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +root.create_scatterplot = function(json_ids, json_data) { + var data, h, halfh, halfw, indID, margin, mychart, totalh, totalw, w; + console.log("TESTING2"); + h = 400; + w = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + halfw = w + margin.left + margin.right; + totalw = halfw * 2; + mychart = scatterplot().xvar(0).yvar(1).xlab("X").ylab("Y").height(h).width(w).margin(margin); + data = json_data; + indID = json_ids; + d3.select("div#comparison_scatterplot").datum({ + data: data, + indID: indID + }).call(mychart); + return mychart.pointsSelect().on("mouseover", function(d) { + return d3.select(this).attr("r", mychart.pointsize() * 3); + }).on("mouseout", function(d) { + return d3.select(this).attr("r", mychart.pointsize()); + }); +}; + +root.create_scatterplots = function(trait_names, json_ids, json_data) { + var brush, brushend, brushmove, brushstart, chart, data, h, halfh, halfw, i, indID, margin, mychart, num_traits, svg, totalh, totalw, w, xscale, xshift, xvar, yscale, yshift, yvar, _i, _j, _k, _ref, _ref1, _ref2, _results; + console.log("json_data:", json_data); + console.log("trait_names:", trait_names); + num_traits = json_data.length; + console.log("num_traits:", num_traits); + h = 300; + w = 400; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * (num_traits - 1); + halfw = w + margin.left + margin.right; + totalw = halfw; + xvar = []; + yvar = []; + xshift = []; + yshift = []; + for (i = _i = 0, _ref = num_traits - 1; 0 <= _ref ? _i <= _ref : _i >= _ref; i = 0 <= _ref ? ++_i : --_i) { + xvar.push(i); + yvar.push(0); + xshift.push(0); + yshift.push(halfh * i); + } + console.log("xvar:", xvar); + console.log("yvar:", yvar); + svg = d3.select("div#comparison_scatterplot").append("svg").attr("height", totalh).attr("width", totalw); + mychart = []; + chart = []; + for (i = _j = 1, _ref1 = num_traits - 1; 1 <= _ref1 ? _j <= _ref1 : _j >= _ref1; i = 1 <= _ref1 ? ++_j : --_j) { + mychart[i - 1] = scatterplot().xvar(xvar[i]).yvar(yvar[i]).nxticks(6).height(h).width(w).margin(margin).pointsize(4).xlab("" + trait_names[i - 1]).ylab("" + trait_names[0]).title("" + trait_names[0] + " vs. " + trait_names[i - 1]); + data = json_data; + indID = json_ids; + chart[i - 1] = svg.append("g").attr("id", "chart" + (i - 1)).attr("transform", "translate(" + xshift[i] + "," + yshift[i - 1] + ")"); + chart[i - 1].datum({ + data: data, + indID: indID + }).call(mychart[i - 1]); + } + brush = []; + brushstart = function(i) { + return function() { + var j, _k, _ref2; + for (j = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; j = 0 <= _ref2 ? ++_k : --_k) { + if (j !== i) { + chart[j].call(brush[j].clear()); + } + } + return svg.selectAll("circle").attr("opacity", 0.6).classed("selected", false); + }; + }; + brushmove = function(i) { + return function() { + var e; + svg.selectAll("circle").classed("selected", false); + e = brush[i].extent(); + return chart[i].selectAll("circle").classed("selected", function(d, j) { + var circ, cx, cy, selected; + circ = d3.select(this); + cx = circ.attr("cx"); + cy = circ.attr("cy"); + selected = e[0][0] <= cx && cx <= e[1][0] && e[0][1] <= cy && cy <= e[1][1]; + if (selected) { + svg.selectAll("circle.pt" + j).classed("selected", true); + } + return selected; + }); + }; + }; + brushend = function() { + return svg.selectAll("circle").attr("opacity", 1); + }; + xscale = d3.scale.linear().domain([margin.left, margin.left + w]).range([margin.left, margin.left + w]); + yscale = d3.scale.linear().domain([margin.top, margin.top + h]).range([margin.top, margin.top + h]); + _results = []; + for (i = _k = 0, _ref2 = num_traits - 2; 0 <= _ref2 ? _k <= _ref2 : _k >= _ref2; i = 0 <= _ref2 ? ++_k : --_k) { + brush[i] = d3.svg.brush().x(xscale).y(yscale).on("brushstart", brushstart(i)).on("brush", brushmove(i)).on("brushend", brushend); + _results.push(chart[i].call(brush[i])); + } + return _results; +}; diff --git a/gn2/wqflask/static/new/javascript/comparison_bar_chart.js b/gn2/wqflask/static/new/javascript/comparison_bar_chart.js new file mode 100644 index 00000000..5e73807c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/comparison_bar_chart.js @@ -0,0 +1,25 @@ +generate_traces = function() { + traces = []; + for (i = 0, _len = js_data.traits.length; i < _len; i++) { + this_trace = { + x: js_data.samples, + y: js_data.sample_data[i], + name: js_data.traits[i], + type: 'bar', + bargap: 20 + } + + traces.push(this_trace) + } + + return traces +} + +create_bar_chart = function() { + var data = generate_traces() + var layout = {barmode: 'group', bargap: 5}; + + Plotly.newPlot('comp_bar_chart', data, layout); +} + +create_bar_chart();
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/corr_matrix.js b/gn2/wqflask/static/new/javascript/corr_matrix.js new file mode 100644 index 00000000..ad0fc8b8 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/corr_matrix.js @@ -0,0 +1,159 @@ +// Generated by CoffeeScript 1.8.0 +var iplotCorr, root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +iplotCorr = function(data, chartOpts) { + var cells, chartdivid, colorScale, corXscale, corYscale, corZscale, corcolors, corr, corr_tip, corrplot, cortitle, drawScatter, height, i, j, margin, nGroup, ncorrX, ncorrY, nind, nvar, pixel_height, pixel_width, rectcolor, scat_tip, scatcolors, scatterplot, scattitle, svg, totalh, totalw, width, zlim, _ref, _ref1, _ref2, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9; + height = (_ref = chartOpts != null ? chartOpts.height : void 0) != null ? _ref : 450; + width = (_ref1 = chartOpts != null ? chartOpts.width : void 0) != null ? _ref1 : height; + margin = (_ref2 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref2 : { + left: 70, + top: 40, + right: 5, + bottom: 70, + inner: 5 + }; + corcolors = (_ref3 = chartOpts != null ? chartOpts.corcolors : void 0) != null ? _ref3 : ["darkslateblue", "white", "crimson"]; + zlim = (_ref4 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref4 : [-1, 0, 1]; + rectcolor = (_ref5 = chartOpts != null ? chartOpts.rectcolor : void 0) != null ? _ref5 : d3.rgb(230, 230, 230); + cortitle = (_ref6 = chartOpts != null ? chartOpts.cortitle : void 0) != null ? _ref6 : ""; + scattitle = (_ref7 = chartOpts != null ? chartOpts.scattitle : void 0) != null ? _ref7 : ""; + scatcolors = (_ref8 = chartOpts != null ? chartOpts.scatcolors : void 0) != null ? _ref8 : null; + chartdivid = (_ref9 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref9 : 'chart'; + totalh = height + margin.top + margin.bottom; + totalw = (width + margin.left + margin.right) * 2; + svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw); + corrplot = svg.append("g").attr("id", "corplot").attr("transform", "translate(" + margin.left + "," + margin.top + ")"); + scatterplot = svg.append("g").attr("id", "scatterplot").attr("transform", "translate(" + (margin.left * 2 + margin.right + width) + "," + margin.top + ")"); + nind = data.indID.length; + nvar = data["var"].length; + ncorrX = data.cols.length; + ncorrY = data.rows.length; + corXscale = d3.scale.ordinal().domain(d3.range(ncorrX)).rangeBands([0, width]); + corYscale = d3.scale.ordinal().domain(d3.range(ncorrY)).rangeBands([0, height]); + corZscale = d3.scale.linear().domain(zlim).range(corcolors); + pixel_width = corXscale(1) - corXscale(0); + pixel_height = corYscale(0) - corYscale(1); + corr = []; + for (i in data.corr) { + for (j in data.corr[i]) { + corr.push({ + row: i, + col: j, + value: data.corr[i][j] + }); + } + corrplot.append("text").attr("class", "corrlabel_y").attr("y", corYscale(i) - pixel_height / 2).attr("x", -margin.left * 0.1).text(data["var"][data.rows[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "end"); + //corrplot.append("text").attr("class", "corrlabel_x").attr("x", corXscale(i) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + + } + scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none"); + corr_tip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return d3.format(".2f")(d.value); + }).direction('e').offset([0, 10]); + corrplot.call(corr_tip); + + cells = corrplot.selectAll("empty").data(corr).enter().append("rect").attr("class", "cell").attr("x", function(d) { + return corXscale(d.col); + }).attr("y", function(d) { + return corYscale(d.row); + }).attr("width", corXscale.rangeBand()).attr("height", corYscale.rangeBand()).attr("fill", function(d) { + return corZscale(d.value); + }).attr("stroke", "none").attr("stroke-width", 2).on("mouseover", function(d) { + d3.select(this).attr("stroke", "black"); + corr_tip.show(d); + //corrplot.append("text").attr("class", "corrlabel").attr("x", corXscale(d.col) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[d.col]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + //return corrplot.append("text").attr("class", "corrlabel_x").attr("y", corYscale(d.row) + pixel_height / 2).attr("x", -margin.left * 0.1).text(data["var"][data.rows[d.row]]).attr("dominant-baseline", "middle").attr("text-anchor", "end"); + return corrplot.append("text").attr("class", "corrlabel_x").attr("x", corXscale(d.col) + pixel_width / 2).attr("y", height + margin.bottom * 0.2).text(data["var"][data.cols[d.col]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + }).on("mouseout", function(d) { + corr_tip.hide(d); + d3.selectAll("text.corrlabel_x").remove(); + return d3.select(this).attr("stroke", "none"); + }).on("click", function(d) { + return drawScatter(d.col, d.row); + }); + nGroup = d3.max(data.group); + if (!(scatcolors != null) || scatcolors.length < nGroup) { + if (nGroup === 1) { + scatcolors = [d3.rgb(150, 150, 150)]; + } else if (nGroup <= 3) { + scatcolors = ["crimson", "green", "darkslateblue"]; + } else { + if (nGroup <= 10) { + colorScale = d3.scale.category10(); + } else { + colorScale = d3.scale.category20(); + } + scatcolors = (function() { + var _results; + _results = []; + for (i in d3.range(nGroup)) { + _results.push(colorScale(i)); + } + return _results; + })(); + } + } + scat_tip = d3.tip().attr('class', 'd3-tip').html(function(d, i) { + return data.indID[i]; + }).direction('e').offset([0, 10]); + scatterplot.call(scat_tip); + drawScatter = function(i, j) { + var xScale, xticks, yScale, yticks; + d3.selectAll("circle.points").remove(); + d3.selectAll("text.axes").remove(); + d3.selectAll("line.axes").remove(); + console.log("data.dat:", data.dat); + console.log("data.cols:", data.cols); + xScale = d3.scale.linear().domain(d3.extent(data.dat[data.cols[i]])).range([margin.inner, width - margin.inner]); + yScale = d3.scale.linear().domain(d3.extent(data.dat[data.rows[j]])).range([height - margin.inner, margin.inner]); + scatterplot.append("text").attr("id", "xaxis").attr("class", "axes").attr("x", width / 2).attr("y", height + margin.bottom * 0.7).text(data["var"][data.cols[i]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("fill", "slateblue"); + scatterplot.append("text").attr("id", "yaxis").attr("class", "axes").attr("x", -margin.left * 0.8).attr("y", height / 2).text(data["var"][data.rows[j]]).attr("dominant-baseline", "middle").attr("text-anchor", "middle").attr("transform", "rotate(270," + (-margin.left * 0.8) + "," + (height / 2) + ")").attr("fill", "slateblue"); + xticks = xScale.ticks(5); + yticks = yScale.ticks(5); + scatterplot.selectAll("empty").data(xticks).enter().append("text").attr("class", "axes").text(function(d) { + return formatAxis(xticks)(d); + }).attr("x", function(d) { + return xScale(d); + }).attr("y", height + margin.bottom * 0.3).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + scatterplot.selectAll("empty").data(yticks).enter().append("text").attr("class", "axes").text(function(d) { + return formatAxis(yticks)(d); + }).attr("x", -margin.left * 0.1).attr("y", function(d) { + return yScale(d); + }).attr("dominant-baseline", "middle").attr("text-anchor", "end"); + scatterplot.selectAll("empty").data(xticks).enter().append("line").attr("class", "axes").attr("x1", function(d) { + return xScale(d); + }).attr("x2", function(d) { + return xScale(d); + }).attr("y1", 0).attr("y2", height).attr("stroke", "white").attr("stroke-width", 1); + scatterplot.selectAll("empty").data(yticks).enter().append("line").attr("class", "axes").attr("y1", function(d) { + return yScale(d); + }).attr("y2", function(d) { + return yScale(d); + }).attr("x1", 0).attr("x2", width).attr("stroke", "white").attr("stroke-width", 1); + return scatterplot.selectAll("empty").data(d3.range(nind)).enter().append("circle").attr("class", "points").attr("cx", function(d) { + return xScale(data.dat[data.cols[i]][d]); + }).attr("cy", function(d) { + return yScale(data.dat[data.rows[j]][d]); + }).attr("r", function(d) { + var x, y; + x = data.dat[data.cols[i]][d]; + y = data.dat[data.rows[j]][d]; + if ((x != "") && (y != "")) { + return 3; + } else { + return null; + } + }).attr("stroke", "black").attr("stroke-width", 1).attr("fill", function(d) { + return scatcolors[data.group[d] - 1]; + }).on("mouseover", scat_tip.show).on("mouseout", scat_tip.hide); + }; + corrplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none"); + scatterplot.append("rect").attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", 1).attr("pointer-events", "none"); + corrplot.append("text").text(cortitle).attr("id", "corrtitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + scatterplot.append("text").text(scattitle).attr("id", "scattitle").attr("x", width / 2).attr("y", -margin.top / 2).attr("dominant-baseline", "middle").attr("text-anchor", "middle"); + return d3.select("div#caption").style("opacity", 1); +}; + +root.corr_matrix = iplotCorr; diff --git a/gn2/wqflask/static/new/javascript/corr_scatter_plot.js b/gn2/wqflask/static/new/javascript/corr_scatter_plot.js new file mode 100644 index 00000000..553423cf --- /dev/null +++ b/gn2/wqflask/static/new/javascript/corr_scatter_plot.js @@ -0,0 +1,73 @@ +// Generated by CoffeeScript 1.8.0 +var Scatter_Plot, root; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +Scatter_Plot = (function() { + function Scatter_Plot() { + var chart, data, g, height, i, main, margin, maxx, maxy, minx, miny, sample1, sample2, samplename, samples_1, samples_2, text, width, x, xAxis, y, yAxis; + data = new Array(); + samples_1 = js_data.samples_1; + samples_2 = js_data.samples_2; + i = 0; + for (samplename in samples_1) { + sample1 = samples_1[samplename]; + sample2 = samples_2[samplename]; + data[i++] = [sample1.value, sample2.value]; + } + margin = { + top: 100, + right: 15, + bottom: 60, + left: 60 + }; + width = js_data.width - margin.left - margin.right; + height = js_data.height - margin.top - margin.bottom; + minx = d3.min(data, function(d) { + return d[0]; + }) * 0.95; + maxx = d3.max(data, function(d) { + return d[0]; + }) * 1.05; + miny = d3.min(data, function(d) { + return d[1]; + }) * 0.95; + maxy = d3.max(data, function(d) { + return d[1]; + }) * 1.05; + x = d3.scale.linear().domain([minx, maxx]).range([0, width]); + y = d3.scale.linear().domain([miny, maxy]).range([height, 0]); + chart = d3.select("#scatter_plot").append("svg:svg").attr("width", width + margin.right + margin.left).attr("height", height + margin.top + margin.bottom).attr("class", "chart"); + main = chart.append("g").attr("transform", "translate(" + margin.left + "," + margin.top + ")").attr("width", width).attr("height", height).attr("class", "main"); + xAxis = d3.svg.axis().scale(x).orient("bottom"); + main.append("g").attr("transform", "translate(0," + height + ")").attr("class", "main axis date").call(xAxis); + yAxis = d3.svg.axis().scale(y).orient("left"); + main.append("g").attr("transform", "translate(0,0)").attr("class", "main axis date").call(yAxis); + g = main.append("svg:g"); + g.selectAll("scatter-dots").data(data).enter().append("svg:circle").attr("cx", function(d) { + return x(d[0]); + }).attr("cy", function(d) { + return y(d[1]); + }).attr("fill", js_data.circle_color).attr("r", js_data.circle_radius); + main.append("line").attr("x1", x(minx)).attr("y1", y(js_data.slope * minx + js_data.intercept)).attr("x2", x(maxx * 0.995)).attr("y2", y(js_data.slope * maxx * 0.995 + js_data.intercept)).style("stroke", js_data.line_color).style("stroke-width", js_data.line_width); + chart.append("text").attr("x", width / 2).attr("y", margin.top / 2 - 25).text("Sample Correlation Scatterplot"); + text = ""; + text += "N=" + js_data.num_overlap; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 - 5).text(text); + text = ""; + text += "r=" + js_data.r_value + "\t"; + text += "p(r)=" + js_data.p_value; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 15).text(text); + text = ""; + text += "slope=" + js_data.slope + "\t"; + text += "intercept=" + js_data.intercept; + chart.append("text").attr("x", margin.left).attr("y", margin.top / 2 + 35).text(text); + chart.append("text").attr("x", width / 2).attr("y", height + margin.top + 35).text(js_data.trait_1); + chart.append("text").attr("x", 20).attr("y", height / 2 + margin.top + 30).attr("transform", "rotate(-90 20," + (height / 2 + margin.top + 30) + ")").text(js_data.trait_2); + } + + return Scatter_Plot; + +})(); + +root.Scatter_Plot = Scatter_Plot; diff --git a/gn2/wqflask/static/new/javascript/create_corr_matrix.js b/gn2/wqflask/static/new/javascript/create_corr_matrix.js new file mode 100644 index 00000000..c0c39fbc --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_corr_matrix.js @@ -0,0 +1,94 @@ +var neg_color_scale = chroma.scale(['#91bfdb', '#ffffff']).domain([-1, -0.4]); +var pos_color_scale = chroma.scale(['#ffffff', '#fc8d59']).domain([0.4, 1]) +$('.corr_cell').each( function () { + corr_value = parseFloat($(this).find('span.corr_value').text()) + if (corr_value >= 0.5){ + $(this).css('background-color', pos_color_scale(parseFloat(corr_value))._rgb) + } + else if (corr_value <= -0.5) { + $(this).css('background-color', neg_color_scale(parseFloat(corr_value))._rgb) + } + else { + $(this).css('background-color', 'white') + } +}); + +$('#short_labels').click( function (){ + if ($('.short_check').css("display") == "none"){ + $('.short_check').css("display", "inline-block") + } else { + $('.short_check').css("display", "none") + } + $('.shortName').each( function() { + if ($(this).css("display") == "none"){ + $(this).css("display", "block"); + } + else { + $(this).css("display", "none"); + } + }); +}); + +$('#long_labels').click( function (){ + if ($('.long_check').css("display") == "none"){ + $('.long_check').css("display", "inline-block") + } else { + $('.long_check').css("display", "none") + } + $('.verboseName').each( function() { + if ($(this).css("display") == "none"){ + $(this).css("display", "block"); + } + else { + $(this).css("display", "none"); + } + }); +}); + +select_all = function() { + $(".trait_checkbox").each(function() { + $(this).prop('checked', true); + }); +}; + +deselect_all = function() { + $(".trait_checkbox").each(function() { + $(this).prop('checked', false); + }); +}; + +change_buttons = function() { + num_checked = $('.trait_checkbox:checked').length; + if (num_checked === 0) { + $("#add").prop("disabled", true); + } else { + $("#add").prop("disabled", false); + } +}; + +add = function() { + var traits; + traits = $("input[name=pca_trait]:checked").map(function() { + return $(this).val(); + }).get(); + + var traits_hash = md5(traits.toString()); + + $.ajax({ + type: "POST", + url: "/collections/store_trait_list", + data: { + hash: traits_hash, + traits: traits.toString() + } + }); + + return $.colorbox({ + href: "/collections/add?hash=" + traits_hash + }); +} + +$("#select_all").click(select_all); +$("#deselect_all").click(deselect_all); +$("#add").click(add); +$(".btn, .trait_checkbox").click(change_buttons); diff --git a/gn2/wqflask/static/new/javascript/create_datatable.js b/gn2/wqflask/static/new/javascript/create_datatable.js new file mode 100644 index 00000000..541dfdf5 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_datatable.js @@ -0,0 +1,117 @@ +create_table = function(tableId="trait_table", tableData = [], columnDefs = [], customSettings = {}) { + + loadDataTable(tableId=tableId, tableData=tableData, customSettings, firstRun=true) + + var widthChange = 0; // For storing the change in width so overall table width can be adjusted by that amount + function loadDataTable(tableId, tableData, customSettings, firstRun=false){ + if (!firstRun){ + columnDefs = setUserColumnsDefWidths(tableId, columnDefs); + } + + tableSettings = { + "drawCallback": function( settings ) { + $('#' + tableId + ' tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected") && event.target.tagName.toLowerCase() !== 'a'){ + $(this).removeClass("selected") + } else if (event.target.tagName.toLowerCase() !== 'a') { + $(this).addClass("selected") + } + change_buttons() + }); + }, + "columns": columnDefs, + "sDom": "iti", + "destroy": true, + "autoWidth": false, + "bSortClasses": false, + "scrollY": "100vh", + "scrollX": "100%", + "scrollCollapse": true, + "scroller": true, + "iDisplayLength": -1, + "initComplete": function (settings) { + // Add JQueryUI resizable functionality to each th in the ScrollHead table + $('#' + tableId + '_wrapper .dataTables_scrollHead thead th').resizable({ + handles: "e", + alsoResize: '#' + tableId + '_wrapper .dataTables_scrollHead table', //Not essential but makes the resizing smoother + resize: function( event, ui ) { + widthChange = ui.size.width - ui.originalSize.width; + }, + stop: function () { + saveColumnSettings(tableId, theTable); + loadDataTable(tableId, tableData, customSettings, firstRun=false); + } + }); + } + } + + if (tableData.length > 0){ + tableSettings["data"] = tableData + } + + // Replace default settings with custom settings or add custom settings if not already set in default settings + $.each(customSettings, function(key, value) { + tableSettings[key] = value + }); + + if (!firstRun){ + $('#' + tableId + '_container').css("width", String($('#' + tableId).width() + widthChange + 17) + "px"); // Change the container width by the change in width of the adjusted column, so the overall table size adjusts properly + + let checkedRows = getCheckedRows(tableId); + theTable = $('#' + tableId).DataTable(tableSettings); + if (checkedRows.length > 0){ + recheckRows(theTable, checkedRows); + } + } else { + theTable = $('#' + tableId).DataTable(tableSettings); + theTable.draw(); + $('#' + tableId + '_container').css("width", String($('#' + tableId).width() + 17) + "px"); + theTable.columns.adjust().draw(); + } + } + + theTable.on( 'order.dt search.dt draw.dt', function () { + theTable.column(1, {search:'applied', order:'applied'}).nodes().each( function (cell, i) { + cell.innerHTML = i+1; + } ); + } ).draw(); + + window.addEventListener('resize', function(){ + theTable.columns.adjust(); + }); + + $('#' + tableId + '_searchbox').on( 'keyup', function () { + theTable.search($(this).val()).draw(); + } ); + + $('.toggle-vis').on('click', function (e) { + e.preventDefault(); + + function toggleColumn(column) { + // Toggle column visibility + column.visible( ! column.visible() ); + if (column.visible()){ + $(this).removeClass("active"); + } else { + $(this).addClass("active"); + } + } + + // Get the column API object + var targetCols = $(this).attr('data-column').split(",") + for (let i = 0; i < targetCols.length; i++){ + var column = theTable.column( targetCols[i] ); + toggleColumn(column); + } + } ); + + $('#redraw').on('click', function (e) { + e.preventDefault(); + trait_table.columns().visible( true ); + $('.toggle-vis.active').removeClass('active'); + }); +} diff --git a/gn2/wqflask/static/new/javascript/create_heatmap.js b/gn2/wqflask/static/new/javascript/create_heatmap.js new file mode 100644 index 00000000..f3ae2a46 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_heatmap.js @@ -0,0 +1,14 @@ +// Generated by CoffeeScript 1.8.0 +var create_heatmap; + +create_heatmap = function() { + var data, h, mychart, w; + h = 500; + w = 1200; + mychart = lodheatmap().height(h).width(w); + data = js_data.json_data; + console.log("data:", data); + return d3.select("div#chart").datum(data).call(mychart); +}; + +create_heatmap(); diff --git a/gn2/wqflask/static/new/javascript/create_lodchart.js b/gn2/wqflask/static/new/javascript/create_lodchart.js new file mode 100644 index 00000000..778eed3a --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_lodchart.js @@ -0,0 +1,50 @@ +//var create_lod_chart; + +create_lod_chart = function() { + var additive, chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; + h = 500; + w = 1200; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + totalw = w + margin.left + margin.right; + if ('additive' in js_data) { + additive = js_data.additive; + } else { + additive = false; + } + console.log("js_data:", js_data); + mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab(js_data.result_score_type + " score").manhattanPlot(js_data.manhattan_plot); + data = js_data.json_data; + d3.select("div#topchart").datum(data).call(mychart); + chrrect = mychart.chrSelect(); + chrrect.on("mouseover", function() { + return d3.select(this).attr("fill", "#E9CFEC"); + }).on("mouseout", function(d, i) { + return d3.select(this).attr("fill", function() { + if (i % 2) { + return "#F1F1F9"; + } + return "#FBFBFF"; + }); + }); + return mychart.markerSelect().on("click", function(d) { + var r; + r = d3.select(this).attr("r"); + return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); + }); +}; + +create_lod_chart() + +/* +$(function() { + return root.create_lod_chart = create_lod_chart; +}); +*/
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/create_manhattan_plot.js b/gn2/wqflask/static/new/javascript/create_manhattan_plot.js new file mode 100644 index 00000000..30af484d --- /dev/null +++ b/gn2/wqflask/static/new/javascript/create_manhattan_plot.js @@ -0,0 +1,68 @@ +// Generated by CoffeeScript 1.8.0 +var create_manhattan_plot; + +create_manhattan_plot = function() { + var chrrect, data, h, halfh, margin, mychart, totalh, totalw, w; + h = 500; + w = 1200; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + halfh = h + margin.top + margin.bottom; + totalh = halfh * 2; + totalw = w + margin.left + margin.right; + console.log("js_data:", js_data); + mychart = lodchart().lodvarname("lod.hk").height(h).width(w).margin(margin).ylab("LOD score").manhattanPlot(js_data.manhattan_plot); + data = js_data.json_data; + d3.select("div#topchart").datum(data).call(mychart); + chrrect = mychart.chrSelect(); + chrrect.on("mouseover", function() { + return d3.select(this).attr("fill", "#E9CFEC"); + }).on("mouseout", function(d, i) { + return d3.select(this).attr("fill", function() { + if (i % 2) { + return "#F1F1F9"; + } + return "#FBFBFF"; + }); + }); + return mychart.markerSelect().on("click", function(d) { + var r; + r = d3.select(this).attr("r"); + return d3.select(this).transition().duration(500).attr("r", r * 3).transition().duration(500).attr("r", r); + }); +}; + +create_manhattan_plot(); + +$("#export").click((function(_this) { + return function() { + var filename, form, svg, svg_xml; + svg = $("#topchart").find("svg")[0]; + svg_xml = (new XMLSerializer).serializeToString(svg); + console.log("svg_xml:", svg_xml); + filename = "manhattan_plot_" + js_data.this_trait; + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }; +})(this)); + +$("#export_pdf").click((function(_this) { + return function() { + var filename, form, svg, svg_xml; + svg = $("#topchart").find("svg")[0]; + svg_xml = (new XMLSerializer).serializeToString(svg); + console.log("svg_xml:", svg_xml); + filename = "manhattan_plot_" + js_data.this_trait; + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }; +})(this)); diff --git a/gn2/wqflask/static/new/javascript/ctl_graph.js b/gn2/wqflask/static/new/javascript/ctl_graph.js new file mode 100644 index 00000000..bd950592 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/ctl_graph.js @@ -0,0 +1,193 @@ +window.onload=function() { + // id of Cytoscape Web container div + //var div_id = "cytoscapeweb"; + + var cy = cytoscape({ + container: $('#cytoscapeweb'), // container to render in + + elements: elements_list, + + style: [ // the stylesheet for the graph + { + selector: 'node', + style: { + 'background-color': '#666', + 'label': 'data(symbol)', + 'font-size': 10 + } + }, + + { + selector: 'edge', + style: { + 'width': 'data(width)', + 'line-color': 'data(color)', + 'target-arrow-color': '#ccc', + 'target-arrow-shape': 'none', + 'font-size': 8, + 'curve-style': 'bezier' + } + } + ], + + zoom: 12, + layout: { name: 'circle', + fit: true, // whether to fit the viewport to the graph + padding: 30 // the padding on fit + //idealEdgeLength: function( edge ){ return edge.data['correlation']*10; }, + }, + + + zoomingEnabled: true, + userZoomingEnabled: true, + panningEnabled: true, + userPanningEnabled: true, + boxSelectionEnabled: false, + selectionType: 'single', + + // rendering options: + styleEnabled: true + }); + + var eles = cy.$() // var containing all elements, so elements can be restored after being removed + + var defaults = { + zoomFactor: 0.05, // zoom factor per zoom tick + zoomDelay: 45, // how many ms between zoom ticks + minZoom: 0.1, // min zoom level + maxZoom: 10, // max zoom level + fitPadding: 30, // padding when fitting + panSpeed: 10, // how many ms in between pan ticks + panDistance: 10, // max pan distance per tick + panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction) + panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed) + panInactiveArea: 8, // radius of inactive area in pan drag box + panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0 + zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution) + fitSelector: undefined, // selector of elements to fit + animateOnFit: function(){ // whether to animate on fit + return false; + }, + fitAnimationDuration: 1000, // duration of animation on fit + + // icon class names + sliderHandleIcon: 'fa fa-minus', + zoomInIcon: 'fa fa-plus', + zoomOutIcon: 'fa fa-minus', + resetIcon: 'fa fa-expand' + }; + + cy.panzoom( defaults ); + + function create_qtips(cy){ + cy.nodes().qtip({ + content: function(){ + gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().sid + '&dataset=' + this.data().dataset + '" >'+this.data().id +'</a>'+'</b><br>' + ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>' + omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>' + qtip_content = gn_link + ncbi_link + omim_link + return qtip_content + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + + cy.edges().qtip({ + content: function(){ + edge_ID = '<b>Edge: ' + this.data().id + '</b><br>' + lod_score = 'LOD: ' + this.data().lod + '<br>' + return edge_ID + lod_score + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + } + + create_qtips(cy) + + $('#slide').change(function() { + eles.restore() + + console.log(eles) + + // nodes_to_restore = eles.filter("node[max_corr >= " + $(this).val() + "], edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]") + // nodes_to_restore.restore() + + // edges_to_restore = eles.filter("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]") + // edges_to_restore.restore() + + //cy.$("node[max_corr >= " + $(this).val() + "]").restore(); + //cy.$("edge[correlation >= " + $(this).val() + "][correlation <= -" + $(this).val() + "]").restore(); + + cy.$("node[max_corr < " + $(this).val() + "]").remove(); + cy.$("edge[correlation < " + $(this).val() + "][correlation > -" + $(this).val() + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + + }); + + $('#reset_graph').click(function() { + eles.restore() + $('#slide').val(0) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + + $('select[name=focus_select]').change(function() { + focus_trait = $(this).val() + + eles.restore() + cy.$('edge[source != "' + focus_trait + '"][target != "' + focus_trait + '"]').remove() + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + + $('select[name=layout_select]').change(function() { + layout_type = $(this).val() + console.log("LAYOUT:", layout_type) + cy.layout({ name: layout_type, + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }); + }); + + $("a#image_link").click(function(e) { + var pngData = cy.png(); + + $(this).attr('href', pngData); + $(this).attr('download', 'network_graph.png'); + + console.log("TESTING:", image_link) + + }); + + +}; + + diff --git a/gn2/wqflask/static/new/javascript/curvechart.js b/gn2/wqflask/static/new/javascript/curvechart.js new file mode 100644 index 00000000..48bf6bf3 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/curvechart.js @@ -0,0 +1,353 @@ +// Generated by CoffeeScript 1.8.0 +var curvechart; + +curvechart = function() { + var axispos, chart, commonX, curvesSelect, height, margin, nxticks, nyticks, rectcolor, rotate_ylab, strokecolor, strokecolorhilit, strokewidth, strokewidthhilit, title, titlepos, width, xlab, xlim, xscale, xticks, ylab, ylim, yscale, yticks; + width = 800; + height = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + xlim = null; + ylim = null; + nxticks = 5; + xticks = null; + nyticks = 5; + yticks = null; + rectcolor = "#e6e6e6"; + strokecolor = null; + strokecolorhilit = null; + strokewidth = 2; + strokewidthhilit = 2; + title = ""; + xlab = "X"; + ylab = "Y"; + rotate_ylab = null; + yscale = d3.scale.linear(); + xscale = d3.scale.linear(); + curvesSelect = null; + commonX = true; + chart = function(selection) { + return selection.each(function(data) { + var curve, curves, g, gEnter, group, i, indID, indtip, j, lastpoint, ngroup, points, pointsg, svg, titlegrp, tmp, v, xaxis, xrange, xs, yaxis, yrange, ys, _i, _j, _len, _ref, _ref1, _ref2, _ref3, _results; + indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null; + indID = indID != null ? indID : (function() { + _results = []; + for (var _i = 1, _ref1 = data.data.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); } + return _results; + }).apply(this); + group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() { + var _results1; + _results1 = []; + for (i in data.data) { + _results1.push(1); + } + return _results1; + })(); + ngroup = d3.max(group); + group = (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = group.length; _j < _len; _j++) { + g = group[_j]; + _results1.push(g - 1); + } + return _results1; + })(); + strokecolor = strokecolor != null ? strokecolor : selectGroupColors(ngroup, "pastel"); + strokecolor = expand2vector(strokecolor, ngroup); + strokecolorhilit = strokecolorhilit != null ? strokecolorhilit : selectGroupColors(ngroup, "dark"); + strokecolorhilit = expand2vector(strokecolorhilit, ngroup); + if (commonX) { + data = (function() { + var _results1; + _results1 = []; + for (i in data.data) { + _results1.push({ + x: data.x, + y: data.data[i] + }); + } + return _results1; + })(); + } else { + data = data.data; + } + xlim = xlim != null ? xlim : d3.extent(pullVarAsArray(data, "x")); + ylim = ylim != null ? ylim : d3.extent(pullVarAsArray(data, "y")); + for (i in data) { + tmp = data[i]; + data[i] = []; + for (j in tmp.x) { + if (!((tmp.x[j] == null) || (tmp.y[j] == null))) { + data[i].push({ + x: tmp.x[j], + y: tmp.y[j] + }); + } + } + } + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", rectcolor).attr("stroke", "none"); + xrange = [margin.left + margin.inner, margin.left + width - margin.inner]; + yrange = [margin.top + height - margin.inner, margin.top + margin.inner]; + xscale.domain(xlim).range(xrange); + yscale.domain(ylim).range(yrange); + xs = d3.scale.linear().domain(xlim).range(xrange); + ys = d3.scale.linear().domain(ylim).range(yrange); + yticks = yticks != null ? yticks : ys.ticks(nyticks); + xticks = xticks != null ? xticks : xs.ticks(nxticks); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) { + return xscale(d); + }).attr("x2", function(d) { + return xscale(d); + }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) { + return xscale(d); + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return formatAxis(xticks)(d); + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab); + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + indtip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return indID[d]; + }).direction('e').offset([0, 10]); + svg.call(indtip); + curve = d3.svg.line().x(function(d) { + return xscale(d.x); + }).y(function(d) { + return yscale(d.y); + }); + curves = g.append("g").attr("id", "curves"); + curvesSelect = curves.selectAll("empty").data(d3.range(data.length)).enter().append("path").datum(function(d) { + return data[d]; + }).attr("d", curve).attr("class", function(d, i) { + return "path" + i; + }).attr("fill", "none").attr("stroke", function(d, i) { + return strokecolor[group[i]]; + }).attr("stroke-width", strokewidth).on("mouseover.panel", function(d, i) { + var circle; + d3.select(this).attr("stroke", strokecolorhilit[group[i]]).moveToFront(); + circle = d3.select("circle#hiddenpoint" + i); + return indtip.show(i, circle.node()); + }).on("mouseout.panel", function(d, i) { + d3.select(this).attr("stroke", strokecolor[group[i]]).moveToBack(); + return indtip.hide(); + }); + lastpoint = (function() { + var _results1; + _results1 = []; + for (i in data) { + _results1.push({ + x: null, + y: null + }); + } + return _results1; + })(); + for (i in data) { + _ref3 = data[i]; + for (_j = 0, _len = _ref3.length; _j < _len; _j++) { + v = _ref3[_j]; + if ((v.x != null) && (v.y != null)) { + lastpoint[i] = v; + } + } + } + pointsg = g.append("g").attr("id", "invisiblepoints"); + points = pointsg.selectAll("empty").data(lastpoint).enter().append("circle").attr("id", function(d, i) { + return "hiddenpoint" + i; + }).attr("cx", function(d) { + return xscale(d.x); + }).attr("cy", function(d) { + return yscale(d.y); + }).attr("r", 1).attr("opacity", 0); + return g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.xlim = function(value) { + if (!arguments.length) { + return xlim; + } + xlim = value; + return chart; + }; + chart.nxticks = function(value) { + if (!arguments.length) { + return nxticks; + } + nxticks = value; + return chart; + }; + chart.xticks = function(value) { + if (!arguments.length) { + return xticks; + } + xticks = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.strokecolor = function(value) { + if (!arguments.length) { + return strokecolor; + } + strokecolor = value; + return chart; + }; + chart.strokecolorhilit = function(value) { + if (!arguments.length) { + return strokecolorhilit; + } + strokecolorhilit = value; + return chart; + }; + chart.strokewidth = function(value) { + if (!arguments.length) { + return strokewidth; + } + strokewidth = value; + return chart; + }; + chart.strokewidthhilit = function(value) { + if (!arguments.length) { + return strokewidthhilit; + } + strokewidthhilit = value; + return chart; + }; + chart.commonX = function(value) { + if (!arguments.length) { + return commonX; + } + commonX = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.xscale = function() { + return xscale; + }; + chart.curvesSelect = function() { + return curvesSelect; + }; + return chart; +}; diff --git a/gn2/wqflask/static/new/javascript/d3panels.min.js b/gn2/wqflask/static/new/javascript/d3panels.min.js new file mode 100644 index 00000000..dfc10643 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/d3panels.min.js @@ -0,0 +1 @@ +!function(){var d3panels={version:"1.7.1"};"use strict";d3panels.formatAxis=function(d){var extra_digits=arguments.length>1&&arguments[1]!==undefined?arguments[1]:0;var gap,ndig;if(d[0]!=null){gap=d[1]-d[0]}else if(d.length>2){gap=d[2]-d[1]}else{gap=d[1]}ndig=Math.floor(d3panels.log10(Math.abs(gap)));if(ndig>0){ndig=0}ndig=Math.abs(ndig)+extra_digits;return function(val){if(val!=null&&val!=="NA"){return d3.format("."+ndig+"f")(val)}return"NA"}};d3panels.unique=function(x){var k,len,output,v;output={};for(k=0,len=x.length;k<len;k++){v=x[k];if(v!=null){output[v]=v}}output=function(){var results;results=[];for(v in output){results.push(output[v])}return results}();return d3panels.forceAsArray(output)};d3panels.pullVarAsArray=function(data,variable){var i,results;results=[];for(i in data){results.push(data[i][variable])}return results};d3panels.reorgByChr=function(uniquechr,chr,vector){var c,i,k,len,result;if(chr.length!==vector.length){d3panels.displayError("reorgByChr: chr.length ("+chr.length+") != vector.length ("+vector.length+")")}result={};for(i=k=0,len=uniquechr.length;k<len;i=++k){c=uniquechr[i];result[c]=function(){var results;results=[];for(i in vector){if(chr[i]===c){results.push(vector[i])}}return results}()}return result};d3panels.reorgLodData=function(data){var i;data.posByChr=d3panels.reorgByChr(data.chrname,data.chr,data.pos);data.lodByChr=d3panels.reorgByChr(data.chrname,data.chr,data.lod);if(data.poslabel!=null){data.poslabelByChr=d3panels.reorgByChr(data.chrname,data.chr,data.poslabel)}if(data.marker!=null){data.markerinfo=function(){var results;results=[];for(i in data.marker){if(data.marker[i]!==""){results.push({name:data.marker[i],chr:data.chr[i],pos:data.pos[i],lod:data.lod[i]})}}return results}()}return data};d3panels.calc_chrscales=function(plot_width,left_margin,gap,chr,start,end){var reverse=arguments.length>6&&arguments[6]!==undefined?arguments[6]:false;var chr_end_pixels,chr_length,chr_start_pixels,domain,i,k,n_chr,range,ref,right,tot_chr_length,tot_pixels,xscale;n_chr=chr.length;chr_length=function(){var results;results=[];for(i in end){results.push(end[i]-start[i])}return results}();tot_chr_length=chr_length.reduce(function(t,s){return t+s});tot_pixels=plot_width-gap*n_chr;chr_start_pixels=[left_margin+gap/2];chr_end_pixels=[left_margin+gap/2+tot_pixels/tot_chr_length*chr_length[0]];for(i=k=1,ref=n_chr-1;1<=ref?k<=ref:k>=ref;i=1<=ref?++k:--k){chr_start_pixels.push(chr_end_pixels[i-1]+gap);chr_end_pixels.push(chr_start_pixels[i]+tot_pixels/tot_chr_length*chr_length[i])}right=plot_width+left_margin*2;xscale={};for(i in chr){domain=[start[i],end[i]];range=[chr_start_pixels[i],chr_end_pixels[i]];if(reverse){domain.reverse();range=[right-range[1],right-range[0]]}xscale[chr[i]]=d3.scaleLinear().domain(domain).range(range)}return xscale};d3panels.selectGroupColors=function(ngroup,palette){var cat20,pastel1,pastel20,set1;if(ngroup===0){return[]}set1=["#e41a1c","#377eb8","#4daf4a","#984ea3","#ff7f00","#ffff33","#a65628","#f781bf","#999999"];pastel1=["#fbb4ae","#b3cde3","#ccebc5","#decbe4","#fed9a6","#ffffcc","#e5d8bd","#fddaec","#f2f2f2"];cat20=["#1f77b4","#aec7e8","#ff7f0e","#ffbb78","#2ca02c","#98df8a","#d62728","#ff9896","#9467bd","#c5b0d5","#8c564b","#c49c94","#e377c2","#f7b6d2","#7f7f7f","#c7c7c7","#bcbd22","#dbdb8d","#17becf","#9edae5"];pastel20=["#8fc7f4","#fed7f8","#ffbf8e","#fffbb8","#8ce08c","#d8ffca","#f68788","#ffd8d6","#d4a7fd","#f5f0f5","#cc968b","#f4dcd4","#f3b7f2","#f7f6f2","#bfbfbf","#f7f7f7","#fcfd82","#fbfbcd","#87feff","#defaf5"];if(palette==="dark"){if(ngroup===1){return["slateblue"]}if(ngroup===2){return["MediumVioletRed","slateblue"]}if(ngroup===3){return["MediumVioletRed","MediumSeaGreen","slateblue"]}if(ngroup<=9){return set1.slice(0,ngroup)}return cat20.slice(0,ngroup)}else{if(ngroup===1){return["#bebebe"]}if(ngroup===2){return["lightpink","lightblue"]}if(ngroup<=9){return pastel1.slice(0,ngroup)}return pastel20.slice(0,ngroup)}};d3panels.expand2vector=function(input,n){var i;if(input==null){return input}if(Array.isArray(input)&&input.length>=n){return input}if(!Array.isArray(input)){input=[input]}if(input.length>1&&n>1){input=function(){var results;results=[];for(i in d3.range(n)){results.push(input[i%input.length])}return results}()}if(input.length===1&&n>1){input=function(){var results;results=[];for(i in d3.range(n)){results.push(input[0])}return results}()}return input};d3panels.median=function(x){var n,xv;if(x==null){return null}x=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];if(xv!=null){results.push(xv)}}return results}();n=x.length;if(!(n>0)){return null}x.sort(function(a,b){return a-b});if(n%2===1){return x[(n-1)/2]}return(x[n/2]+x[n/2-1])/2};d3panels.pad_vector=function(x){var pad=arguments.length>1&&arguments[1]!==undefined?arguments[1]:null;if(pad==null){return[x[0]-(x[1]-x[0])].concat(x).concat([x[x.length-1]+(x[x.length-1]-x[x.length-2])])}return[x[0]-pad].concat(x).concat(x[x.length-1]+pad)};d3panels.calc_midpoints=function(x){var i,k,ref,results;results=[];for(i=k=0,ref=x.length-2;0<=ref?k<=ref:k>=ref;i=0<=ref?++k:--k){results.push((x[i]+x[i+1])/2)}return results};d3panels.calc_cell_rect=function(cells,xmid,ymid){var bottom,cell,k,left,len,results,right,top;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];left=xmid[cell.xindex];right=xmid[1+cell.xindex];top=ymid[cell.yindex];bottom=ymid[1+cell.yindex];cell.left=d3.min([left,right]);cell.width=Math.abs(right-left);cell.top=d3.min([top,bottom]);results.push(cell.height=Math.abs(bottom-top))}return results};d3panels.calc_chrcell_rect=function(cells,xmid,ymid){var bottom,cell,k,left,len,results,right,top;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];left=xmid[cell.chr][cell.posindex];right=xmid[cell.chr][1+cell.posindex];top=ymid[cell.lodindex];bottom=ymid[1+cell.lodindex];cell.left=d3.min([left,right]);cell.width=Math.abs(right-left);cell.top=d3.min([top,bottom]);results.push(cell.height=Math.abs(bottom-top))}return results};d3panels.calc_2dchrcell_rect=function(cells,xmid,ymid){var bottom,cell,k,left,len,results,right,top;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];left=xmid[cell.chrx][cell.xindexByChr];right=xmid[cell.chrx][1+cell.xindexByChr];top=ymid[cell.chry][cell.yindexByChr];bottom=ymid[cell.chry][1+cell.yindexByChr];cell.left=d3.min([left,right]);cell.width=Math.abs(right-left);cell.top=d3.min([top,bottom]);results.push(cell.height=Math.abs(bottom-top))}return results};d3panels.maxdiff=function(x){var d,i,k,ref,result;if(x.length<2){return null}result=x[1]-x[0];if(x.length<3){return result}for(i=k=2,ref=x.length;2<=ref?k<ref:k>ref;i=2<=ref?++k:--k){d=x[i]-x[i-1];if(d>result){result=d}}return result};d3panels.matrixMin=function(mat){var i,j,result;result=mat[0][0];for(i in mat){for(j in mat[i]){if(!(result!=null)||result>mat[i][j]&&mat[i][j]!=null){result=mat[i][j]}}}return result};d3panels.matrixMax=function(mat){var i,j,result;result=mat[0][0];for(i in mat){for(j in mat[i]){if(!(result!=null)||result<mat[i][j]&&mat[i][j]!=null){result=mat[i][j]}}}return result};d3panels.matrixMaxAbs=function(mat){var i,j,result;result=Math.abs(mat[0][0]);for(i in mat){for(j in mat[i]){if(!(result!=null)||result<Math.abs(mat[i][j])&&mat[i][j]!=null){result=Math.abs(mat[i][j])}}}return result};d3panels.matrixExtent=function(mat){return[d3panels.matrixMin(mat),d3panels.matrixMax(mat)]};d3panels.forceAsArray=function(x){if(x==null){return x}if(Array.isArray(x)){return x}return[x]};d3panels.missing2null=function(vec){var missingvalues=arguments.length>1&&arguments[1]!==undefined?arguments[1]:["NA",""];return vec.map(function(value){if(missingvalues.indexOf(value)>-1){return null}else{return value}})};d3panels.displayError=function(message){var divid=arguments.length>1&&arguments[1]!==undefined?arguments[1]:null;var div;div="div.error";if(divid!=null){div+="#"+divid}if(d3.select(div).empty()){d3.select("body").insert("div",":first-child").attr("class","error")}return d3.select(div).append("p").text(message)};d3panels.sumArray=function(vec){var x;vec=function(){var k,len,results;results=[];for(k=0,len=vec.length;k<len;k++){x=vec[k];if(x!=null){results.push(x)}}return results}();if(!(vec.length>0)){return null}return vec.reduce(function(a,b){return a*1+b*1})};d3panels.calc_crosstab=function(data){var col,cs,i,k,l,ncol,nrow,ref,ref1,result,row,rs;nrow=data.ycat.length;ncol=data.xcat.length;result=function(){var k,ref,results;results=[];for(row=k=0,ref=nrow;0<=ref?k<=ref:k>=ref;row=0<=ref?++k:--k){results.push(function(){var l,ref1,results1;results1=[];for(col=l=0,ref1=ncol;0<=ref1?l<=ref1:l>=ref1;col=0<=ref1?++l:--l){results1.push(0)}return results1}())}return results}();for(i in data.x){result[data.y[i]][data.x[i]]+=1}rs=d3panels.rowSums(result);cs=d3panels.colSums(result);for(i=k=0,ref=ncol;0<=ref?k<ref:k>ref;i=0<=ref?++k:--k){result[nrow][i]=cs[i]}for(i=l=0,ref1=nrow;0<=ref1?l<ref1:l>ref1;i=0<=ref1?++l:--l){result[i][ncol]=rs[i]}result[nrow][ncol]=d3panels.sumArray(rs);return result};d3panels.rowSums=function(mat){var k,len,results,x;results=[];for(k=0,len=mat.length;k<len;k++){x=mat[k];results.push(d3panels.sumArray(x))}return results};d3panels.transpose=function(mat){var i,j,k,ref,results;results=[];for(j=k=0,ref=mat[0].length;0<=ref?k<ref:k>ref;j=0<=ref?++k:--k){results.push(function(){var l,ref1,results1;results1=[];for(i=l=0,ref1=mat.length;0<=ref1?l<ref1:l>ref1;i=0<=ref1?++l:--l){results1.push(mat[i][j])}return results1}())}return results};d3panels.colSums=function(mat){return d3panels.rowSums(d3panels.transpose(mat))};d3panels.log2=function(x){if(x==null){return x}return Math.log(x)/Math.log(2)};d3panels.log10=function(x){if(x==null){return x}return Math.log(x)/Math.log(10)};d3panels.abs=function(x){if(x==null){return x}return Math.abs(x)};d3panels.mean_by_group=function(g,y){var i,means,n;means={};n={};for(i in g){if(n[g[i]]!=null){if(y[i]!=null){means[g[i]]+=y[i]}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){means[g[i]]=y[i]}if(y[i]!=null){n[g[i]]=1}}}for(i in means){means[i]/=n[i]}return means};d3panels.sd_by_group=function(g,y){var dev,i,means,n,sds;means=d3panels.mean_by_group(g,y);sds={};n={};for(i in g){dev=y[i]-means[g[i]];if(n[g[i]]!=null){if(y[i]!=null){sds[g[i]]+=dev*dev}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){sds[g[i]]=dev*dev}if(y[i]!=null){n[g[i]]=1}}}for(i in sds){sds[i]=n[i]<2?null:Math.sqrt(sds[i]/(n[i]-1))}return sds};d3panels.count_groups=function(g,y){var i,n;n={};for(i in g){if(n[g[i]]!=null){if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){n[g[i]]=1}}}return n};d3panels.ci_by_group=function(g,y){var m=arguments.length>2&&arguments[2]!==undefined?arguments[2]:2;var ci,dev,i,means,n,sds;means=d3panels.mean_by_group(g,y);sds={};n={};for(i in g){dev=y[i]-means[g[i]];if(n[g[i]]!=null){if(y[i]!=null){sds[g[i]]+=dev*dev}if(y[i]!=null){n[g[i]]+=1}}else{if(y[i]!=null){sds[g[i]]=dev*dev}if(y[i]!=null){n[g[i]]=1}}}for(i in sds){sds[i]=n[i]<2?null:Math.sqrt(sds[i]/(n[i]-1))}ci={};for(i in means){ci[i]={mean:means[i],low:n[i]>0?means[i]-m*sds[i]/Math.sqrt(n[i]):means[i],high:n[i]>0?means[i]+m*sds[i]/Math.sqrt(n[i]):means[i]}}return ci};d3panels.pad_ylim=function(ylim){var p=arguments.length>1&&arguments[1]!==undefined?arguments[1]:.025;var d;d=ylim[1]-ylim[0];return[ylim[0]-d*p,ylim[1]+d*p]};d3panels.add_chrname_start_end=function(data){var c,i,k,l,len,len1,ref,ref1,these_pos;if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(data.chrstart==null){data.chrstart=[];ref=data.chrname;for(k=0,len=ref.length;k<len;k++){c=ref[k];these_pos=function(){var results;results=[];for(i in data.chr){if(data.chr[i]===c){results.push(data.pos[i])}}return results}();data.chrstart.push(d3.min(these_pos))}}if(data.chrend==null){data.chrend=[];ref1=data.chrname;for(l=0,len1=ref1.length;l<len1;l++){c=ref1[l];these_pos=function(){var results;results=[];for(i in data.chr){if(data.chr[i]===c){results.push(data.pos[i])}}return results}();data.chrend.push(d3.max(these_pos))}}data.start=d3panels.forceAsArray(data.start);data.end=d3panels.forceAsArray(data.end);return data};d3panels.calc_breaks=function(number,low,high){var d,i,results;if(low>=high){d3panels.displayError("calc_breaks: should have low < high");if(low>high){var _ref=[high,low];low=_ref[0];high=_ref[1]}if(low===high){low-=.5;high+=.5}}if(number<2){d3panels.displayError("calc_breaks: number should be >= 2");number=2}d=(high-low)/(number-1);results=[];for(i in d3.range(number)){results.push(low+d*i)}return results};d3panels.calc_freq=function(values,breaks){var return_counts=arguments.length>2&&arguments[2]!==undefined?arguments[2]:false;var br,i,k,len,n,ref,result,v,z;v=values.slice(0);v.sort(function(a,b){return+a-b});br=breaks.slice(0);br.sort(function(a,b){return+a-b});br[0]-=1e-6;br[br.length-1]+=1e-6;result=function(){var k,len,ref,results;ref=d3.range(br.length-1);results=[];for(k=0,len=ref.length;k<len;k++){i=ref[k];results.push(0)}return results}();n=v.length;v=function(){var k,len,results;results=[];for(k=0,len=v.length;k<len;k++){z=v[k];if(z>br[0]&&z<br[br.length-1]){results.push(z)}}return results}();if(v.length<n){d3panels.displayError("calc_freq: values out of range of breaks")}n=v.length;ref=d3.range(br.length-1);for(k=0,len=ref.length;k<len;k++){i=ref[k];result[i]=function(){var l,len1,results;results=[];for(l=0,len1=v.length;l<len1;l++){z=v[l];if(z>=br[i]&&z<br[i+1]){results.push(z)}}return results}().length;if(!return_counts){result[i]/=n*(br[i+1]-br[i])}}return result};d3panels.calc_hist_path=function(freq,breaks){var i,result;if(freq.length!==breaks.length-1){d3panels.displayError("freq.length ("+freq.length+") should be breaks.length - 1 ("+(breaks.length-1)+")")}result=[{x:breaks[0],y:0}];for(i in freq){result.push({x:breaks[i],y:freq[i]});result.push({x:breaks[+i+1],y:freq[i]})}result.push({x:breaks[breaks.length-1],y:0});return result};d3panels.index_of_nearest=function(d,vec){var abs_diff;abs_diff=vec.map(function(val){return Math.abs(val-d)});return abs_diff.indexOf(d3.min(abs_diff))};d3panels.check_listarg_v_default=function(arg,defaults){var key;for(key in defaults){if(arg[key]==null){arg[key]=defaults[key]}}return arg};d3panels.object_position=function(object){var obj,x,y;obj=object.node().getBoundingClientRect();x=obj.left/2+obj.right/2;y=obj.top/2+obj.bottom/2;return{x:x,y:y}};"use strict";d3panels.lod2dheatmap=function(chartOpts){var cellSelect,cells,celltip,chart,chrGap,colors,equalCells,height,hilitcolor,margin,nullcolor,oneAtTop,ref,ref1,ref10,ref11,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,width,xscale,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:800;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:60};chrGap=(ref3=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref3:6;equalCells=(ref4=chartOpts!=null?chartOpts.equalCells:void 0)!=null?ref4:false;oneAtTop=(ref5=chartOpts!=null?chartOpts.oneAtTop:void 0)!=null?ref5:false;colors=(ref6=chartOpts!=null?chartOpts.colors:void 0)!=null?ref6:["slateblue","white","crimson"];nullcolor=(ref7=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref7:"#e6e6e6";zlim=(ref8=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref8:null;zthresh=(ref9=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref9:null;hilitcolor=(ref10=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref10:"black";tipclass=(ref11=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref11:"tooltip";xscale=null;yscale=null;zscale=null;celltip=null;cells=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cellg,chr,i,indexWithinChr,j,k,l,len,len1,len2,m,myframe,n_pos,posByChr,ref12,ref13,ref14,tooltipfunc,x,xmid_scaled,y,ymid_scaled,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});if(data.chr==null){d3panels.displayError("lod2dheatmap: data.chr is missing")}if(data.pos==null){d3panels.displayError("lod2dheatmap: data.pos is missing")}if(data.lod==null){d3panels.displayError("lod2dheatmap: data.lod is missing")}n_pos=data.chr.length;if(data.pos.length!==n_pos){d3panels.displayError("lod2dheatmap: data.pos.length ("+data.pos.length+") != data.chr.length ("+n_pos+")")}if(data.lod.length!==n_pos){d3panels.displayError("lod2dheatmap: data.lod.length ("+data.lod.length+") != data.chr.length ("+n_pos+")")}for(i in data.lod){if(data.lod[i].length!==n_pos){d3panels.displayError("lod2dheatmap: data.lod["+i+"].length ("+data.lod[i].length+") != data.chr.length ("+n_pos+")")}}if(data.poslabel!=null){if(data.poslabel.length!==n_pos){d3panels.displayError("lod2dheatmap: data.poslabel.length ("+data.poslabel.length+") != data.chr.length ("+n_pos+")")}}else{data.poslabel=function(){var results;results=[];for(i in data.chr){results.push(data.chr[i]+"@"+d3panels.formatAxis(data.pos)(data.pos[i]))}return results}()}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(equalCells){data.pos=[];ref12=data.chrname;for(k=0,len=ref12.length;k<len;k++){chr=ref12[k];data.pos=data.pos.concat(function(){var results;results=[];for(i in data.chr){if(data.chr[i]===chr){results.push(+i)}}return results}())}}data=d3panels.add_chrname_start_end(data);if(equalCells){chrGap=(width-margin.left-margin.right-2*data.chrname.length)/data.chr.length+2}chartOpts.chrGap=chrGap;chartOpts.width=width;chartOpts.height=height;chartOpts.margin=margin;myframe=d3panels.chr2dpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();posByChr=d3panels.reorgByChr(data.chrname,data.chr,data.pos);xmid_scaled={};ymid_scaled={};ref13=data.chrname;for(l=0,len1=ref13.length;l<len1;l++){chr=ref13[l];xmid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref14,results;ref14=posByChr[chr];results=[];for(m=0,len2=ref14.length;m<len2;m++){x=ref14[m];results.push(xscale[chr](x))}return results}(),chrGap-2));ymid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref14,results;ref14=posByChr[chr];results=[];for(m=0,len2=ref14.length;m<len2;m++){y=ref14[m];results.push(yscale[chr](y))}return results}(),oneAtTop?chrGap-2:2-chrGap))}zmin=d3panels.matrixMin(data.lod);zmax=d3panels.matrixMaxAbs(data.lod);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("lod2dheatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;indexWithinChr=[];ref14=data.chrname;for(m=0,len2=ref14.length;m<len2;m++){chr=ref14[m];indexWithinChr=indexWithinChr.concat(function(){var results;results=[];for(i in posByChr[chr]){results.push(+i)}return results}())}cells=[];for(i in data.chr){for(j in data.chr){if(Math.abs(data.lod[i][j])>=zthresh){cells.push({lod:data.lod[i][j],chrx:data.chr[i],chry:data.chr[j],poslabelx:data.poslabel[i],poslabely:data.poslabel[j],xindex:i,yindex:j,xindexByChr:indexWithinChr[i],yindexByChr:indexWithinChr[j]})}}}d3panels.calc_2dchrcell_rect(cells,xmid_scaled,ymid_scaled);cellg=svg.append("g").attr("id","cells");cellSelect=cellg.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return d.left}).attr("y",function(d){return d.top}).attr("width",function(d){return d.width}).attr("height",function(d){return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.lod!=null){return zscale(d.lod)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").on("mouseover",function(d){return d3.select(this).attr("stroke",hilitcolor).raise()}).on("mouseout",function(){return d3.select(this).attr("stroke","none")});tooltipfunc=function tooltipfunc(d){var z;z=d3.format(".2f")(Math.abs(d.lod));return"("+d.poslabelx+","+d.poslabely+") → "+z};return celltip=d3panels.tooltip_create(d3.select("body"),cellg.selectAll("rect"),{tipclass:tipclass},tooltipfunc)};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return zscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.panelframe=function(chartOpts){var axispos,box,boxcolor,boxwidth,chart,height,margin,nxticks,nyticks,plot_height,plot_width,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,ref18,ref19,ref2,ref20,ref21,ref22,ref23,ref24,ref25,ref26,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,v_over_h,width,xNA,xNA_size,xlab,xlabels,xlim,xlineOpts,xlines,xscale,xscale_wnull,xticklab,xticks,yNA,yNA_size,ylab,ylabels,ylim,ylineOpts,ylines,yscale,yscale_wnull,yticklab,yticks;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40,inner:3};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:"X";ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"Y";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;xNA=(ref9=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref9:false;yNA=(ref10=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref10:false;xNA_size=(ref11=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref11:{width:20,gap:10};yNA_size=(ref12=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref12:{width:20,gap:10};xlim=(ref13=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref13:[0,1];ylim=(ref14=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref14:[0,1];nxticks=(ref15=chartOpts!=null?chartOpts.nxticks:void 0)!=null?ref15:5;xticks=(ref16=chartOpts!=null?chartOpts.xticks:void 0)!=null?ref16:null;xticklab=(ref17=chartOpts!=null?chartOpts.xticklab:void 0)!=null?ref17:null;nyticks=(ref18=chartOpts!=null?chartOpts.nyticks:void 0)!=null?ref18:5;yticks=(ref19=chartOpts!=null?chartOpts.yticks:void 0)!=null?ref19:null;yticklab=(ref20=chartOpts!=null?chartOpts.yticklab:void 0)!=null?ref20:null;rectcolor=(ref21=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref21:"#e6e6e6";boxcolor=(ref22=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref22:"black";boxwidth=(ref23=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref23:2;xlineOpts=(ref24=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref24:{color:"white",width:2};ylineOpts=(ref25=chartOpts!=null?chartOpts.ylineOpts:void 0)!=null?ref25:{color:"white",width:2};v_over_h=(ref26=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref26:false;xscale=null;yscale=null;xNA=xNA;yNA=yNA;xlines=null;ylines=null;xlabels=null;ylabels=null;plot_width=null;plot_height=null;box=null;svg=null;xscale_wnull=null;yscale_wnull=null;chart=function chart(selection){var boxes,boxes2include,d,g,i,inner_height,inner_width,xNA_xpos,xaxis,xrange,yNA_ypos,yaxis,ylabpos_x,ylabpos_y,yrange;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40,inner:3});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});xNA_size=d3panels.check_listarg_v_default(xNA_size,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA_size,{width:20,gap:10});xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"white",width:2});ylineOpts=d3panels.check_listarg_v_default(ylineOpts,{color:"white",width:2});svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");if(!xNA){xNA_size={width:0,gap:0}}if(!yNA){yNA_size={width:0,gap:0}}plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);inner_width=width-(margin.right+margin.left+xNA_size.width+xNA_size.gap);inner_height=height-(margin.top+margin.bottom+yNA_size.width+yNA_size.gap);boxes={left:[margin.left+xNA_size.width+xNA_size.gap,margin.left,margin.left,margin.left+xNA_size.width+xNA_size.gap],width:[inner_width,xNA_size.width,xNA_size.width,inner_width],top:[margin.top,margin.top,height-(margin.bottom+yNA_size.width),height-(margin.bottom+yNA_size.width)],height:[inner_height,inner_height,yNA_size.width,yNA_size.width]};xNA_xpos=xNA?margin.left+xNA_size.width/2:-5e4;yNA_ypos=yNA?height-margin.bottom-yNA_size.width/2:-5e4;xrange=[boxes.left[0],boxes.left[0]+boxes.width[0]];yrange=[boxes.top[0]+boxes.height[0],boxes.top[0]];for(i in boxes.left){if(boxes.width[i]>0&&boxes.height[i]>0){g.append("rect").attr("x",boxes.left[i]).attr("y",boxes.top[i]).attr("height",boxes.height[i]).attr("width",boxes.width[i]).attr("fill",rectcolor).attr("stroke","none").attr("shape-rendering","crispEdges")}}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1;if(v_over_h){yaxis=g.append("g").attr("class","y axis");xaxis=g.append("g").attr("class","x axis")}else{xaxis=g.append("g").attr("class","x axis");yaxis=g.append("g").attr("class","y axis")}xaxis.append("text").attr("class","title").text(xlab).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(ylab).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");xscale=d3.scaleLinear().domain(xlim).range([xrange[0]+margin.inner,xrange[1]-margin.inner]);yscale=d3.scaleLinear().domain(ylim).range([yrange[0]-margin.inner,yrange[1]+margin.inner]);xscale_wnull=function xscale_wnull(val){if(val==null){return xNA_xpos}return xscale(val)};yscale_wnull=function yscale_wnull(val){if(val==null){return yNA_ypos}return yscale(val)};xticks=xticks!=null?xticks:xscale.ticks(nxticks);if(xticklab!=null&&xticklab.length!==xticks.length){d3panels.displayError("panelframe: xticklab.length ("+xticklab.length+") != xticks.length ("+xticks.length+")")}if(!(xticklab!=null&&xticklab.length===xticks.length)){xticklab=function(){var j,len,results;results=[];for(j=0,len=xticks.length;j<len;j++){d=xticks[j];results.push(d3panels.formatAxis(xticks)(d))}return results}()}if(xNA){xticks=[null].concat(xticks)}if(xNA){xticklab=["NA"].concat(xticklab)}yticks=yticks!=null?yticks:yscale.ticks(nyticks);if(yticklab!=null&&yticklab.length!==yticks.length){d3panels.displayError("panelframe: yticklab.length ("+yticklab.length+") != yticks.length ("+yticks.length+")")}if(!(yticklab!=null&&yticklab.length===yticks.length)){yticklab=function(){var j,len,results;results=[];for(j=0,len=yticks.length;j<len;j++){d=yticks[j];results.push(d3panels.formatAxis(yticks)(d))}return results}()}if(yNA){yticks=[null].concat(yticks)}if(yNA){yticklab=["NA"].concat(yticklab)}ylines=yaxis.append("g").attr("id","ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1",function(d){return yscale_wnull(d)}).attr("y2",function(d){return yscale_wnull(d)}).attr("x1",function(d,i){if(i<yticks.length){return xrange[0]}return margin.left}).attr("x2",function(d,i){if(i<yticks.length){return xrange[1]}return margin.left+xNA_size.width}).attr("fill","none").attr("stroke",ylineOpts.color).attr("stroke-width",ylineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");xlines=xaxis.append("g").attr("id","xlines").selectAll("empty").data(xticks.concat(xticks)).enter().append("line").attr("x1",function(d){return xscale_wnull(d)}).attr("x2",function(d){return xscale_wnull(d)}).attr("y1",function(d,i){if(i<xticks.length){return yrange[0]}return height-margin.bottom}).attr("y2",function(d,i){if(i<xticks.length){return yrange[1]}return height-margin.bottom-yNA_size.width}).attr("fill","none").attr("stroke",xlineOpts.color).attr("stroke-width",xlineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(xticklab).enter().append("text").attr("x",function(d,i){return xscale_wnull(xticks[i])}).attr("y",height-margin.bottom+axispos.xlabel).text(function(d){return d});ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y",function(d,i){return yscale_wnull(yticks[i])}).attr("x",margin.left-axispos.ylabel).text(function(d){return d});boxes2include=function(){var results;results=[];for(i in boxes.left){if(boxes.width[i]>0&&boxes.height[i]>0){results.push(i)}}return results}();box=svg.append("g").attr("id","box");return box.selectAll("empty").data(boxes2include).enter().append("rect").attr("x",function(i){return boxes.left[i]}).attr("y",function(i){return boxes.top[i]}).attr("height",function(i){return boxes.height[i]}).attr("width",function(i){return boxes.width[i]}).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale_wnull};chart.yscale=function(){return yscale_wnull};chart.xNA=function(){return xNA};chart.yNA=function(){return yNA};chart.xlines=function(){return xlines};chart.ylines=function(){return ylines};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.chrpanelframe=function(chartOpts){var altrectcolor,axispos,box,boxcolor,boxwidth,chart,chrGap,chrSelect,chrlinecolor,chrlines,chrlinewidth,height,horizontal,margin,nyticks,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,ref18,ref19,ref2,ref20,ref21,ref22,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,width,xlab,xlabels,xlineOpts,xscale,ylab,ylabels,ylim,ylineOpts,yscale,yticklab,yticks;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:null;ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"LOD score";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;ylim=(ref9=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref9:[0,1];nyticks=(ref10=chartOpts!=null?chartOpts.nyticks:void 0)!=null?ref10:5;yticks=(ref11=chartOpts!=null?chartOpts.yticks:void 0)!=null?ref11:null;yticklab=(ref12=chartOpts!=null?chartOpts.yticklab:void 0)!=null?ref12:null;rectcolor=(ref13=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref13:"#e6e6e6";altrectcolor=(ref14=chartOpts!=null?chartOpts.altrectcolor:void 0)!=null?ref14:"#d4d4d4";chrlinecolor=(ref15=chartOpts!=null?chartOpts.chrlinecolor:void 0)!=null?ref15:"";chrlinewidth=(ref16=chartOpts!=null?chartOpts.chrlinewidth:void 0)!=null?ref16:2;boxcolor=(ref17=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref17:"black";boxwidth=(ref18=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref18:2;xlineOpts=(ref19=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref19:{color:"#d4d4d4",width:2};ylineOpts=(ref20=chartOpts!=null?chartOpts.ylineOpts:void 0)!=null?ref20:{color:"white",width:2};chrGap=(ref21=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref21:6;horizontal=(ref22=chartOpts.horizontal)!=null?ref22:false;xscale=null;yscale=null;xlabels=null;ylabels=null;chrSelect=null;chrlines=null;box=null;svg=null;chart=function chart(selection,data){var c,d,g,plot_height,plot_width,thechr,xaxis,xlines,xticks,yaxis,ylabpos_x,ylabpos_y,ylines;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"white",width:2});ylineOpts=d3panels.check_listarg_v_default(ylineOpts,{color:"white",width:2});if(data.chr==null){d3panels.displayError("chrpanelframe: data.chr is missing")}if(data.end==null){d3panels.displayError("chrpanelframe: data.end is missing")}if(xlab==null){xlab=data.chr.length===1?"Position":"Chromosome"}svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);if(!(data!=null?data.start:void 0)){data.start=function(){var j,len,ref23,results;ref23=data.chr;results=[];for(j=0,len=ref23.length;j<len;j++){c=ref23[j];results.push(0)}return results}()}if(data.chr.length!==data.start.length){d3panels.displayError("chrpanelframe: data.start.length ("+data.start.length+") != data.chr.length ("+data.chr.length+")")}if(data.chr.length!==data.end.length){d3panels.displayError("chrpanelframe: data.end.length ("+data.end.length+") != data.chr.length ("+data.chr.length+")")}if(horizontal){xscale=d3panels.calc_chrscales(plot_height,margin.top,chrGap,data.chr,data.start,data.end);yscale=d3.scaleLinear().domain(ylim.reverse()).range([plot_width+margin.left,margin.left])}else{xscale=d3panels.calc_chrscales(plot_width,margin.left,chrGap,data.chr,data.start,data.end);yscale=d3.scaleLinear().domain(ylim).range([plot_height+margin.top,margin.top])}g.append("rect").attr("x",margin.left).attr("width",plot_width).attr("y",margin.top).attr("height",plot_height).attr("fill",rectcolor).attr("shape-rendering","crispEdges");if(altrectcolor!==""){chrSelect=g.append("g").selectAll("empty").data(data.chr).enter().append("rect").attr("x",function(d,i){if(horizontal){return margin.left}return xscale[d](data.start[i])-chrGap/2}).attr("width",function(d,i){if(horizontal){return plot_width}return xscale[d](data.end[i])-xscale[d](data.start[i])+chrGap}).attr("y",function(d,i){if(horizontal){return xscale[d](data.start[i])-chrGap/2}return margin.top}).attr("height",function(d,i){if(horizontal){return xscale[d](data.end[i])-xscale[d](data.start[i])+chrGap}return plot_height}).attr("fill",function(d,i){if(i%2===0){return rectcolor}return altrectcolor}).attr("shape-rendering","crispEdges")}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);if(horizontal){rotate_ylab=rotate_ylab!=null?rotate_ylab:xlab.length>1}else{rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1}xaxis=g.append("g").attr("class",function(){if(horizontal){return"y axis"}return"x axis"});yaxis=g.append("g").attr("class",function(){if(horizontal){return"x axis"}return"y axis"});xaxis.append("text").attr("class","title").text(function(){if(horizontal){return ylab}return xlab}).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(function(){if(horizontal){return xlab}return ylab}).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");if(data.chr.length>1){xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x",function(d,i){if(horizontal){return margin.left-axispos.ylabel}return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}).attr("y",function(d,i){if(horizontal){return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}return height-margin.bottom+axispos.xlabel}).text(function(d){return d})}else{thechr=data.chr[0];xticks=xscale[thechr].ticks(5);xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(xticks).enter().append("text").attr("x",function(d){if(horizontal){return margin.left-axispos.ylabel}return xscale[thechr](d)}).attr("y",function(d,i){if(horizontal){return xscale[thechr](d)}return height-margin.bottom+axispos.xlabel}).text(function(d){return d});xlines=xaxis.append("g").attr("id","xlines").selectAll("empty").data(xticks).enter().append("line").attr("x1",function(d){if(horizontal){return margin.left}return xscale[thechr](d)}).attr("x2",function(d){if(horizontal){return margin.left+plot_width}return xscale[thechr](d)}).attr("y1",function(d,i){if(horizontal){return xscale[thechr](d)}return margin.top}).attr("y2",function(d,i){if(horizontal){return xscale[thechr](d)}return plot_height+margin.top}).attr("fill","none").attr("stroke",xlineOpts.color).attr("stroke-width",xlineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none")}yticks=yticks!=null?yticks:yscale.ticks(nyticks);if(yticklab!=null&&yticklab.length!==yticks.length){displayError("chrpanelframe: yticklab.length ("+yticklab.length+") != yticks.length ("+yticks.length+")")}if(!(yticklab!=null&&yticklab.length===yticks.length)){yticklab=function(){var j,len,results;results=[];for(j=0,len=yticks.length;j<len;j++){d=yticks[j];results.push(d3panels.formatAxis(yticks)(d))}return results}()}ylines=yaxis.append("g").attr("id","ylines").selectAll("empty").data(yticks.concat(yticks)).enter().append("line").attr("y1",function(d){if(horizontal){return margin.top}return yscale(d)}).attr("y2",function(d){if(horizontal){return margin.top+plot_height}return yscale(d)}).attr("x1",function(d,i){if(horizontal){return yscale(d)}return margin.left}).attr("x2",function(d,i){if(horizontal){return yscale(d)}return plot_width+margin.left}).attr("fill","none").attr("stroke",ylineOpts.color).attr("stroke-width",ylineOpts.width).attr("shape-rendering","crispEdges").style("pointer-events","none");ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(yticklab).enter().append("text").attr("y",function(d,i){if(horizontal){return height-margin.bottom+axispos.xlabel}return yscale(yticks[i])}).attr("x",function(d,i){if(horizontal){return yscale(yticks[i])}return margin.left-axispos.ylabel}).text(function(d){return d});if(chrlinecolor!==""&&data.chr.length>1){chrlines=svg.append("g").attr("id","chrlines");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("x1",function(d,i){if(horizontal){return margin.left}return xscale[d](data.end[i])+chrGap/2}).attr("x2",function(d,i){if(horizontal){return margin.left+plot_width}return xscale[d](data.end[i])+chrGap/2}).attr("y1",function(d,i){if(horizontal){return xscale[d](data.end[i])+chrGap/2}return margin.top}).attr("y2",function(d,i){if(horizontal){return xscale[d](data.end[i])+chrGap/2}return margin.top+plot_height}).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges")}return box=svg.append("rect").attr("class","box").attr("x",margin.left).attr("y",margin.top).attr("height",plot_height).attr("width",plot_width).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.chrSelect=function(){return chrSelect};chart.chrlines=function(){return chrlines};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.chr2dpanelframe=function(chartOpts){var altrectcolor,axispos,box,boxcolor,boxwidth,chart,chrGap,chrSelect,chrlinecolor,chrlines,chrlinewidth,height,margin,oneAtTop,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,title,titlepos,width,xlab,xlabels,xscale,ylab,ylabels,yscale;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:800;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:60};axispos=(ref3=chartOpts!=null?chartOpts.axispos:void 0)!=null?ref3:{xtitle:25,ytitle:45,xlabel:5,ylabel:5};titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";xlab=(ref6=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref6:"Chromosome";ylab=(ref7=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref7:"Chromosome";rotate_ylab=(ref8=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref8:null;rectcolor=(ref9=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref9:"#e6e6e6";altrectcolor=(ref10=chartOpts!=null?chartOpts.altrectcolor:void 0)!=null?ref10:"#d4d4d4";chrlinecolor=(ref11=chartOpts!=null?chartOpts.chrlinecolor:void 0)!=null?ref11:"";chrlinewidth=(ref12=chartOpts!=null?chartOpts.chrlinewidth:void 0)!=null?ref12:2;boxcolor=(ref13=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref13:"black";boxwidth=(ref14=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref14:2;chrGap=(ref15=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref15:6;oneAtTop=(ref16=chartOpts!=null?chartOpts.oneAtTop:void 0)!=null?ref16:false;xscale=null;yscale=null;xlabels=null;ylabels=null;chrSelect=null;chrlines=null;box=null;svg=null;chart=function chart(selection,data){var c,chrRect,chrx,chry,g,j,k,len,len1,plot_height,plot_width,ref17,ref18,x,xaxis,y,yaxis,ylabpos_x,ylabpos_y;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});axispos=d3panels.check_listarg_v_default(axispos,{xtitle:25,ytitle:45,xlabel:5,ylabel:5});if(data.chr==null){d3panels.displayError("chr2dpanelframe: data.chr is missing")}if(data.end==null){d3panels.displayError("chr2dpanelframe: data.end is missing")}svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");g=svg.append("g").attr("id","frame");plot_width=width-(margin.left+margin.right);plot_height=height-(margin.top+margin.bottom);if(!(data!=null?data.start:void 0)){data.start=function(){var j,len,ref17,results;ref17=data.chr;results=[];for(j=0,len=ref17.length;j<len;j++){c=ref17[j];results.push(0)}return results}()}if(data.chr.length!==data.start.length){d3panels.displayError("chr2dpanelframe: data.start.length ("+data.start.length+") != data.chr.length ("+data.chr.length+")")}if(data.chr.length!==data.end.length){d3panels.displayError("chr2dpanelframe: data.end.length ("+data.end.length+") != data.chr.length ("+data.chr.length+")")}xscale=d3panels.calc_chrscales(plot_width,margin.left,chrGap,data.chr,data.start,data.end);yscale=d3panels.calc_chrscales(plot_height,margin.top,chrGap,data.chr,data.start,data.end,!oneAtTop);g.append("rect").attr("x",margin.left).attr("width",plot_width).attr("y",margin.top).attr("height",plot_height).attr("fill",rectcolor).attr("shape-rendering","crispEdges");chrRect=[];ref17=data.chr;for(x=j=0,len=ref17.length;j<len;x=++j){chrx=ref17[x];ref18=data.chr;for(y=k=0,len1=ref18.length;k<len1;y=++k){chry=ref18[y];chrRect.push({chrx:chrx,xi:x,chry:chry,yi:y,odd:(x+y)%2})}}if(altrectcolor!==""){chrSelect=g.append("g").selectAll("empty").data(chrRect).enter().append("rect").attr("x",function(d){return xscale[d.chrx](data.start[d.xi])-chrGap/2}).attr("width",function(d){return xscale[d.chrx](data.end[d.xi])-xscale[d.chrx](data.start[d.xi])+chrGap}).attr("y",function(d){if(oneAtTop){return yscale[d.chry](data.start[d.yi])-chrGap/2}return yscale[d.chry](data.end[d.yi])-chrGap/2}).attr("height",function(d){if(oneAtTop){return yscale[d.chry](data.end[d.yi])-yscale[d.chry](data.start[d.yi])+chrGap}return yscale[d.chry](data.start[d.yi])-yscale[d.chry](data.end[d.yi])+chrGap}).attr("fill",function(d,i){if(!d.odd){return rectcolor}return altrectcolor}).attr("shape-rendering","crispEdges")}g.append("g").attr("class","title").append("text").text(title).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",titlepos);rotate_ylab=rotate_ylab!=null?rotate_ylab:ylab.length>1;xaxis=g.append("g").attr("class","x axis");yaxis=g.append("g").attr("class","y axis");xaxis.append("text").attr("class","title").text(function(){return xlab}).attr("x",(width-margin.left-margin.right)/2+margin.left).attr("y",plot_height+margin.top+axispos.xtitle);ylabpos_y=(height-margin.top-margin.bottom)/2+margin.top;ylabpos_x=margin.left-axispos.ytitle;yaxis.append("text").attr("class","title").text(function(){return ylab}).attr("y",ylabpos_y).attr("x",ylabpos_x).attr("transform",rotate_ylab?"rotate(270,"+ylabpos_x+","+ylabpos_y+")":"");xlabels=xaxis.append("g").attr("id","xlabels").selectAll("empty").data(data.chr).enter().append("text").attr("x",function(d,i){return(xscale[d](data.start[i])+xscale[d](data.end[i]))/2}).attr("y",height-margin.bottom+axispos.xlabel).text(function(d){return d});ylabels=yaxis.append("g").attr("id","ylabels").selectAll("empty").data(data.chr).enter().append("text").attr("y",function(d,i){return(yscale[d](data.start[i])+yscale[d](data.end[i]))/2}).attr("x",margin.left-axispos.ylabel).text(function(d){return d});if(chrlinecolor!==""&&data.chr.length>1){chrlines=svg.append("g").attr("id","chrlines");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("x1",function(d,i){return xscale[d](data.end[i])+chrGap/2}).attr("x2",function(d,i){return xscale[d](data.end[i])+chrGap/2}).attr("y1",margin.top).attr("y2",margin.top+plot_height).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges");chrlines.selectAll("empty").data(data.chr.slice(0,+(data.chr.length-2)+1||9e9)).enter().append("line").attr("y1",function(d,i){if(oneAtTop){return yscale[d](data.end[i])+chrGap/2}return yscale[d](data.end[i])-chrGap/2}).attr("y2",function(d,i){if(oneAtTop){return yscale[d](data.end[i])+chrGap/2}return yscale[d](data.end[i])-chrGap/2}).attr("x1",margin.left).attr("x2",margin.left+plot_width).attr("stroke",chrlinecolor).attr("stroke-width",chrlinewidth).attr("shape-rendering","crispEdges")}return box=svg.append("rect").attr("class","box").attr("x",margin.left).attr("y",margin.top).attr("height",plot_height).attr("width",plot_width).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth).attr("shape-rendering","crispEdges")};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xlabels=function(){return xlabels};chart.ylabels=function(){return ylabels};chart.chrSelect=function(){return chrSelect};chart.chrlines=function(){return chrlines};chart.plot_width=function(){return plot_width};chart.plot_height=function(){return plot_height};chart.width=function(){return width};chart.height=function(){return height};chart.margin=function(){return margin};chart.box=function(){return box};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.cichart=function(chartOpts){var chart,horizontal,ref,ref1,ref10,ref11,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,segcolor,segments,segstrokewidth,segwidth,svg,tip,tipclass,v_over_h,vertsegcolor,xcatlabels,xlab,xlineOpts,xscale,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xcatlabels=(ref=chartOpts!=null?chartOpts.xcatlabels:void 0)!=null?ref:null;segwidth=(ref1=chartOpts!=null?chartOpts.segwidth:void 0)!=null?ref1:.4;segcolor=(ref2=chartOpts!=null?chartOpts.segcolor:void 0)!=null?ref2:"slateblue";segstrokewidth=(ref3=chartOpts!=null?chartOpts.segstrokewidth:void 0)!=null?ref3:"3";vertsegcolor=(ref4=chartOpts!=null?chartOpts.vertsegcolor:void 0)!=null?ref4:"slateblue";xlab=(ref5=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref5:"Group";ylab=(ref6=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref6:"Response";ylim=(ref7=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref7:null;xlineOpts=(ref8=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref8:{color:"#CDCDCD",width:5};horizontal=(ref9=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref9:false;v_over_h=(ref10=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref10:horizontal;tipclass=(ref11=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref11:"tooltip";xscale=null;yscale=null;segments=null;tip=null;svg=null;chart=function chart(selection,data){var direction,high,i,low,mean,myframe,ncat,segmentGroup,tipfunc,xlim,xticks,xval,yval;xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"#CDCDCD",width:5});if(data.mean==null){d3panels.displayError("cichart: data.mean is missing")}if(data.low==null){d3panels.displayError("cichart: data.low is missing")}if(data.high==null){d3panels.displayError("cichart: data.high is missing")}mean=data.mean;low=data.low;high=data.high;ncat=mean.length;if(ncat!==low.length){d3panels.displayError("cichart: low.length ["+low.length+"] != mean.length ["+ncat+"]")}if(ncat!==high.length){d3panels.displayError("cichart: high.length ["+high.length+"] != mean.length ["+ncat+"]")}xticks=function(){var results;results=[];for(i in mean){results.push(+i+1)}return results}();xcatlabels=xcatlabels!=null?xcatlabels:xticks;if(xcatlabels.length!==mean.length){d3panels.displayError("cichart: xcatlabels.length ["+xcatlabels.length+"] != mean.length ["+ncat+"]")}ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(low.concat(high)));xlim=[.5,mean.length+.5];segcolor=d3panels.expand2vector(d3panels.forceAsArray(segcolor),mean.length);vertsegcolor=d3panels.expand2vector(d3panels.forceAsArray(vertsegcolor),mean.length);if(horizontal){chartOpts.ylim=xlim.reverse();chartOpts.xlim=ylim;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.yNA=chartOpts.xNA;chartOpts.xNA=chartOpts.yNA;chartOpts.yticks=xticks;chartOpts.yticklab=xcatlabels;chartOpts.v_over_h=v_over_h}else{chartOpts.ylim=ylim;chartOpts.xlim=xlim;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.ylineOpts=chartOpts.ylineOpts;chartOpts.xlineOpts=xlineOpts;chartOpts.xticks=xticks;chartOpts.xticklab=xcatlabels;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();segmentGroup=svg.append("g").attr("id","segments");segments=segmentGroup.selectAll("empty").data(low).enter().append("line").attr("x1",function(d,i){if(!horizontal){return xscale(i+1)}return xscale(d)}).attr("x2",function(d,i){if(!horizontal){return xscale(i+1)}return xscale(high[i])}).attr("y1",function(d,i){if(!horizontal){return yscale(d)}return yscale(i+1)}).attr("y2",function(d,i){if(!horizontal){return yscale(high[i])}return yscale(i+1)}).attr("fill","none").attr("stroke",function(d,i){return vertsegcolor[i]}).attr("stroke-width",segstrokewidth).attr("shape-rendering","crispEdges");yval=mean.concat(low,high);xval=function(){var results;results=[];for(i in yval){results.push(+(i%ncat)+1)}return results}();segments=segmentGroup.selectAll("empty").data(yval).enter().append("line").attr("x1",function(d,i){if(horizontal){return xscale(d)}else{if(i<ncat){return xscale(xval[i]-segwidth/2)}return xscale(xval[i]-segwidth/3)}}).attr("x2",function(d,i){if(horizontal){return xscale(d)}else{if(i<ncat){return xscale(xval[i]+segwidth/2)}return xscale(xval[i]+segwidth/3)}}).attr("y1",function(d,i){if(horizontal){if(i<ncat){return yscale(xval[i]-segwidth/2)}return yscale(xval[i]-segwidth/3)}else{return yscale(d)}}).attr("y2",function(d,i){if(horizontal){if(i<ncat){return yscale(xval[i]+segwidth/2)}return yscale(xval[i]+segwidth/3)}else{return yscale(d)}}).attr("fill","none").attr("stroke",function(d,i){return segcolor[i%mean.length]}).attr("stroke-width",segstrokewidth).attr("shape-rendering","crispEdges");direction=horizontal?"north":"east";tipfunc=function tipfunc(d,i){var f,index;index=i%mean.length;f=d3panels.formatAxis([low[index],mean[index]],1);return f(mean[index])+" ("+f(low[index])+" - "+f(high[index])+")"};tip=d3panels.tooltip_create(d3.select("body"),segments,{direction:direction,tipclass:tipclass},tipfunc);return myframe.box().raise()};chart.yscale=function(){return yscale};chart.xscale=function(){return xscale};chart.segments=function(){return segments};chart.tip=function(){return tip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(tip);return null};return chart};"use strict";d3panels.crosstab=function(chartOpts){var bordercolor,cellPad,chart,colrect,fontsize,height,hilitcolor,margin,rectcolor,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rowrect,svg,title,titlepos,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:600;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:300;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:80,right:40,bottom:20};cellPad=(ref3=chartOpts!=null?chartOpts.cellPad:void 0)!=null?ref3:null;titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:50;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";fontsize=(ref6=chartOpts!=null?chartOpts.fontsize:void 0)!=null?ref6:null;rectcolor=(ref7=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref7:"#e6e6e6";hilitcolor=(ref8=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref8:"#e9cfec";bordercolor=(ref9=chartOpts!=null?chartOpts.bordercolor:void 0)!=null?ref9:"black";rowrect=null;colrect=null;svg=null;chart=function chart(selection,data){var borders,cell,cellHeight,cellWidth,cells,collab,denom,i,j,k,l,n,ncol,nrow,plot_height,plot_width,rect,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref17,rowlab,tab,titles,values,xscale,xv,yscale,yv;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:60});if(data.x==null){d3panels.displayError("crosstab: data.x is missing")}if(data.y==null){d3panels.displayError("crosstab: data.y is missing")}n=data.x.length;if(data.y.length!==n){d3panels.displayError("crosstab: data.x.length ["+data.x.length+"] != data.y.length ["+data.y.length+"]")}data.xcat=(ref10=data!=null?data.xcat:void 0)!=null?ref10:function(){var k,len,ref11,results;ref11=d3.range(d3.max(data.x));results=[];for(k=0,len=ref11.length;k<len;k++){xv=ref11[k];results.push(xv+1)}return results}();data.ycat=(ref11=data!=null?data.ycat:void 0)!=null?ref11:function(){var k,len,ref12,results;ref12=d3.range(d3.max(data.y));results=[];for(k=0,len=ref12.length;k<len;k++){yv=ref12[k];results.push(yv+1)}return results}();ncol=data.xcat.length;if(d3.max(data.x)>ncol||d3.min(data.x)<=0){d3panels.displayError("crosstab: data.x should be in range 1-"+ncol+" [was "+d3.min(data.x)+" - "+d3.max(data.x)+"]")}nrow=data.ycat.length;if(d3.max(data.y)>nrow||d3.min(data.y)<=0){d3panels.displayError("crosstab: data.y should be in range 1-"+nrow+" [was "+d3.min(data.y)+" - "+d3.max(data.y)+"]")}data.x=function(){var k,len,ref12,results;ref12=data.x;results=[];for(k=0,len=ref12.length;k<len;k++){xv=ref12[k];results.push(xv-1)}return results}();data.y=function(){var k,len,ref12,results;ref12=data.y;results=[];for(k=0,len=ref12.length;k<len;k++){yv=ref12[k];results.push(yv-1)}return results}();tab=d3panels.calc_crosstab(data);data.xlabel=(ref12=data!=null?data.xlabel:void 0)!=null?ref12:"";data.ylabel=(ref13=data!=null?data.ylabel:void 0)!=null?ref13:"";cells=[];for(i=k=0,ref14=nrow;0<=ref14?k<=ref14:k>=ref14;i=0<=ref14?++k:--k){for(j=l=0,ref15=ncol;0<=ref15?l<=ref15:l>=ref15;j=0<=ref15?++l:--l){cell={value:tab[i][j],row:i,col:j,shaded:false,rowpercent:"",colpercent:""};if(i<nrow-1&&(j<ncol-1||j===ncol)){cell.shaded=true}if(j<ncol-1&&(i<nrow-1||i===nrow)){cell.shaded=true}if(i<nrow-1){denom=tab[nrow][j]-tab[nrow-1][j];cell.colpercent=denom>0?Math.round(100*tab[i][j]/denom)+"%":"—"}else if(i===nrow-1){denom=tab[nrow][j];cell.colpercent=denom>0?"("+Math.round(100*tab[i][j]/denom)+"%)":"—"}else{cell.colpercent=cell.value}if(j<ncol-1){denom=tab[i][ncol]-tab[i][ncol-1];cell.rowpercent=denom>0?Math.round(100*tab[i][j]/denom)+"%":"—"}else if(j===ncol-1){denom=tab[i][ncol];cell.rowpercent=denom>0?"("+Math.round(100*tab[i][j]/denom)+"%)":"—"}else{cell.rowpercent=cell.value}cells.push(cell)}}plot_width=width-margin.left-margin.right;plot_height=height-margin.top-margin.bottom;cellWidth=plot_width/(ncol+2);cellHeight=plot_height/(nrow+2);fontsize=fontsize!=null?fontsize:cellHeight*.5;cellPad=cellPad!=null?cellPad:cellWidth*.1;xscale=d3.scaleBand().domain(function(){var results=[];for(var m=0,ref16=ncol+1;0<=ref16?m<=ref16:m>=ref16;0<=ref16?m++:m--){results.push(m)}return results}.apply(this)).range([margin.left,width-margin.right]);yscale=d3.scaleBand().domain(function(){var results=[];for(var m=0,ref17=nrow+1;0<=ref17?m<=ref17:m>=ref17;0<=ref17?m++:m--){results.push(m)}return results}.apply(this)).range([margin.top,height-margin.bottom]);svg=selection.append("svg").attr("width",width).attr("height",height).attr("class","d3panels");rect=svg.append("g").attr("id","value_rect");rect.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return xscale(d.col+1)}).attr("y",function(d){return yscale(d.row+1)}).attr("width",cellWidth).attr("height",cellHeight).attr("fill",function(d){if(d.shaded){return rectcolor}else{return"none"}}).attr("stroke",function(d){if(d.shaded){return rectcolor}else{return"none"}}).attr("stroke-width",0).style("pointer-events","none").attr("shape-rendering","crispEdges");values=svg.append("g").attr("id","values");values.selectAll("empty").data(cells).enter().append("text").attr("x",function(d){return xscale(d.col+1)+cellWidth-cellPad}).attr("y",function(d){return yscale(d.row+1)+cellHeight/2}).text(function(d){return d.value}).attr("class",function(d){return"crosstab row"+d.row+" col"+d.col}).style("font-size",fontsize).style("pointer-events","none");colrect=svg.append("g").attr("id","colrect");colrect.selectAll("empty").data(data.xcat.concat("Total")).enter().append("rect").attr("x",function(d,i){return xscale(i+1)}).attr("y",yscale(0)).attr("width",cellWidth).attr("height",cellHeight).attr("fill","white").attr("stroke","white").attr("shape-rendering","crispEdges").on("mouseover",function(d,i){d3.select(this).attr("fill",hilitcolor).attr("stroke",hilitcolor);return values.selectAll(".col"+i).text(function(d){return d.colpercent})}).on("mouseout",function(d,i){d3.select(this).attr("fill","white").attr("stroke","white");return values.selectAll("text.col"+i).text(function(d){return d.value})});collab=svg.append("g").attr("id","collab");collab.selectAll("empty").data(data.xcat.concat("Total")).enter().append("text").attr("x",function(d,i){return xscale(i+1)+cellWidth-cellPad}).attr("y",yscale(0)+cellHeight/2).text(function(d){return d}).attr("class","crosstab").style("font-size",fontsize).style("pointer-events","none");rowrect=svg.append("g").attr("id","rowrect");rowrect.selectAll("empty").data(data.ycat.concat("Total")).enter().append("rect").attr("x",xscale(0)).attr("y",function(d,i){return yscale(i+1)}).attr("width",cellWidth).attr("height",cellHeight).attr("fill","white").attr("stroke","white").attr("shape-rendering","crispEdges").on("mouseover",function(d,i){d3.select(this).attr("fill",hilitcolor).attr("stroke",hilitcolor);return values.selectAll(".row"+i).text(function(d){return d.rowpercent})}).on("mouseout",function(d,i){d3.select(this).attr("fill","white").attr("stroke","white");return values.selectAll(".row"+i).text(function(d){return d.value})});rowlab=svg.append("g").attr("id","rowlab");rowlab.selectAll("empty").data(data.ycat.concat("Total")).enter().append("text").attr("x",xscale(0)+cellWidth-cellPad).attr("y",function(d,i){return yscale(i+1)+cellHeight/2}).text(function(d){return d}).attr("class","crosstab").style("font-size",fontsize).style("pointer-events","none");borders=svg.append("g").attr("id","borders");borders.append("rect").attr("x",xscale(1)).attr("y",yscale(1)).attr("width",cellWidth*ncol).attr("height",cellHeight*nrow).attr("fill","none").attr("stroke",bordercolor).attr("stroke-width",2).style("pointer-events","none").attr("shape-rendering","crispEdges");borders.append("rect").attr("x",xscale(ncol+1)).attr("y",yscale(nrow+1)).attr("width",cellWidth).attr("height",cellHeight).attr("fill","none").attr("stroke",bordercolor).attr("stroke-width",2).style("pointer-events","none").attr("shape-rendering","crispEdges");titles=svg.append("g").attr("id","titles");titles.append("text").attr("class","crosstabtitle").attr("x",margin.left+(ncol+1)*cellWidth/2).attr("y",margin.top-cellHeight/2).text(data.xlabel).style("font-size",fontsize).style("font-weight","bold");titles.append("text").attr("class","crosstab").attr("x",xscale(0)+cellWidth-cellPad).attr("y",yscale(0)+cellHeight/2).text(data.ylabel).style("font-size",fontsize).style("font-weight","bold");return titles.append("text").attr("class","crosstabtitle").attr("x",margin.left+(width-margin.left-margin.right)/2).attr("y",margin.top-titlepos).text(title).style("font-size",fontsize)};chart.rowrect=function(){return rowrect};chart.colrect=function(){return colrect};chart.svg=function(){return svg};chart.remove=function(){svg.remove();return null};return chart};"use strict";d3panels.curvechart=function(chartOpts){var chart,curves,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref2,ref3,ref4,ref5,ref6,svg,tipclass,xlim,xscale,ylim,yscale;if(chartOpts==null){chartOpts={}}xlim=(ref=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref:null;ylim=(ref1=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref1:null;linecolor=(ref2=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref2:null;linecolorhilit=(ref3=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref3:null;linewidth=(ref4=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref4:2;linewidthhilit=(ref5=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref5:2;tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";xscale=null;yscale=null;curves=null;indtip=null;svg=null;chart=function chart(selection,data){var add_curves,i,j,myframe,n_ind,ref7,x,y;if(data.x==null){d3panels.displayError("curvechart: data.x is missing")}if(data.y==null){d3panels.displayError("curvechart: data.y is missing")}x=data.x;y=data.y;n_ind=y.length;if(x.length===1&&y.length>1){for(j=i=2,ref7=n_ind;2<=ref7?i<=ref7:i>=ref7;j=2<=ref7?++i:--i){x.push(x[0])}}if(x.length!==n_ind){d3panels.displayError("curvechart: data.x.length ("+x.length+") != data.y.length ("+n_ind+")")}xlim=xlim!=null?xlim:d3panels.matrixExtent(x);ylim=ylim!=null?ylim:d3panels.matrixExtent(y);chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();add_curves=d3panels.add_curves({linecolor:linecolor,linecolorhilit:linecolorhilit,linewidth:linewidth,linewidthhilit:linewidthhilit,tipclass:tipclass});add_curves(myframe,data);curves=add_curves.curves();indtip=add_curves.indtip();return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";var indexOf=[].indexOf;d3panels.dotchart=function(chartOpts){var chart,horizontal,indtip,jitter,pointcolor,points,pointsize,pointstroke,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,v_over_h,xNA,xNA_size,xcategories,xcatlabels,xlab,xlineOpts,xscale,yNA,yNA_size,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xcategories=(ref=chartOpts!=null?chartOpts.xcategories:void 0)!=null?ref:null;xcatlabels=(ref1=chartOpts!=null?chartOpts.xcatlabels:void 0)!=null?ref1:null;xNA=(ref2=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref2:{handle:true,force:false};yNA=(ref3=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref3:{handle:true,force:false};xNA_size=(ref4=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref4:{width:20,gap:10};yNA_size=(ref5=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref5:{width:20,gap:10};ylim=(ref6=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref6:null;xlab=(ref7=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref7:"Group";ylab=(ref8=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref8:"Response";xlineOpts=(ref9=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref9:{color:"#cdcdcd",width:5};pointcolor=(ref10=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref10:null;pointstroke=(ref11=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref11:"black";pointsize=(ref12=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref12:3;jitter=(ref13=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref13:"beeswarm";tipclass=(ref14=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref14:"tooltip";horizontal=(ref15=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref15:false;v_over_h=(ref16=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref16:horizontal;xscale=null;yscale=null;xNA=xNA;yNA=yNA;points=null;indtip=null;svg=null;chart=function chart(selection,data){var force,g,group,i,indID,jitter_width,myframe,ngroup,pointGroup,ref17,ref18,ref19,ref20,scaledPoints,u,x,xlim,xv,y;xNA=d3panels.check_listarg_v_default(xNA,{handle:true,force:false});yNA=d3panels.check_listarg_v_default(yNA,{handle:true,force:false});xNA_size=d3panels.check_listarg_v_default(xNA,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA,{width:20,gap:10});if(data.x==null){d3panels.displayError("dotchart: data.x is missing")}if(data.y==null){d3panels.displayError("dotchart: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);indID=(ref17=data!=null?data.indID:void 0)!=null?ref17:function(){var results=[];for(var j=1,ref18=x.length;1<=ref18?j<=ref18:j>=ref18;1<=ref18?j++:j--){results.push(j)}return results}.apply(this);if(x.length!==y.length){d3panels.displayError("dotchart: length(x) ["+x.length+"] != length(y) ["+y.length+"]")}if(indID.length!==x.length){d3panels.displayError("dotchart: length(indID) ["+indID.length+"] != length(x) ["+x.length+"]")}group=(ref19=data!=null?data.group:void 0)!=null?ref19:function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){i=x[j];results.push(1)}return results}();group=d3panels.expand2vector(group,x.length);ngroup=d3.max(group);group=function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("dotchart: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==x.length){d3panels.displayError("dotchart: group.length ("+group.length+") != x.length ("+x.length+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}xcategories=xcategories!=null?xcategories:d3panels.unique(x);xcategories=d3panels.forceAsArray(xcategories);xcatlabels=xcatlabels!=null?xcatlabels:xcategories;xcatlabels=d3panels.forceAsArray(xcatlabels);if(xcatlabels.length!==xcategories.length){d3panels.displayError("dotchart: xcatlabels.length ["+xcatlabels.length+"] != xcategories.length ["+xcategories.length+"]")}if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){xv=x[j];results.push(xv!=null&&!(indexOf.call(xcategories,xv)>=0))}return results}())>0){d3panels.displayError("dotchart: Some x values not in xcategories");console.log("xcategories:");console.log(xcategories);console.log("x:");console.log(x);for(i in x){if(x[i]!=null&&!(ref20=x[i],indexOf.call(xcategories,ref20)>=0)){x[i]=null}}}ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(y));xlim=[d3.min(xcategories)-.5,d3.max(xcategories)+.5];xNA.handle=xNA.force||xNA.handle&&!x.every(function(v){return v!=null});yNA.handle=yNA.force||yNA.handle&&!y.every(function(v){return v!=null});if(horizontal){chartOpts.ylim=xlim.reverse();chartOpts.xlim=ylim;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.yNA=xNA.handle;chartOpts.xNA=yNA.handle;chartOpts.xNA_size=yNA_size;chartOpts.yNA_size=xNA_size;chartOpts.yticks=xcategories;chartOpts.yticklab=xcatlabels;chartOpts.v_over_h=v_over_h}else{chartOpts.ylim=ylim;chartOpts.xlim=xlim;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.ylineOpts=chartOpts.ylineOpts;chartOpts.xlineOpts=xlineOpts;chartOpts.xNA=xNA.handle;chartOpts.yNA=yNA.handle;chartOpts.xNA_size=xNA_size;chartOpts.yNA_size=yNA_size;chartOpts.xticks=xcategories;chartOpts.xticklab=xcatlabels;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();if(horizontal){scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(y[i]),y:yscale(x[i])})}return results}()}else{scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(x[i]),y:yscale(y[i])})}return results}()}pointGroup=svg.append("g").attr("id","points");points=pointGroup.selectAll("empty").data(scaledPoints).enter().append("circle").attr("class",function(d,i){return"pt"+i}).attr("r",pointsize).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width","1").attr("cx",function(d){return d.x}).attr("cy",function(d){return d.y});indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]});if(jitter==="random"){jitter_width=.2;u=function(){var results;results=[];for(i in scaledPoints){results.push((Math.random()-.5)*jitter_width)}return results}();if(horizontal){points.attr("cy",function(d,i){if(x[i]!=null){return yscale(x[i]+u[i])}return yscale(x[i])+u[i]/jitter_width*xNA_size.width/2})}else{points.attr("cx",function(d,i){if(x[i]!=null){return xscale(x[i]+u[i])}return xscale(x[i])+u[i]/jitter_width*xNA_size.width/2})}}else if(jitter==="beeswarm"){if(horizontal){d3.range(scaledPoints.length).map(function(i){return scaledPoints[i].fx=scaledPoints[i].x});force=d3.forceSimulation(scaledPoints).force("y",d3.forceY(function(d){return d.y})).force("collide",d3.forceCollide(pointsize*1.1)).stop()}else{d3.range(scaledPoints.length).map(function(i){return scaledPoints[i].fy=scaledPoints[i].y});force=d3.forceSimulation(scaledPoints).force("x",d3.forceX(function(d){return d.x})).force("collide",d3.forceCollide(pointsize*1.1)).stop()}(function(){var results=[];for(var j=0;j<=30;j++){results.push(j)}return results}).apply(this).map(function(d){force.tick();return points.attr("cx",function(d){return d.x}).attr("cy",function(d){return d.y})})}else if(jitter!=="none"){d3panels.displayError('dotchart: jitter should be "beeswarm", "random", or "none"')}return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xNA=function(){return xNA.handle};chart.yNA=function(){return yNA.handle};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.heatmap=function(chartOpts){var cellSelect,cells,celltip,chart,colors,hilitcolor,margin,nullcolor,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,ref8,svg,tipclass,xlim,xscale,ylim,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}margin=(ref=chartOpts!=null?chartOpts.margin:void 0)!=null?ref:{left:60,top:40,right:40,bottom:40,inner:0};xlim=(ref1=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref1:null;ylim=(ref2=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref2:null;nullcolor=(ref3=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref3:"#e6e6e6";colors=(ref4=chartOpts!=null?chartOpts.colors:void 0)!=null?ref4:["slateblue","white","crimson"];zlim=(ref5=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref5:null;zthresh=(ref6=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref6:null;hilitcolor=(ref7=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref7:"black";tipclass=(ref8=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref8:"tooltip";xscale=null;yscale=null;zscale=null;cells=null;celltip=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cell,cellrect,i,j,myframe,nx,ny,ref10,ref9,tooltipfunc,xlabels,xmid,xmid_scaled,xv,ylabels,ymid,ymid_scaled,yv,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40,inner:0});if(!(data.x!=null||data.xcat!=null)){d3panels.displayError("heatmap: data.x is missing")}if(!(data.y!=null||data.ycat!=null)){d3panels.displayError("heatmap: data.y is missing")}if(data.z==null){d3panels.displayError("heatmap: data.z is missing")}if(data.xcat!=null){data.x=function(){var results;results=[];for(i in data.xcat){results.push(+i)}return results}();xlim=xlim!=null?xlim:[-.5,data.x.length-.5];chartOpts.xticks=data.x;chartOpts.xlineOpts={color:"none",width:0};chartOpts.xlab=(ref9=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref9:""}if(data.ycat!=null){data.y=function(){var results;results=[];for(i in data.ycat){results.push(+i)}return results}();ylim=ylim!=null?ylim:[-.5,data.x.length-.5];chartOpts.yticks=data.y;chartOpts.ylineOpts={color:"none",width:0};chartOpts.ylab=(ref10=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref10:""}nx=data.x.length;ny=data.y.length;if(data.z.length!==nx){d3panels.displayError("heatmap: data.x.length ("+nx+") != data.z.length ("+data.z.length+")")}for(i in data.z){if(data.z[i].length!==ny){d3panels.displayError("heatmap: data.y.length ("+ny+") != data.z["+i+"].length ("+data.z[i].length+")")}}cells=[];for(i in data.z){for(j in data.z[i]){cells.push({x:data.x[i],y:data.y[j],z:data.z[i][j],xindex:+i,yindex:+j})}}xmid=d3panels.calc_midpoints(d3panels.pad_vector(data.x));ymid=d3panels.calc_midpoints(d3panels.pad_vector(data.y));xlim=xlim!=null?xlim:d3.extent(xmid);ylim=ylim!=null?ylim:d3.extent(ymid);zmin=d3panels.matrixMin(data.z);zmax=d3panels.matrixMaxAbs(data.z);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("heatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;cells=function(){var k,len,results;results=[];for(k=0,len=cells.length;k<len;k++){cell=cells[k];if(Math.abs(cell.z)>=zthresh){results.push(cell)}}return results}();chartOpts.margin=margin;chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();xlabels=myframe.xlabels();ylabels=myframe.ylabels();xmid_scaled=function(){var k,len,results;results=[];for(k=0,len=xmid.length;k<len;k++){xv=xmid[k];results.push(xscale(xv))}return results}();ymid_scaled=function(){var k,len,results;results=[];for(k=0,len=ymid.length;k<len;k++){yv=ymid[k];results.push(yscale(yv))}return results}();d3panels.calc_cell_rect(cells,xmid_scaled,ymid_scaled);cellrect=svg.append("g").attr("id","cells");cellSelect=cellrect.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){return d.left}).attr("y",function(d){return d.top}).attr("width",function(d){return d.width}).attr("height",function(d){return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.z!=null){return zscale(d.z)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").attr("shape-rendering","crispEdges").on("mouseover",function(d){d3.select(this).attr("stroke",hilitcolor).raise();if(data.xcat!=null){svg.select("text#xlab"+d.x).attr("opacity",1)}if(data.ycat!=null){return svg.select("text#ylab"+d.y).attr("opacity",1)}}).on("mouseout",function(d){d3.select(this).attr("stroke","none");if(data.xcat!=null){svg.select("text#xlab"+d.x).attr("opacity",0)}if(data.ycat!=null){return svg.select("text#ylab"+d.y).attr("opacity",0)}});tooltipfunc=function tooltipfunc(d,i){var x,y,z;x=d3panels.formatAxis(data.x)(d.x);y=d3panels.formatAxis(data.y)(d.y);z=d3panels.formatAxis([0,zmax/100])(d.z);if(data.xcat!=null&&data.ycat!=null){return""+z}if(data.xcat!=null){return"("+y+") → "+z}if(data.ycat!=null){return"("+x+") → "+z}return"("+x+", "+y+") → "+z};celltip=d3panels.tooltip_create(d3.select("body"),cellrect.selectAll("rect"),{tipclass:tipclass},tooltipfunc);if(data.xcat!=null){xlabels.text(function(d,i){return data.xcat[i]}).attr("opacity",0).attr("id",function(d,i){return"xlab"+data.x[i]})}if(data.ycat!=null){ylabels.text(function(d,i){return data.ycat[i]}).attr("opacity",0).attr("id",function(d,i){return"ylab"+data.y[i]})}return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return zscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.lodchart=function(chartOpts){var chart,chrSelect,linecolor,linewidth,markerSelect,markertip,pointcolor,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,ref5,ref6,_svg,tipclass,_xscale,ylim,_yscale;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:"darkslateblue";linewidth=(ref1=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref1:2;pointcolor=(ref2=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref2:"#e9cfec";pointsize=(ref3=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref3:0;pointstroke=(ref4=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref4:"black";ylim=(ref5=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref5:null;tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";_xscale=null;_yscale=null;chrSelect=null;markerSelect=null;markertip=null;_svg=null;chart=function chart(selection,data){var add2chart,i,myframe,self_chart;if(data.chr==null){d3panels.displayError("lodchart: data.chr is missing")}if(data.pos==null){d3panels.displayError("lodchart: data.pos is missing")}if(data.lod==null){d3panels.displayError("lodchart: data.lod is missing")}if(data.marker==null){d3panels.displayError("lodchart: data.marker is missing")}if(data.pos.length!==data.chr.length){d3panels.displayError("lodchart: data.pos.length ("+data.pos.length+") != data.chr.length ("+data.chr.length+")")}if(data.lod.length!==data.chr.length){d3panels.displayError("lodchart: data.lod.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}if(data.marker==null){data.marker=[function(){var results;results=[];for(i in data.chr){results.push("")}return results}()]}if(data.marker.length!==data.chr.length){d3panels.displayError("lodchart: data.marker.length ("+data.marker.length+") != data.chr.length ("+data.chr.length+")")}data=d3panels.add_chrname_start_end(data);data=d3panels.reorgLodData(data);chartOpts.ylim=ylim!=null?ylim:[0,d3.max(data.lod)*1.05];myframe=d3panels.chrpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});_svg=myframe.svg();_xscale=myframe.xscale();_yscale=myframe.yscale();chrSelect=myframe.chrSelect();self_chart={svg:function svg(){return _svg},xscale:function xscale(){return _xscale},yscale:function yscale(){return _yscale}};add2chart=d3panels.add_lodcurve(chartOpts);add2chart(self_chart,data);markerSelect=add2chart.markerSelect();markertip=add2chart.markertip();return myframe.box().raise()};chart.xscale=function(){return _xscale};chart.yscale=function(){return _yscale};chart.chrSelect=function(){return chrSelect};chart.markerSelect=function(){return markerSelect};chart.markertip=function(){return markertip};chart.svg=function(){return _svg};chart.remove=function(){_svg.remove();d3panels.tooltip_destroy(markertip);return null};return chart};"use strict";d3panels.add_lodcurve=function(chartOpts){var chart,g,horizontal,linecolor,linedash,linewidth,markerSelect,markertip,pointcolor,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,ref5,ref6,ref7,tipclass;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:"darkslateblue";linewidth=(ref1=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref1:2;linedash=(ref2=chartOpts!=null?chartOpts.linedash:void 0)!=null?ref2:"";pointcolor=(ref3=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref3:"#e9cfec";pointsize=(ref4=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref4:0;pointstroke=(ref5=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref5:"black";tipclass=(ref6=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref6:"tooltip";horizontal=(ref7=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref7:false;markerSelect=null;markertip=null;g=null;chart=function chart(prevchart,data){var bigpointsize,chr,curves,hiddenpoints,i,j,len,lodcurve,markerpoints,ref8,svg,xscale,yscale;if(data.chr==null){d3panels.displayError("add_lodcurve: data.chr is missing")}if(data.pos==null){d3panels.displayError("add_lodcurve: data.pos is missing")}if(data.lod==null){d3panels.displayError("add_lodcurve: data.lod is missing")}if(data.marker==null){d3panels.displayError("add_lodcurve: data.marker is missing")}if(data.pos.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.pos.length ("+data.pos.length+") != data.chr.length ("+data.chr.length+")")}if(data.lod.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.lod.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}if(data.marker==null){data.marker=[function(){var results;results=[];for(i in data.chr){results.push("")}return results}()]}if(data.marker.length!==data.chr.length){d3panels.displayError("add_lodcurve: data.marker.length ("+data.lod.length+") != data.chr.length ("+data.chr.length+")")}data=d3panels.add_chrname_start_end(data);if(!(data.posByChr!=null&&data.lodByChr!=null&&data.markerinfo!=null)){data=d3panels.reorgLodData(data)}svg=prevchart.svg();g=svg.append("g").attr("id","lod_curve");xscale=prevchart.xscale();yscale=prevchart.yscale();lodcurve=function lodcurve(chr){return d3.line().x(function(d,i){if(horizontal){return yscale(data.lodByChr[chr][i])}return xscale[chr](d)}).y(function(d,i){if(horizontal){return xscale[chr](d)}return yscale(data.lodByChr[chr][i])})};if(linewidth>0){curves=g.append("g").attr("id","curves");ref8=data.chrname;for(j=0,len=ref8.length;j<len;j++){chr=ref8[j];curves.append("path").datum(data.posByChr[chr]).attr("d",lodcurve(chr)).attr("stroke",linecolor).attr("fill","none").attr("stroke-width",linewidth).attr("stroke-dasharray",linedash).style("pointer-events","none")}}if(pointsize>0){markerpoints=g.append("g").attr("id","markerpoints_visible");markerpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx",function(d){if(horizontal){return yscale(d.lod)}return xscale[d.chr](d.pos)}).attr("cy",function(d){if(horizontal){return xscale[d.chr](d.pos)}return yscale(d.lod)}).attr("r",function(d){if(d.lod!=null){return pointsize}else{return null}}).attr("fill",pointcolor).attr("stroke",pointstroke).attr("pointer-events","hidden")}hiddenpoints=g.append("g").attr("id","markerpoints_hidden");bigpointsize=d3.max([2*pointsize,3]);markerSelect=hiddenpoints.selectAll("empty").data(data.markerinfo).enter().append("circle").attr("cx",function(d){if(horizontal){return yscale(d.lod)}return xscale[d.chr](d.pos)}).attr("cy",function(d){if(horizontal){return xscale[d.chr](d.pos)}return yscale(d.lod)}).attr("id",function(d){return d.name}).attr("r",function(d){if(d.lod!=null){return bigpointsize}else{return null}}).attr("opacity",0).attr("fill",pointcolor).attr("stroke",pointstroke).attr("stroke-width","1").on("mouseover",function(d){return d3.select(this).attr("opacity",1)}).on("mouseout",function(){return d3.select(this).attr("opacity",0)});return markertip=d3panels.tooltip_create(d3.select("body"),markerSelect,{tipclass:tipclass},function(d,i){return[d.name," LOD = "+d3.format(".2f")(d.lod)]})};chart.markerSelect=function(){return markerSelect};chart.markertip=function(){return markertip};chart.remove=function(){g.remove();d3panels.tooltip_destroy(markertip);return null};return chart};"use strict";d3panels.add_curves=function(chartOpts){var chart,curveGroup,curves,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref2,ref3,ref4,tipclass;if(chartOpts==null){chartOpts={}}linecolor=(ref=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref:null;linecolorhilit=(ref1=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref1:null;linewidth=(ref2=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref2:2;linewidthhilit=(ref3=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref3:2;tipclass=(ref4=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref4:"tooltip";curves=null;indtip=null;curveGroup=null;chart=function chart(prevchart,data){var curvefunc,dataByPoint,g,group,i,indID,j,k,n_ind,ngroup,ref5,ref6,ref7,svg,x,xscale,y,yscale;if(data.x==null){d3panels.displayError("add_curves: data.x is missing")}if(data.y==null){d3panels.displayError("add_curves: data.y is missing")}x=function(){var k,len,ref5,results;ref5=data.x;results=[];for(k=0,len=ref5.length;k<len;k++){x=ref5[k];results.push(d3panels.missing2null(x))}return results}();y=function(){var k,len,ref5,results;ref5=data.y;results=[];for(k=0,len=ref5.length;k<len;k++){y=ref5[k];results.push(d3panels.missing2null(y))}return results}();n_ind=y.length;if(x.length===1&&y.length>1){for(j=k=2,ref5=n_ind;2<=ref5?k<=ref5:k>=ref5;j=2<=ref5?++k:--k){x.push(x[0])}}if(x.length!==n_ind){d3panels.displayError("add_curves: data.x.length ("+x.length+") != data.y.length ("+n_ind+")")}indID=(ref6=data!=null?data.indID:void 0)!=null?ref6:function(){var results=[];for(var l=1;1<=n_ind?l<=n_ind:l>=n_ind;1<=n_ind?l++:l--){results.push(l)}return results}.apply(this);if(indID.length!==n_ind){d3panels.displayError("add_curves: data.indID.length ("+indID.length+") != data.y.length ("+n_ind+")")}group=(ref7=data!=null?data.group:void 0)!=null?ref7:function(){var results;results=[];for(i in y){results.push(1)}return results}();group=d3panels.expand2vector(group,n_ind);ngroup=d3.max(group);group=function(){var l,len,results;results=[];for(l=0,len=group.length;l<len;l++){g=group[l];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var l,len,results;results=[];for(l=0,len=group.length;l<len;l++){g=group[l];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_curves: group values out of range");console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==n_ind){d3panels.displayError("add_curves: data.group.length ("+group.length+") != data.y.length ("+n_ind+")")}for(i in y){if(x[i].length!==y[i].length){d3panels.displayError("add_curves: length(x) ("+x[i].length+") != length(y) ("+y[i].length+") for individual "+indID[i]+" (index "+(i+1)+")")}}linecolor=linecolor!=null?linecolor:d3panels.selectGroupColors(ngroup,"pastel");linecolor=d3panels.expand2vector(linecolor,ngroup);linecolorhilit=linecolorhilit!=null?linecolorhilit:d3panels.selectGroupColors(ngroup,"dark");linecolorhilit=d3panels.expand2vector(linecolorhilit,ngroup);svg=prevchart.svg();xscale=prevchart.xscale();yscale=prevchart.yscale();dataByPoint=[];for(i in y){dataByPoint.push(function(){var results;results=[];for(j in y[i]){if(x[i][j]!=null&&y[i][j]!=null){results.push({x:x[i][j],y:y[i][j]})}}return results}())}curvefunc=d3.line().x(function(d){return xscale(d.x)}).y(function(d){return yscale(d.y)});curveGroup=svg.append("g").attr("id","curves");curves=curveGroup.selectAll("empty").data(d3.range(n_ind)).enter().append("path").datum(function(d){return dataByPoint[d]}).attr("d",curvefunc).attr("class",function(d,i){return"path"+i}).attr("fill","none").attr("stroke",function(d,i){return linecolor[group[i]]}).attr("stroke-width",linewidth).on("mouseover.panel",function(d,i){return d3.select(this).attr("stroke",linecolorhilit[group[i]]).attr("stroke-width",linewidthhilit).raise()}).on("mouseout.panel",function(d,i){return d3.select(this).attr("stroke",linecolor[group[i]]).attr("stroke-width",linewidth)});indtip=d3panels.tooltip_create(d3.select("body"),curves,{tipclass:tipclass},function(d,i){return indID[i]});return prevchart.box().raise()};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.remove=function(){curveGroup.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.add_points=function(chartOpts){var chart,indtip,jitter,pointGroup,pointcolor,points,pointsize,pointstroke,ref,ref1,ref2,ref3,ref4,tipclass;if(chartOpts==null){chartOpts={}}pointcolor=(ref=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref:null;pointsize=(ref1=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref1:3;pointstroke=(ref2=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref2:"black";jitter=(ref3=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref3:"beeswarm";tipclass=(ref4=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref4:"tooltip";points=null;indtip=null;pointGroup=null;chart=function chart(prevchart,data){var force,g,group,i,indID,ngroup,ref5,ref6,ref7,scaledPoints,svg,ux,uy,x,xscale,xwid,y,yscale,ywid;if(data.x==null){d3panels.displayError("add_points: data.x is missing")}if(data.y==null){d3panels.displayError("add_points: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);if(x.length!==y.length){d3panels.displayError("add_points: x.length ("+x.length+") != y.length ("+y.length+")")}indID=(ref5=data!=null?data.indID:void 0)!=null?ref5:null;indID=indID!=null?indID:function(){var results=[];for(var j=1,ref6=x.length;1<=ref6?j<=ref6:j>=ref6;1<=ref6?j++:j--){results.push(j)}return results}.apply(this);if(indID.length!==x.length){d3panels.displayError("add_points: indID.length ("+indID.length+") != x.length ("+x.length+")")}group=(ref7=data!=null?data.group:void 0)!=null?ref7:function(){var j,len,results;results=[];for(j=0,len=x.length;j<len;j++){i=x[j];results.push(1)}return results}();group=d3panels.expand2vector(group,x.length);ngroup=d3.max(group);group=function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var j,len,results;results=[];for(j=0,len=group.length;j<len;j++){g=group[j];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_points: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==x.length){d3panels.displayError("add_points: group.length ("+group.length+") != x.length ("+x.length+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}svg=prevchart.svg();xscale=prevchart.xscale();yscale=prevchart.yscale();pointGroup=svg.append("g").attr("id","points");points=pointGroup.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx",function(d,i){return xscale(x[i])}).attr("cy",function(d,i){return yscale(y[i])}).attr("class",function(d,i){return"pt"+i}).attr("r",pointsize).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width","1");indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]});if(prevchart.xNA()||prevchart.yNA()){if(jitter==="random"){xwid=20-pointsize-2;xwid=xwid<=2?2:xwid;ywid=20-pointsize-2;ywid=ywid<=2?2:ywid;ux=function(){var results;results=[];for(i in x){results.push((Math.random()-.5)*xwid)}return results}();uy=function(){var results;results=[];for(i in x){results.push((Math.random()-.5)*ywid)}return results}();points.attr("cx",function(d,i){if(x[i]!=null){return xscale(x[i])}return xscale(x[i])+ux[i]}).attr("cy",function(d,i){if(y[i]!=null){return yscale(y[i])}return yscale(y[i])+uy[i]})}else if(jitter==="beeswarm"){scaledPoints=function(){var results;results=[];for(i in x){results.push({x:xscale(x[i]),y:yscale(y[i]),xnull:x[i]==null,ynull:y[i]==null})}return results}();d3.range(scaledPoints.length).map(function(i){if(!scaledPoints[i].xnull){scaledPoints[i].fx=scaledPoints[i].x}if(!scaledPoints[i].ynull){return scaledPoints[i].fy=scaledPoints[i].y}});force=d3.forceSimulation(scaledPoints).force("x",d3.forceX(function(d){return d.x})).force("y",d3.forceY(function(d){return d.y})).force("collide",d3.forceCollide(pointsize*1.1)).stop();(function(){var results=[];for(var j=0;j<=30;j++){results.push(j)}return results}).apply(this).map(function(d){force.tick();return points.attr("cx",function(d,i){return scaledPoints[i].x}).attr("cy",function(d,i){return scaledPoints[i].y})})}else if(jitter!=="none"){d3panels.displayError('add_points: jitter should be "beeswarm", "random", or "none"')}}return prevchart.box().raise()};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.remove=function(){pointGroup.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.lodheatmap=function(chartOpts){var cellSelect,cells,celltip,chart,chrGap,colors,equalCells,height,hilitcolor,horizontal,margin,nullcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,width,xlab,xscale,ylab,ylim,yscale,zlim,zscale,zthresh;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:500;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:40,bottom:40};colors=(ref3=chartOpts!=null?chartOpts.colors:void 0)!=null?ref3:["slateblue","white","crimson"];nullcolor=(ref4=chartOpts!=null?chartOpts.nullcolor:void 0)!=null?ref4:"#e6e6e6";xlab=(ref5=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref5:null;ylab=(ref6=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref6:"";ylim=(ref7=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref7:null;zlim=(ref8=chartOpts!=null?chartOpts.zlim:void 0)!=null?ref8:null;zthresh=(ref9=chartOpts!=null?chartOpts.zthresh:void 0)!=null?ref9:null;horizontal=(ref10=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref10:false;hilitcolor=(ref11=chartOpts!=null?chartOpts.hilitcolor:void 0)!=null?ref11:"black";chrGap=(ref12=chartOpts!=null?chartOpts.chrGap:void 0)!=null?ref12:6;equalCells=(ref13=chartOpts!=null?chartOpts.equalCells:void 0)!=null?ref13:false;tipclass=(ref14=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref14:"tooltip";xscale=null;yscale=null;zscale=null;cells=null;celltip=null;svg=null;cellSelect=null;chart=function chart(selection,data){var cellg,celltipfunc,chr,direction,i,j,k,l,len,len1,len2,len3,len4,lod,m,myframe,n,n_lod,n_pos,o,pos,ref15,ref16,ref17,ref18,ref19,x,xmid_scaled,y,ylabels,ymid,ymid_scaled,yv,zmax,zmin;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:40,bottom:40});if(data.chr==null){d3panels.displayError("lodheatmap: data.chr is missing")}if(data.pos==null){d3panels.displayError("lodheatmap: data.pos is missing")}if(data.lod==null){d3panels.displayError("lodheatmap: data.lod is missing")}if(data.ycat!=null){data.y=function(){var results;results=[];for(i in data.ycat){results.push(i+1)}return results}()}if(data.y==null){data.ycat=function(){var results;results=[];for(i in data.lod[0]){results.push(i+1)}return results}();data.y=function(){var results;results=[];for(i in data.lod[0]){results.push(i+1)}return results}()}data.y=function(){var k,len,ref15,results;ref15=data.y;results=[];for(k=0,len=ref15.length;k<len;k++){yv=ref15[k];results.push(+yv)}return results}();n_pos=data.chr.length;n_lod=data.y.length;if(n_pos!==data.pos.length){d3panels.displayError("lodheatmap: data.pos.length ("+data.pos.length+") != data.chr.length ("+n_pos+")")}if(n_pos!==data.lod.length){d3panels.displayError("lodheatmap: data.lod.length ("+data.lod.length+") != data.chr.length ("+n_pos+")")}for(i in data.lod){if(data.lod[i].length!==data.y.length){d3panels.displayError("lodheatmap: data.lod["+i+"].length ("+data.lod[i].length+") != data.y.length ("+n_lod+")")}}if(data.poslabel!=null){if(data.poslabel.length!==n_pos){d3panels.displayError("lodheatmap: data.poslabel.length ("+data.poslabel.length+") != data.chr.length ("+n_pos+")")}}else{data.poslabel=function(){var results;results=[];for(i in data.chr){results.push(data.chr[i]+"@"+d3panels.formatAxis(data.pos)(data.pos[i]))}return results}()}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);if(equalCells){data.pos=[];ref15=data.chrname;for(k=0,len=ref15.length;k<len;k++){chr=ref15[k];data.pos=data.pos.concat(function(){var results;results=[];for(i in data.chr){if(data.chr[i]===chr){results.push(+i)}}return results}())}}data=d3panels.add_chrname_start_end(data);if(equalCells){chrGap=(width-margin.left-margin.right-2*data.chrname.length)/data.chr.length+2}data=d3panels.reorgLodData(data);ymid=d3panels.calc_midpoints(d3panels.pad_vector(data.y));chartOpts.ylim=ylim!=null?ylim:d3.extent(ymid);chartOpts.horizontal=horizontal;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.chrGap=chrGap;chartOpts.width=width;chartOpts.height=height;chartOpts.margin=margin;if(data.ycat!=null){chartOpts.yticks=data.y;chartOpts.yticklab=data.ycat}myframe=d3panels.chrpanelframe(chartOpts);myframe(selection,{chr:data.chrname,start:data.chrstart,end:data.chrend});svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();ylabels=myframe.ylabels();ymid_scaled=function(){var l,len1,results;results=[];for(l=0,len1=ymid.length;l<len1;l++){y=ymid[l];results.push(yscale(y))}return results}();xmid_scaled={};ref16=data.chrname;for(l=0,len1=ref16.length;l<len1;l++){chr=ref16[l];xmid_scaled[chr]=d3panels.calc_midpoints(d3panels.pad_vector(function(){var len2,m,ref17,results;ref17=data.posByChr[chr];results=[];for(m=0,len2=ref17.length;m<len2;m++){x=ref17[m];results.push(xscale[chr](x))}return results}(),(chrGap-2)/2))}zmin=d3panels.matrixMin(data.lod);zmax=d3panels.matrixMaxAbs(data.lod);zlim=zlim!=null?zlim:[-zmax,0,zmax];if(zlim.length!==colors.length){d3panels.displayError("lodheatmap: zlim.length ("+zlim.length+") != colors.length ("+colors.length+")")}zscale=d3.scaleLinear().domain(zlim).range(colors);zthresh=zthresh!=null?zthresh:zmin-1;cells=[];ref17=data.chrname;for(m=0,len2=ref17.length;m<len2;m++){chr=ref17[m];ref18=data.posByChr[chr];for(i=n=0,len3=ref18.length;n<len3;i=++n){pos=ref18[i];ref19=data.lodByChr[chr][i];for(j=o=0,len4=ref19.length;o<len4;j=++o){lod=ref19[j];if(Math.abs(lod)>=zthresh){cells.push({lod:lod,chr:chr,pos:pos,poslabel:data.poslabelByChr[chr][i],posindex:+i,lodindex:+j})}}}}d3panels.calc_chrcell_rect(cells,xmid_scaled,ymid_scaled);cellg=svg.append("g").attr("id","cells");cellSelect=cellg.selectAll("empty").data(cells).enter().append("rect").attr("x",function(d){if(horizontal){return d.top}return d.left}).attr("y",function(d){if(horizontal){return d.left}return d.top}).attr("width",function(d){if(horizontal){return d.height}return d.width}).attr("height",function(d){if(horizontal){return d.width}return d.height}).attr("class",function(d,i){return"cell"+i}).attr("fill",function(d){if(d.lod!=null){return zscale(d.lod)}else{return nullcolor}}).attr("stroke","none").attr("stroke-width","1").attr("shape-rendering","crispEdges").on("mouseover",function(d){d3.select(this).attr("stroke",hilitcolor).raise();if(data.ycat!=null){return svg.select("text#ylab"+d.lodindex).attr("opacity",1)}}).on("mouseout",function(d){d3.select(this).attr("stroke","none");if(data.ycat!=null){return svg.select("text#ylab"+d.lodindex).attr("opacity",0)}});if(data.ycat!=null){svg.selectAll("g#ylines").remove();ylabels.attr("opacity",0).attr("id",function(d,i){return"ylab"+i})}celltipfunc=function celltipfunc(d){var lodlabel,z;z=d3.format(".2f")(Math.abs(d.lod));lodlabel=data.ycat!=null?data.ycat[d.lodindex]:d3panels.formatAxis(data.y)(data.y[d.lodindex]);if(horizontal){return lodlabel+", "+d.poslabel+" → "+z}return d.poslabel+", "+lodlabel+" → "+z};direction=horizontal?"north":"east";celltip=d3panels.tooltip_create(d3.select("body"),cellg.selectAll("rect"),{direction:direction,tipclass:tipclass},celltipfunc);return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.zscale=function(){return yscale};chart.cells=function(){return cellSelect};chart.celltip=function(){return celltip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(celltip);return null};return chart};"use strict";d3panels.mapchart=function(chartOpts){var chart,horizontal,linecolor,linecolorhilit,linewidth,markerSelect,martip,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,shiftStart,svg,tickwidth,tipclass,v_over_h,xlab,xlineOpts,xscale,ylab,yscale;if(chartOpts==null){chartOpts={}}tickwidth=(ref=chartOpts!=null?chartOpts.tickwidth:void 0)!=null?ref:10;linecolor=(ref1=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref1:"slateblue";linecolorhilit=(ref2=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref2:"Orchid";linewidth=(ref3=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref3:3;xlab=(ref4=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref4:"Chromosome";ylab=(ref5=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref5:"Position (cM)";xlineOpts=(ref6=chartOpts!=null?chartOpts.xlineOpts:void 0)!=null?ref6:{color:"#cdcdcd",width:5};horizontal=(ref7=chartOpts!=null?chartOpts.horizontal:void 0)!=null?ref7:false;v_over_h=(ref8=chartOpts!=null?chartOpts.v_over_h:void 0)!=null?ref8:horizontal;shiftStart=(ref9=chartOpts!=null?chartOpts.shiftStart:void 0)!=null?ref9:false;tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;markerSelect=null;martip=null;svg=null;chart=function chart(selection,data){var chr,chrscale,direction,extentByChr,i,j,k,l,len,len1,markerpos,markers,minpos,myframe,n_chr,n_pos,pos,ref11,ref12,these_index,these_pos,tipfunc,x,xlim,xticklab,xticks,ylim;xlineOpts=d3panels.check_listarg_v_default(xlineOpts,{color:"#cdcdcd",width:5});if(data.chr==null){d3panels.displayError("mapchart: data.chr is missing")}if(data.pos==null){d3panels.displayError("mapchart: data.pos is missing")}if(data.marker==null){d3panels.displayError("mapchart: data.marker is missing")}n_pos=data.pos.length;if(data.chr.length!==n_pos){d3panels.displayError("mapchart: data.chr.length ("+data.chr.length+") != data.pos.length ("+n_pos+")")}if(data.marker.length!==n_pos){d3panels.displayError("mapchart: data.marker.length ("+data.marker.length+") != data.pos.length ("+n_pos+")")}if(data.chrname==null){data.chrname=d3panels.unique(data.chr)}data.chrname=d3panels.forceAsArray(data.chrname);data.adjpos=data.pos.slice(0);if(shiftStart){ref11=data.chrname;for(k=0,len=ref11.length;k<len;k++){chr=ref11[k];these_pos=function(){var results;results=[];for(i in data.pos){if(data.chr[i]===chr){results.push(data.pos[i])}}return results}();these_index=function(){var results;results=[];for(i in data.pos){if(data.chr[i]===chr){results.push(i)}}return results}();minpos=d3.min(these_pos);these_pos=function(){var l,len1,results;results=[];for(l=0,len1=these_pos.length;l<len1;l++){x=these_pos[l];results.push(x-minpos)}return results}();for(j in these_pos){data.adjpos[these_index[j]]=these_pos[j]}}}extentByChr={};ref12=data.chrname;for(l=0,len1=ref12.length;l<len1;l++){chr=ref12[l];pos=function(){var results;results=[];for(i in data.adjpos){if(data.chr[i]===chr){results.push(data.adjpos[i])}}return results}();extentByChr[chr]=d3.extent(pos)}ylim=ylim!=null?ylim:d3.extent(data.adjpos);n_chr=data.chrname.length;xlim=[.5,n_chr+.5];xticks=function(){var len2,m,ref13,results;ref13=d3.range(n_chr);results=[];for(m=0,len2=ref13.length;m<len2;m++){i=ref13[m];results.push(i+1)}return results}();xticklab=data.chrname;chartOpts.xNA=false;chartOpts.yNA=false;if(horizontal){chartOpts.xlim=ylim;chartOpts.ylim=xlim.reverse();chartOpts.xlineOpts=chartOpts.ylineOpts;chartOpts.ylineOpts=xlineOpts;chartOpts.xlab=ylab;chartOpts.ylab=xlab;chartOpts.xticks=chartOpts.yticks;chartOpts.yticks=xticks;chartOpts.nxticks=chartOpts.nyticks;chartOpts.xticklab=chartOpts.yticklab;chartOpts.yticklab=xticklab;chartOpts.v_over_h=v_over_h}else{chartOpts.xlim=xlim;chartOpts.ylim=ylim.reverse();chartOpts.xlineOpts=xlineOpts;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.xticks=xticks;chartOpts.xticklab=xticklab;chartOpts.v_over_h=v_over_h}myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();chrscale=function chrscale(chr){var chrpos;chrpos=data.chrname.indexOf(chr)+1;if(!horizontal){return xscale(chrpos)}return yscale(chrpos)};svg.append("g").attr("id","chromosomes").selectAll("empty").data(data.chrname).enter().append("line").attr("x1",function(d){if(horizontal){return xscale(extentByChr[d][0])}return chrscale(d)}).attr("x2",function(d){if(horizontal){return xscale(extentByChr[d][1])}return chrscale(d)}).attr("y1",function(d){if(horizontal){return chrscale(d)}return yscale(extentByChr[d][0])}).attr("y2",function(d){if(horizontal){return chrscale(d)}return yscale(extentByChr[d][1])}).attr("fill","none").attr("stroke",linecolor).attr("stroke-width",linewidth).attr("shape-rendering","crispEdges").style("pointer-events","none");markerpos={};for(i in data.marker){markerpos[data.marker[i]]=d3.format(".1f")(data.pos[i])}markers=svg.append("g").attr("id","points");markerSelect=markers.selectAll("empty").data(data.marker).enter().append("line").attr("x1",function(d,i){if(horizontal){return xscale(data.adjpos[i])}return chrscale(data.chr[i])-tickwidth}).attr("x2",function(d,i){if(horizontal){return xscale(data.adjpos[i])}return chrscale(data.chr[i])+tickwidth}).attr("y1",function(d,i){if(horizontal){return chrscale(data.chr[i])-tickwidth}return yscale(data.adjpos[i])}).attr("y2",function(d,i){if(horizontal){return chrscale(data.chr[i])+tickwidth}return yscale(data.adjpos[i])}).attr("id",function(d){return d}).attr("fill","none").attr("stroke",linecolor).attr("stroke-width",linewidth).attr("shape-rendering","crispEdges").on("mouseover.paneltip",function(d){return d3.select(this).attr("stroke",linecolorhilit)}).on("mouseout.paneltip",function(){return d3.select(this).attr("stroke",linecolor)});tipfunc=function tipfunc(d,i){return d+" ("+markerpos[d]+")"};direction=horizontal?"north":"east";martip=d3panels.tooltip_create(d3.select("body"),markers.selectAll("line"),{direction:direction,tipclass:tipclass},tipfunc);return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.markerSelect=function(){return markerSelect};chart.martip=function(){return martip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(martip);return null};return chart};"use strict";d3panels.scatterplot=function(chartOpts){var chart,indtip,jitter,pointcolor,points,pointsize,pointstroke,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,xNA,xNA_size,xlim,xscale,yNA,yNA_size,ylim,yscale;if(chartOpts==null){chartOpts={}}xNA=(ref=chartOpts!=null?chartOpts.xNA:void 0)!=null?ref:{handle:true,force:false};yNA=(ref1=chartOpts!=null?chartOpts.yNA:void 0)!=null?ref1:{handle:true,force:false};xNA_size=(ref2=chartOpts!=null?chartOpts.xNA_size:void 0)!=null?ref2:{width:20,gap:10};yNA_size=(ref3=chartOpts!=null?chartOpts.yNA_size:void 0)!=null?ref3:{width:20,gap:10};xlim=(ref4=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref4:null;ylim=(ref5=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref5:null;pointcolor=(ref6=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref6:null;pointstroke=(ref7=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref7:"black";pointsize=(ref8=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref8:3;jitter=(ref9=chartOpts!=null?chartOpts.jitter:void 0)!=null?ref9:"beeswarm";tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;xNA=xNA;yNA=yNA;points=null;indtip=null;svg=null;chart=function chart(selection,data){var addpts,myframe,x,y;xNA=d3panels.check_listarg_v_default(xNA,{handle:true,force:false});yNA=d3panels.check_listarg_v_default(yNA,{handle:true,force:false});xNA_size=d3panels.check_listarg_v_default(xNA,{width:20,gap:10});yNA_size=d3panels.check_listarg_v_default(yNA,{width:20,gap:10});if(data.x==null){d3panels.displayError("scatterplot: data.x is missing")}if(data.y==null){d3panels.displayError("scatterplot: data.y is missing")}x=d3panels.missing2null(data.x);y=d3panels.missing2null(data.y);if(x.length!==y.length){d3panels.displayError("scatterplot: x.length ("+x.length+") != y.length ("+y.length+")")}xNA.handle=xNA.force||xNA.handle&&!x.every(function(v){return v!=null});yNA.handle=yNA.force||yNA.handle&&!y.every(function(v){return v!=null});xlim=xlim!=null?xlim:d3panels.pad_ylim(d3.extent(x));ylim=ylim!=null?ylim:d3panels.pad_ylim(d3.extent(y));chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=xNA.handle;chartOpts.yNA=yNA.handle;chartOpts.xNA_size=xNA_size;chartOpts.yNA_size=yNA_size;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();addpts=d3panels.add_points({pointcolor:pointcolor,pointstroke:pointstroke,pointsize:pointsize,jitter:jitter,tipclass:tipclass});addpts(myframe,{x:x,y:y,indID:data.indID,group:data.group});points=addpts.points();return indtip=addpts.indtip()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.xNA=function(){return xNA.handle};chart.yNA=function(){return yNA.handle};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.trichart=function(chartOpts){var boxcolor,boxwidth,chart,gridcolor,gridlines,gridwidth,height,indtip,labelpos,labels,margin,pointcolor,points,pointsize,pointstroke,pscale,rectcolor,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,svg,tipclass,title,titlepos,width,xscale,yscale;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:600;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:520;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:60,top:40,right:60,bottom:10};labelpos=(ref3=chartOpts!=null?chartOpts.labelpos:void 0)!=null?ref3:10;titlepos=(ref4=chartOpts!=null?chartOpts.titlepos:void 0)!=null?ref4:20;title=(ref5=chartOpts!=null?chartOpts.title:void 0)!=null?ref5:"";labels=(ref6=chartOpts!=null?chartOpts.labels:void 0)!=null?ref6:["(1,0,0)","(0,1,0)","(0,0,1)"];rectcolor=(ref7=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref7:"#e6e6e6";boxcolor=(ref8=chartOpts!=null?chartOpts.boxcolor:void 0)!=null?ref8:"black";boxwidth=(ref9=chartOpts!=null?chartOpts.boxwidth:void 0)!=null?ref9:2;pointcolor=(ref10=chartOpts!=null?chartOpts.pointcolor:void 0)!=null?ref10:null;pointstroke=(ref11=chartOpts!=null?chartOpts.pointstroke:void 0)!=null?ref11:"black";pointsize=(ref12=chartOpts!=null?chartOpts.pointsize:void 0)!=null?ref12:3;gridlines=(ref13=chartOpts!=null?chartOpts.gridlines:void 0)!=null?ref13:0;gridcolor=(ref14=chartOpts!=null?chartOpts.gridcolor:void 0)!=null?ref14:"white";gridwidth=(ref15=chartOpts!=null?chartOpts.gridwidth:void 0)!=null?ref15:1;tipclass=(ref16=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref16:"tooltip";xscale=null;yscale=null;pscale=null;points=null;indtip=null;svg=null;chart=function chart(selection,data){var d,first,flag_length_not_3,flag_out_of_range,flag_sum_not_1,frame,framefunc,g,gr,group,i,indID,indices,j,len,n,ngroup,p,p1,p2,p3,p4,plot_height,plot_width,ref17,ref18,second,sum,v,vertices,vv,xlim,xy,ylim;margin=d3panels.check_listarg_v_default(margin,{left:60,top:40,right:60,bottom:10});if(data.p==null){d3panels.displayError("trichart: data.p is missing")}p=function(){var j,len,ref17,results;ref17=data.p;results=[];for(j=0,len=ref17.length;j<len;j++){v=ref17[j];results.push(d3panels.missing2null(v))}return results}();flag_length_not_3=false;flag_sum_not_1=false;flag_out_of_range=false;for(j=0,len=p.length;j<len;j++){v=p[j];if(v.length!==3){flag_length_not_3=true}sum=d3panels.sumArray(v);if(d3panels.abs(sum-1)>1e-6){flag_sum_not_1}if(d3panels.sumArray(function(){var k,len1,results;results=[];for(k=0,len1=v.length;k<len1;k++){vv=v[k];results.push(vv<0||vv>1)}return results}())>0){flag_out_of_range=true}}if(flag_length_not_3){d3panels.displayError("trichart: points not all of length 3")}if(flag_sum_not_1){d3panels.displayError("trichart: points not all summing to 1")}if(flag_out_of_range){d3panels.displayError("trichart: points not all in [0,1]")}n=p.length;indID=(ref17=data!=null?data.indID:void 0)!=null?ref17:function(){var results;results=[];for(i in p){results.push(+i+1)}return results}();if(indID.length!==n){d3panels.displayError("trichart: data.indID.length ("+indID.length+") != data.p.length ("+n+")")}group=(ref18=data!=null?data.group:void 0)!=null?ref18:function(){var results;results=[];for(i in p){results.push(1)}return results}();group=d3panels.expand2vector(group,n);ngroup=d3.max(group);group=function(){var k,len1,results;results=[];for(k=0,len1=group.length;k<len1;k++){g=group[k];results.push(g!=null?g-1:g)}return results}();if(d3panels.sumArray(function(){var k,len1,results;results=[];for(k=0,len1=group.length;k<len1;k++){g=group[k];results.push(g<0||g>ngroup-1)}return results}())>0){d3panels.displayError("add_points: group values out of range");console.log("ngroup: "+ngroup);console.log("distinct groups: "+d3panels.unique(group))}if(group.length!==n){d3panels.displayError("trichart: data.group.length ("+group.length+") != data.p.length ("+n+")")}pointcolor=pointcolor!=null?pointcolor:d3panels.selectGroupColors(ngroup,"dark");pointcolor=d3panels.expand2vector(pointcolor,ngroup);if(pointcolor.length<ngroup){d3panels.displayError("add_points: pointcolor.length ("+pointcolor.length+") < ngroup ("+ngroup+")")}xlim=[0,2/Math.sqrt(3)];ylim=[0,1];plot_height=height-margin.top-margin.bottom;plot_width=width-margin.left-margin.right;if(plot_height>plot_width/xlim[1]){d=plot_height-plot_width/xlim[1];margin.top+=d/2;margin.bottom+=d/2;plot_height-=d}else{d=plot_width-plot_height*xlim[1];margin.left+=d/2;margin.right+=d/2;plot_width-=d}xscale=d3.scaleLinear().domain(xlim).range([margin.left,margin.left+plot_width]);yscale=d3.scaleLinear().domain(ylim).range([plot_height+margin.top,margin.top]);pscale=function pscale(p){sum=d3panels.sumArray(p);return{x:xscale((p[0]*2+p[1])/Math.sqrt(3)/sum),y:yscale(p[1]/sum)}};xy=function(){var k,len1,results;results=[];for(k=0,len1=p.length;k<len1;k++){v=p[k];results.push({x:(v[0]*2+v[1])/Math.sqrt(3),y:v[1]})}return results}();svg=selection.append("svg");svg.attr("width",width).attr("height",height).attr("class","d3panels");frame=svg.append("g").attr("id","frame");vertices=[{x:xlim[0],y:ylim[0]},{x:xlim[1]/2,y:ylim[1]},{x:xlim[1],y:ylim[0]}];framefunc=d3.line().x(function(d){return xscale(vertices[d].x)}).y(function(d){return yscale(vertices[d].y)});indices=function(){var results;results=[];for(i in vertices){results.push(+i)}return results}().concat(0);frame.append("path").datum(indices).attr("d",framefunc).attr("fill",rectcolor).attr("stroke",boxcolor).attr("stroke-width",boxwidth);if(gridlines>0){gr=function(){var results=[];for(var k=1;1<=gridlines?k<=gridlines:k>=gridlines;1<=gridlines?k++:k--){results.push(k)}return results}.apply(this).map(function(i){return i/(gridlines+1)});p1=gr.map(function(x){return[x,0,1-x]});p2=gr.map(function(x){return[x,1-x,0]});p3=gr.map(function(x){return[0,1-x,x]});p4=gr.map(function(x){return[1-x,0,x]});first=p1.concat(p2).concat(p3);second=p2.concat(p3).concat(p4);g=frame.append("g").attr("class","gridlines").selectAll("empty").data(first).enter().append("line").attr("x1",function(d){return pscale(d).x}).attr("y1",function(d){return pscale(d).y}).attr("x2",function(d,i){return pscale(second[i]).x}).attr("y2",function(d,i){return pscale(second[i]).y}).attr("stroke",gridcolor).attr("stroke-width",gridwidth).attr("shape-rendering","crispEdges").style("pointer-events","none").attr("fill","none");frame.append("path").datum(indices).attr("d",framefunc).attr("fill","none").attr("stroke",boxcolor).attr("stroke-width",boxwidth)}frame.append("g").attr("class","title").append("text").text(title).attr("x",plot_width/2+margin.left).attr("y",margin.top-titlepos);frame.append("g").attr("id","labels").selectAll("empty").data(vertices).enter().append("text").attr("x",function(d,i){return xscale(d.x)+[-1,+1,+1][i]*labelpos}).attr("y",function(d){return yscale(d.y)}).style("dominant-baseline","middle").style("text-anchor",function(d,i){return["end","start","start"][i]}).text(function(d,i){return labels[i]});points=svg.append("g").attr("id","points").selectAll("empty").data(p).enter().append("circle").attr("r",pointsize).attr("cx",function(d){return pscale(d).x}).attr("cy",function(d){return pscale(d).y}).attr("fill",function(d,i){return pointcolor[group[i]]}).attr("stroke",pointstroke).attr("stroke-width",1);return indtip=d3panels.tooltip_create(d3.select("body"),points,{tipclass:tipclass},function(d,i){return indID[i]})};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.pscale=function(){return pscale};chart.points=function(){return points};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_destroy(indtip);return null};return chart};"use strict";d3panels.histchart=function(chartOpts){var chart,curves,density,indtip,linecolor,linecolorhilit,linewidth,linewidthhilit,ref,ref1,ref10,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,rotate_ylab,svg,tipclass,xlab,xlim,xscale,ylab,ylim,yscale;if(chartOpts==null){chartOpts={}}xlim=(ref=chartOpts!=null?chartOpts.xlim:void 0)!=null?ref:null;ylim=(ref1=chartOpts!=null?chartOpts.ylim:void 0)!=null?ref1:null;xlab=(ref2=chartOpts!=null?chartOpts.xlab:void 0)!=null?ref2:"";ylab=(ref3=chartOpts!=null?chartOpts.ylab:void 0)!=null?ref3:"";rotate_ylab=(ref4=chartOpts!=null?chartOpts.rotate_ylab:void 0)!=null?ref4:null;linecolor=(ref5=chartOpts!=null?chartOpts.linecolor:void 0)!=null?ref5:null;linecolorhilit=(ref6=chartOpts!=null?chartOpts.linecolorhilit:void 0)!=null?ref6:null;linewidth=(ref7=chartOpts!=null?chartOpts.linewidth:void 0)!=null?ref7:2;linewidthhilit=(ref8=chartOpts!=null?chartOpts.linewidthhilit:void 0)!=null?ref8:2;density=(ref9=chartOpts!=null?chartOpts.density:void 0)!=null?ref9:true;tipclass=(ref10=chartOpts!=null?chartOpts.tipclass:void 0)!=null?ref10:"tooltip";xscale=null;yscale=null;curves=null;indtip=null;svg=null;chart=function chart(selection,data){var add_curves,breaks,brlim,d,f,freq,i,j,k,l,len,len1,maxn,maxpos,myframe,n_ind,p,path_data,path_x,path_y,pt,ref11,x,xv,xx;if(data.x==null){d3panels.displayError("histchart: data.x is missing")}x=data.x;data.group=function(){var results;results=[];for(i in x){results.push(+i+1)}return results}();n_ind=x.length;if(data.breaks==null){maxn=d3.max(function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];results.push(xv.length)}return results}());data.breaks=[2*Math.ceil(Math.sqrt(maxn)+1)]}breaks=d3panels.forceAsArray(data.breaks);xlim=xlim!=null?xlim:d3panels.matrixExtent(x);if(breaks.length===1){breaks=d3panels.calc_breaks(breaks[0],xlim[0],xlim[1])}brlim=[d3.min(breaks)-1e-6,d3.max(breaks)+1e-6];x=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xx=x[k];results.push(function(){var l,len1,results1;results1=[];for(l=0,len1=xx.length;l<len1;l++){xv=xx[l];if(xv>=brlim[0]&xv<=brlim[1]){results1.push(xv)}}return results1}())}return results}();freq=function(){var k,len,results;results=[];for(k=0,len=x.length;k<len;k++){xv=x[k];results.push(d3panels.calc_freq(xv,breaks,!density))}return results}();maxpos=[];for(k=0,len=freq.length;k<len;k++){f=freq[k];pt={x:breaks[1],y:f[0]};ref11=d3.range(f.length);for(l=0,len1=ref11.length;l<len1;l++){j=ref11[l];if(f[j]>pt.y){pt.y=f[j];pt.x=breaks[j+1]}}maxpos.push(pt)}ylim=ylim!=null?ylim:[0,d3panels.matrixMax(freq)*1.05];chartOpts.xlim=xlim;chartOpts.ylim=ylim;chartOpts.xNA=false;chartOpts.yNA=false;chartOpts.xlab=xlab;chartOpts.ylab=ylab;chartOpts.rotate_ylab=rotate_ylab;myframe=d3panels.panelframe(chartOpts);myframe(selection);svg=myframe.svg();xscale=myframe.xscale();yscale=myframe.yscale();path_data=function(){var len2,m,results;results=[];for(m=0,len2=freq.length;m<len2;m++){f=freq[m];results.push(d3panels.calc_hist_path(f,breaks))}return results}();path_x=function(){var len2,m,results;results=[];for(m=0,len2=path_data.length;m<len2;m++){p=path_data[m];results.push(function(){var len3,n,results1;results1=[];for(n=0,len3=p.length;n<len3;n++){d=p[n];results1.push(d.x)}return results1}())}return results}();path_y=function(){var len2,m,results;results=[];for(m=0,len2=path_data.length;m<len2;m++){p=path_data[m];results.push(function(){var len3,n,results1;results1=[];for(n=0,len3=p.length;n<len3;n++){d=p[n];results1.push(d.y)}return results1}())}return results}();add_curves=d3panels.add_curves({linecolor:linecolor,linecolorhilit:linecolorhilit,linewidth:linewidth,linewidthhilit:linewidthhilit,tipclass:tipclass});add_curves(myframe,{x:path_x,y:path_y,indID:data.indID,group:data.group});curves=add_curves.curves();indtip=add_curves.indtip();return myframe.box().raise()};chart.xscale=function(){return xscale};chart.yscale=function(){return yscale};chart.curves=function(){return curves};chart.indtip=function(){return indtip};chart.svg=function(){return svg};chart.remove=function(){svg.remove();d3panels.tooltip_dstroy(indtip);return null};return chart};"use strict";d3panels.slider=function(chartOpts){var buttoncolor,buttondotcolor,buttondotsize,buttonround,buttonsize,buttonstroke,_chart,height,margin,nticks,rectcolor,rectheight,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,slider_svg,stopindex,textsize,tickgap,tickheight,ticks,ticks_at_stops,value,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:80;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:25,right:25,inner:0,top:40,bottom:40};rectheight=(ref3=chartOpts!=null?chartOpts.rectheight:void 0)!=null?ref3:10;rectcolor=(ref4=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref4:"#ccc";buttonsize=(ref5=chartOpts!=null?chartOpts.buttonsize:void 0)!=null?ref5:rectheight*2;buttoncolor=(ref6=chartOpts!=null?chartOpts.buttoncolor:void 0)!=null?ref6:"#eee";buttonstroke=(ref7=chartOpts!=null?chartOpts.buttonstroke:void 0)!=null?ref7:"black";buttonround=(ref8=chartOpts!=null?chartOpts.buttonround:void 0)!=null?ref8:buttonsize*.2;buttondotcolor=(ref9=chartOpts!=null?chartOpts.buttondotcolor:void 0)!=null?ref9:"slateblue";buttondotsize=(ref10=chartOpts!=null?chartOpts.buttondotsize:void 0)!=null?ref10:buttonsize/4;tickheight=(ref11=chartOpts!=null?chartOpts.tickheight:void 0)!=null?ref11:10;tickgap=(ref12=chartOpts!=null?chartOpts.tickgap:void 0)!=null?ref12:tickheight/2;textsize=(ref13=chartOpts!=null?chartOpts.textsize:void 0)!=null?ref13:14;nticks=(ref14=chartOpts!=null?chartOpts.nticks:void 0)!=null?ref14:5;ticks=(ref15=chartOpts!=null?chartOpts.ticks:void 0)!=null?ref15:null;ticks_at_stops=(ref16=chartOpts!=null?chartOpts.ticks_at_stops:void 0)!=null?ref16:true;value=0;stopindex=0;slider_svg=null;_chart=function chart(selection,callback,range,stops,initial_value){var button,clamp_pixels,dragged,end_drag,xcscale,xscale;margin=d3panels.check_listarg_v_default(margin,{left:25,right:25,inner:0,top:40,bottom:40});margin.left+=margin.inner;margin.right+=margin.inner;if(range==null){range=[margin.left,width-margin.right]}if(margin.top!=null&&margin.top+margin.bottom>0){margin.top=height*margin.top/(margin.top+margin.bottom)}else{margin.top=height/2}if(initial_value!=null){value=initial_value;if(value<range[0]){value=range[0]}if(value>range[1]){value=range[1]}if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops)}if(stops!=null){value=stops[stopindex]}}else{if(stops!=null){stopindex=Math.floor(Math.random()*stops.length);value=stops[stopindex]}else{value=(range[1]-range[0])*Math.random()+range[0]}}slider_svg=selection.insert("svg").attr("height",height).attr("width",width);xcscale=d3.scaleLinear().range([margin.left,width-margin.right]).domain(range).clamp(true);xscale=function xscale(d){if(stops!=null){return xcscale(stops[d3panels.index_of_nearest(d,stops)])}return xcscale(d)};clamp_pixels=function clamp_pixels(pixels,interval){if(pixels<interval[0]){return interval[0]}if(pixels>interval[1]){return interval[1]}return pixels};slider_svg.insert("rect").attr("x",margin.left).attr("y",margin.top-rectheight/2).attr("rx",rectheight*.3).attr("ry",rectheight*.3).attr("width",width-margin.left-margin.right).attr("height",rectheight).attr("fill",rectcolor);if(ticks==null){ticks=xcscale.ticks(nticks)}slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top+rectheight/2+tickgap).attr("y2",margin.top+rectheight/2+tickgap+tickheight).attr("stroke","black").attr("shape-rendering","crispEdges");slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x",function(d){return xcscale(d)}).attr("y",margin.top+rectheight/2+tickgap*2+tickheight).text(function(d){return d}).style("font-size",textsize).style("dominant-baseline","hanging").style("text-anchor","middle").style("pointer-events","none").style("-webkit-user-select","none").style("-moz-user-select","none").style("-ms-user-select","none");if(stops!=null&&ticks_at_stops){slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top-rectheight/2-tickgap).attr("y2",margin.top-rectheight/2-tickgap-tickheight).attr("stroke","black").attr("shape-rendering","crispEdges")}button=slider_svg.insert("g").attr("id","button").attr("transform","translate("+xscale(value)+",0)");button.insert("rect").attr("x",-buttonsize/2).attr("y",margin.top-buttonsize/2).attr("height",buttonsize).attr("width",buttonsize).attr("rx",buttonround).attr("ry",buttonround).attr("stroke",buttonstroke).attr("stroke-width",2).attr("fill",buttoncolor);button.insert("circle").attr("cx",0).attr("cy",margin.top).attr("r",buttondotsize).attr("fill",buttondotcolor);dragged=function dragged(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value=xcscale.invert(clamped_pixels);d3.select(this).attr("transform","translate("+xcscale(value)+",0)");if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops);value=stops[stopindex]}if(callback!=null){return callback(_chart)}};end_drag=function end_drag(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value=xcscale.invert(clamped_pixels);if(stops!=null){stopindex=d3panels.index_of_nearest(value,stops);value=stops[stopindex]}if(callback!=null){callback(_chart)}return d3.select(this).attr("transform","translate("+xcscale(value)+",0)")};button.call(d3.drag().on("drag",dragged).on("end",end_drag));if(callback!=null){return callback(_chart)}};_chart.value=function(){return value};_chart.stopindex=function(){return stopindex};_chart.remove=function(){return slider_svg.remove()};return _chart};"use strict";d3panels.double_slider=function(chartOpts){var buttoncolor,buttondotcolor,buttondotsize,buttonround,buttonsize,buttonstroke,_chart,height,margin,nticks,rectcolor,rectheight,ref,ref1,ref10,ref11,ref12,ref13,ref14,ref15,ref16,ref2,ref3,ref4,ref5,ref6,ref7,ref8,ref9,slider_svg,stopindex,textsize,tickgap,tickheight,ticks,ticks_at_stops,value,width;if(chartOpts==null){chartOpts={}}width=(ref=chartOpts!=null?chartOpts.width:void 0)!=null?ref:800;height=(ref1=chartOpts!=null?chartOpts.height:void 0)!=null?ref1:80;margin=(ref2=chartOpts!=null?chartOpts.margin:void 0)!=null?ref2:{left:25,right:25,inner:0,top:40,bottom:40};rectheight=(ref3=chartOpts!=null?chartOpts.rectheight:void 0)!=null?ref3:10;rectcolor=(ref4=chartOpts!=null?chartOpts.rectcolor:void 0)!=null?ref4:"#ccc";buttonsize=(ref5=chartOpts!=null?chartOpts.buttonsize:void 0)!=null?ref5:rectheight*2;buttoncolor=(ref6=chartOpts!=null?chartOpts.buttoncolor:void 0)!=null?ref6:"#eee";buttonstroke=(ref7=chartOpts!=null?chartOpts.buttonstroke:void 0)!=null?ref7:"black";buttonround=(ref8=chartOpts!=null?chartOpts.buttonround:void 0)!=null?ref8:buttonsize*.2;buttondotcolor=(ref9=chartOpts!=null?chartOpts.buttondotcolor:void 0)!=null?ref9:["slateblue","orchid"];buttondotsize=(ref10=chartOpts!=null?chartOpts.buttondotsize:void 0)!=null?ref10:buttonsize/4;tickheight=(ref11=chartOpts!=null?chartOpts.tickheight:void 0)!=null?ref11:10;tickgap=(ref12=chartOpts!=null?chartOpts.tickgap:void 0)!=null?ref12:tickheight/2;textsize=(ref13=chartOpts!=null?chartOpts.textsize:void 0)!=null?ref13:14;nticks=(ref14=chartOpts!=null?chartOpts.nticks:void 0)!=null?ref14:5;ticks=(ref15=chartOpts!=null?chartOpts.ticks:void 0)!=null?ref15:null;ticks_at_stops=(ref16=chartOpts!=null?chartOpts.ticks_at_stops:void 0)!=null?ref16:true;value=[0,0];stopindex=[0,0];slider_svg=null;if(!Array.isArray(buttoncolor)){buttoncolor=[buttoncolor,buttoncolor]}if(!Array.isArray(buttonstroke)){buttonstroke=[buttonstroke,buttonstroke]}if(!Array.isArray(buttondotcolor)){buttondotcolor=[buttondotcolor,buttondotcolor]}_chart=function chart(selection,callback1,callback2,range,stops,initial_value){var buttons,callbacks,clamp_pixels,dragged,end_drag,start_drag,xcscale,xscale;margin=d3panels.check_listarg_v_default(margin,{left:25,right:25,inner:0,top:40,bottom:40});callbacks=[callback1,callback2];margin.left+=margin.inner;margin.right+=margin.inner;if(range==null){range=[margin.left,width-margin.right]}if(margin.top!=null&&margin.top+margin.bottom>0){margin.top=height*margin.top/(margin.top+margin.bottom)}else{margin.top=height/2}if(initial_value!=null){value=initial_value.map(function(d){if(d<range[0]){return range[0]}if(d>range[1]){return range[1]}return d});if(stops!=null){stopindex=value.map(function(d){return d3panels.index_of_nearest(d,stops)})}if(stops!=null){value=stopindex.map(function(i){return stops[i]})}}else{if(stops!=null){stopindex=[0,1].map(function(i){return Math.floor(Math.random()*stops.length)});value=stopindex.map(function(i){return stops[i]})}else{value=[0,1].map(function(i){return(range[1]-range[0])*Math.random()+range[0]})}}slider_svg=selection.insert("svg").attr("height",height).attr("width",width);xcscale=d3.scaleLinear().range([margin.left,width-margin.right]).domain(range).clamp(true);xscale=function xscale(d){if(stops!=null){return xcscale(stops[d3panels.index_of_nearest(d,stops)])}return xcscale(d)};clamp_pixels=function clamp_pixels(pixels,interval){if(pixels<interval[0]){return interval[0]}if(pixels>interval[1]){return interval[1]}return pixels};slider_svg.insert("rect").attr("x",margin.left).attr("y",margin.top-rectheight/2).attr("rx",rectheight*.3).attr("ry",rectheight*.3).attr("width",width-margin.left-margin.right).attr("height",rectheight).attr("fill",rectcolor);if(ticks==null){ticks=xcscale.ticks(nticks)}slider_svg.selectAll("empty").data(ticks).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top+rectheight/2+tickgap).attr("y2",margin.top+rectheight/2+tickgap+tickheight).attr("stroke","black").attr("shape-rendering","crispEdges");slider_svg.selectAll("empty").data(ticks).enter().insert("text").attr("x",function(d){return xcscale(d)}).attr("y",margin.top+rectheight/2+tickgap*2+tickheight).text(function(d){return d}).style("font-size",textsize).style("dominant-baseline","hanging").style("text-anchor","middle").style("pointer-events","none").style("-webkit-user-select","none").style("-moz-user-select","none").style("-ms-user-select","none");if(stops!=null&&ticks_at_stops){slider_svg.selectAll("empty").data(stops).enter().insert("line").attr("x1",function(d){return xcscale(d)}).attr("x2",function(d){return xcscale(d)}).attr("y1",margin.top-rectheight/2-tickgap).attr("y2",margin.top-rectheight/2-tickgap-tickheight).attr("stroke","black").attr("shape-rendering","crispEdges")}buttons=[0,1].map(function(i){return slider_svg.insert("g").attr("id","button"+(i+1)).attr("transform",function(d){return"translate("+xscale(value[i])+",0)"})});[0,1].map(function(i){buttons[i].insert("rect").attr("x",-buttonsize/2).attr("y",margin.top-buttonsize/2).attr("height",buttonsize).attr("width",buttonsize).attr("rx",buttonround).attr("ry",buttonround).attr("stroke",buttonstroke[i]).attr("stroke-width",2).attr("fill",buttoncolor[i]);return buttons[i].insert("circle").attr("cx",0).attr("cy",margin.top).attr("r",buttondotsize).attr("fill",buttondotcolor[i])});start_drag=function start_drag(i){return function(d){return buttons[i].raise()}};dragged=function dragged(i){return function(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value[i]=xcscale.invert(clamped_pixels);d3.select(this).attr("transform","translate("+xcscale(value[i])+",0)");if(stops!=null){stopindex[i]=d3panels.index_of_nearest(value[i],stops);value[i]=stops[stopindex[i]]}if(callbacks[i]!=null){return callbacks[i](_chart)}}};end_drag=function end_drag(i){return function(d){var clamped_pixels,pixel_value;pixel_value=d3.event.x;clamped_pixels=clamp_pixels(pixel_value,[margin.left,width-margin.right]);value[i]=xcscale.invert(clamped_pixels);if(stops!=null){stopindex[i]=d3panels.index_of_nearest(value[i],stops);value[i]=stops[stopindex[i]]}if(callbacks[i]!=null){callbacks[i](_chart)}return d3.select(this).attr("transform","translate("+xcscale(value[i])+",0)")}};return[0,1].map(function(i){buttons[i].call(d3.drag().on("start",start_drag(i)).on("drag",dragged(i)).on("end",end_drag(i)));if(callbacks[i]!=null){return callbacks[i](_chart)}})};_chart.value=function(){return value};_chart.stopindex=function(){return stopindex};_chart.remove=function(){return slider_svg.remove()};return _chart};"use strict";d3panels.tooltip_create=function(selection,objects,options,tooltip_func){var direction,fill,fontcolor,fontsize,in_duration,out_duration,pad,ref,ref1,ref2,ref3,ref4,tipclass,tipdiv,tipgroup,triChar,tridiv;tipclass=(ref=options!=null?options.tipclass:void 0)!=null?ref:"d3panels-tooltip";direction=(ref1=options!=null?options.direction:void 0)!=null?ref1:"east";out_duration=(ref2=options!=null?options.out_duration:void 0)!=null?ref2:1e3;in_duration=(ref3=options!=null?options.in_duration:void 0)!=null?ref3:0;pad=(ref4=options!=null?options.pad:void 0)!=null?ref4:8;fill=options!=null?options.fill:void 0;fontcolor=options!=null?options.fontcolor:void 0;fontsize=options!=null?options.fontsize:void 0;tipgroup=selection.append("g").attr("class","d3panels-tooltip "+tipclass).style("opacity",0).datum({direction:direction,pad:pad});tipdiv=tipgroup.append("div").attr("class","d3panels-tooltip "+tipclass);if(direction==="east"){triChar="â—€"}else if(direction==="west"){triChar="â–¶"}else if(direction==="north"){triChar="â–¼"}else if(direction==="south"){triChar="â–²"}else{d3panels.displayError("tooltip_create: invalid direction ("+direction+")")}tridiv=tipgroup.append("div").attr("class","d3panels-tooltip-tri "+tipclass).html(triChar);if(fill!=null){tipdiv.style("background",fill)}if(fontcolor!=null){tipdiv.style("color",fontcolor)}if(fontsize!=null){tipdiv.style("font-size",fontsize+"px")}if(fill!=null){tridiv.style("color",fill)}if(fontsize!=null){tridiv.style("font-size",fontsize+"px")}objects.on("mouseover."+tipclass,function(d,i){var mouseX,mouseY;mouseX=d3.event.pageX*1;mouseY=d3.event.pageY*1;tipdiv.html(tooltip_func(d,i));d3panels.tooltip_move(tipgroup,mouseX,mouseY);return d3panels.tooltip_show(tipgroup,in_duration)});objects.on("mouseout."+tipclass,function(d){return d3panels.tooltip_hide(tipgroup,out_duration)});return tipgroup};d3panels.tooltip_move=function(tipgroup,x,y){var direction,divpad,fontsize,pad,posX,posY,shiftX,shiftY,tipbox_height,tipbox_width,tipdiv,triX,triY,tridiv;tipdiv=tipgroup.select("div.d3panels-tooltip");tridiv=tipgroup.select("div.d3panels-tooltip-tri");tipbox_height=tipdiv.node().getBoundingClientRect().height*1;tipbox_width=tipdiv.node().getBoundingClientRect().width*1;fontsize=tridiv.style("font-size").replace("px","")*1;pad=tipgroup.datum().pad*1+fontsize;direction=tipgroup.datum().direction;shiftX=shiftY=0;if(direction==="east"){posX=x+pad;posY=y-tipbox_height/2;divpad=tipdiv.style("padding-left").replace("px","")*1;shiftX=-fontsize-divpad;shiftY=tipbox_height/2-fontsize/2}else if(direction==="west"){posX=x-tipbox_width*1-pad;posY=y-tipbox_height/2;divpad=tipdiv.style("padding-right").replace("px","")*1;shiftX=tipbox_width-fontsize+divpad;shiftY=tipbox_height/2-fontsize/2}else if(direction==="north"){posX=x-tipbox_width/2;posY=y-tipbox_height-pad;divpad=tipdiv.style("padding-bottom").replace("px","")*1;shiftX=tipbox_width/2-fontsize;shiftY=tipbox_height+divpad/2-fontsize/2}else if(direction==="south"){posX=x-tipbox_width/2;posY=y+pad;divpad=tipdiv.style("padding-top").replace("px","")*1;shiftX=+tipbox_width/2-fontsize;shiftY=-fontsize}tipdiv.style("left",posX+"px").style("top",posY+"px");triX=posX+shiftX;triY=posY+shiftY;return tridiv.style("left",triX+"px").style("top",triY+"px").style("width",tipbox_width).style("height",tipbox_height)};d3panels.tooltip_text=function(tipgroup,text){return tipgroup.select("div.d3panels-tooltip").html(text)};d3panels.tooltip_show=function(tipgroup,duration){return tipgroup.transition().duration(duration).style("opacity",1)};d3panels.tooltip_hide=function(tipgroup,duration){return tipgroup.transition().duration(duration).style("opacity",0)};d3panels.tooltip_destroy=function(tipgroup){return tipgroup.remove()};if(typeof define==="function"&&define.amd)this.d3panels=d3panels,define(d3panels);else if(typeof module==="object"&&module.exports)module.exports=d3panels;else this.d3panels=d3panels}();
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/dataset_select_menu_orig.js b/gn2/wqflask/static/new/javascript/dataset_select_menu_orig.js new file mode 100644 index 00000000..25a703e6 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/dataset_select_menu_orig.js @@ -0,0 +1,330 @@ +var apply_default, check_search_term, dataset_info, group_info, make_default, open_window, populate_dataset, populate_group, populate_species, populate_type, process_json, redo_dropdown; +process_json = function(data) { + window.jdata = data; + populate_species(); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return apply_default(); + } +}; + +range = function(size, startAt=0) { + return [...Array(size).keys()].map(idx => idx + startAt); +}; + +indicate_error = function (jqXHR, textStatus, errorThrown) { + errorElement = document.createElement("span"); + errorElement.setAttribute("class", "alert-danger"); + errorText = document.createTextNode( + "There was an error retrieving and setting the menu. Try again later."); + errorElement.appendChild(errorText); + if (document.getElementById("search")){ + form = document.getElementById("search").getElementsByTagName("form")[0]; + form.prepend(errorElement); + disable_element = function(select) { + select.setAttribute("disabled", "disabled"); + }; + Array.from(form.getElementsByTagName("select")).forEach(disable_element); + Array.from(form.getElementsByTagName("textarea")).forEach(disable_element); + } +}; + +defaultStatusCodeFunctions = range(200, 400).reduce( + function(acc, scode) { + acc[scode] = indicate_error; + return acc; + }, {}); + +if (typeof gn_server_url === 'undefined'){ + gn_server_url = $("#search form").attr("data-gn_server_url") +} + +$.ajax(gn_server_url +'/menu/generate/json', { + dataType: 'json', + success: process_json, + error: indicate_error, + statusCode: { + ...defaultStatusCodeFunctions, + } +}); + +populate_species = function() { + var species_list; + species_list = this.jdata.species; + redo_dropdown($('#species'), species_list); + return populate_group(); +}; +window.populate_species = populate_species; + +populate_group = function() { + var group_list, species; + species = $('#species').val(); + group_list = this.jdata.groups[species]; + for (_i = 0, _len = group_list.length; _i < (_len - 1); _i++) { + if (group_list[_i][0] == "BXD300"){ + group_list.splice(_i, 1) + } + } + redo_dropdown($('#group'), group_list); + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } +}; +window.populate_group = populate_group; + +populate_type = function() { + var group, species, type_list; + species = $('#species').val(); + group = $('#group').val(); + type_list = this.jdata.types[species][group]; + redo_dropdown($('#type'), type_list); + return populate_dataset(); +}; +window.populate_type = populate_type; + +populate_dataset = function() { + var dataset_list, group, species, type; + species = $('#species').val(); + group = $('#group').val(); + type = $('#type').val(); + dataset_list = this.jdata.datasets[species][group][type]; + return redo_dropdown($('#dataset'), dataset_list); +}; +window.populate_dataset = populate_dataset; + +redo_dropdown = function(dropdown, items) { + var item, _i, _len, _results; + dropdown.empty(); + _results = []; + + if (dropdown.attr('id') == "species"){ + species_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + species_family = item[2].toString() + species_family_list.push([item[0], item[1], species_family]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = species_family_list.length; _i < _len; _i++) { + item = species_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == species_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == species_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && this_opt_group != null && item[2] == "None"){ + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else if (dropdown.attr('id') == "group"){ + group_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + group_family = item[2].toString().split(":")[1] + group_family_list.push([item[0], item[1], group_family]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = group_family_list.length; _i < _len; _i++) { + item = group_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == group_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == group_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && this_opt_group != null && item[2] == "None"){ + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else if (dropdown.attr('id') == "type"){ + type_family_list = []; + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + type_family_list.push([item[0], item[1], item[2]]) + } + + current_family = "" + this_opt_group = null + for (_i = 0, _len = type_family_list.length; _i < _len; _i++) { + item = type_family_list[_i]; + if (item[2] != "None" && current_family == ""){ + current_family = item[2] + this_opt_group = $("<optgroup label=\"" + item[2] + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] == current_family){ + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else if (current_family != "" && item[2] != current_family && item[2] != "None"){ + current_family = item[2] + _results.push(dropdown.append(this_opt_group)) + this_opt_group = $("<optgroup label=\"" + current_family + "\">") + this_opt_group.append($("<option />").val(item[0]).text(item[1])); + if (_i == type_family_list.length - 1){ + _results.push(dropdown.append(this_opt_group)) + } + } else { + _results.push(dropdown.append(this_opt_group)) + current_family = "" + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } else { + for (_i = 0, _len = items.length; _i < _len; _i++) { + item = items[_i]; + if (item.length > 2){ + _results.push(dropdown.append($("<option data-id=\""+item[0]+"\" />").val(item[1]).text(item[2]))); + } else { + _results.push(dropdown.append($("<option />").val(item[0]).text(item[1]))); + } + } + } + + return _results; +}; + +$('#species').change((function(_this) { + return function() { + return populate_group(); + }; +})(this)); + +$('#group').change((function(_this) { + return function() { + if ($('#type').length > 0) { //This is to determine if it's the index page or the submit_trait page (which only has species and group selection and no make default option) + return populate_type(); + } + else { + return false + } + }; +})(this)); + +$('#type').change((function(_this) { + return function() { + return populate_dataset(); + }; +})(this)); + +open_window = function(url, name) { + var options; + options = "menubar=yes,toolbar=yes,titlebar=yes,location=yes,resizable=yes,status=yes,scrollbars=yes,directories=yes,width=900"; + return open(url, name, options).focus(); +}; + +group_info = function() { + var group, species, url; + species = $('#species').val(); + group = $('#group').val(); + url = "http://gn1.genenetwork.org/" + species + "Cross.html#" + group; + return open_window(url, "_blank"); +}; +$('#group_info').click(group_info); + +dataset_info = function() { + var dataset, url; + accession_id = $('#dataset option:selected').data("id"); + if (accession_id != "None") { + url = "https://info.genenetwork.org/infofile/source.php?GN_AccesionId=" + accession_id + } else { + species = $('#species').val(); + group = $('#group').val(); + url = "https://info.genenetwork.org/species/source.php?SpeciesName=" + species + "&InbredSetName=" + group + } + return open_window(url, "_blank"); +}; +$('#dataset_info').click(dataset_info); + +make_default = function() { + var holder, item, jholder, _i, _len, _ref; + alert("The current settings are now your default.") + holder = {}; + _ref = ['species', 'group', 'type', 'dataset']; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + holder[item] = $("#" + item).val(); + } + jholder = JSON.stringify(holder); + return $.cookie('search_defaults', jholder, { + expires: 365 + }); +}; + +apply_default = function() { + var defaults, item, populate_function, _i, _len, _ref, _results; + defaults = $.cookie('search_defaults'); + if (defaults) { + defaults = $.parseJSON(defaults); + } else { + defaults = { + species: "mouse", + group: "BXD", + type: "Hippocampus mRNA", + dataset: "HC_M2_0606_P" + }; + } + + _ref = [['species', 'group'], ['group', 'type'], ['type', 'dataset'], ['dataset', null]]; + _results = []; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + item = _ref[_i]; + $("#" + item[0]).val(defaults[item[0]]); + if (item[1]) { + populate_function = "populate_" + item[1]; + _results.push(window[populate_function]()); + } else { + _results.push(void 0); + } + } + return _results; +}; + +check_search_term = function() { + var or_search_term, and_search_term; + or_search_term = $('#or_search').val(); + and_search_term = $('#and_search').val(); + if (or_search_term === "" && and_search_term === "") { + alert("Please enter one or more search terms or search equations."); + return false; + } +}; + +$("#make_default").click(make_default); diff --git a/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js b/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js new file mode 100644 index 00000000..f883c0d9 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/draw_corr_scatterplot.js @@ -0,0 +1,913 @@ +var chart; +var srchart; + +x_val_range = js_data.x_range[1] - js_data.x_range[0] +y_val_range = js_data.y_range[1] - js_data.y_range[0] + +if (x_val_range >= 2 && x_val_range < 9){ + x_tick_digits = '.1f' +} else if (x_val_range >= 0.8 && x_val_range < 2) { + x_tick_digits = '.2f' +} else if (x_val_range < 0.8) { + x_tick_digits = '.3f' +} else { + x_tick_digits = 'f' +} + +if (y_val_range >= 2 && y_val_range < 8){ + y_tick_digits = '.1f' +} else if (y_val_range >= 0.8 && y_val_range < 2) { + y_tick_digits = '.2f' +} else if (y_val_range < 0.8) { + y_tick_digits = '.3f' +} else { + y_tick_digits = 'f' +} + +console.log("y_digits:", y_tick_digits) + +var layout = { + height: 700, + width: 800, + margin: { + l: 70, + r: 30, + t: 90, + b: 50 + }, + xaxis: { + range: [js_data.x_range[0], js_data.x_range[1]], + title: js_data.trait_1, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + ticklen: 4, + tickformat: x_tick_digits + }, + yaxis: { + range: [js_data.y_range[0], js_data.y_range[1]], + title: js_data.trait_2, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + ticklen: 4, + tickformat: y_tick_digits, + automargin: true + }, + hovermode: "closest", + showlegend: false, + annotations:[{ + xref: 'paper', + yref: 'paper', + x: 1, + xanchor: 'right', + y: 1.05, + yanchor: 'top', + text: '<i>r</i> = ' + js_data.r_value.toFixed(3) + ', <i>p</i> = ' + js_data.p_value.toExponential(3) + ', <i>n</i> = ' + js_data.num_overlap, + showarrow: false, + font: { + size: 14 + }, + } + ] +} + +var sr_layout = { + height: 700, + width: 800, + margin: { + l: 60, + r: 30, + t: 80, + b: 50 + }, + xaxis: { + range: [js_data.sr_range[0], js_data.sr_range[1]], + title: js_data.trait_1, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + yaxis: { + range: [js_data.sr_range[0], js_data.sr_range[1]], + title: js_data.trait_2, + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + }, + hovermode: "closest", + showlegend: false, + annotations:[{ + xref: 'paper', + yref: 'paper', + x: 1, + xanchor: 'right', + y: 1.05, + yanchor: 'top', + text: '<i>rho</i> = ' + js_data.srr_value.toFixed(3) + ', <i>P</i> = ' + js_data.srp_value.toExponential(3) + ', <i>n</i> = ' + js_data.num_overlap, + showarrow: false, + font: { + size: 14 + }, + } +] +} + +var modebar_options = { + modeBarButtonsToAdd:[{ + name: 'Export as SVG', + icon: Plotly.Icons.camera, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'svg'}) + } + }, + { + name: 'Export as JPEG', + icon: Plotly.Icons.disk, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'jpeg'}) + } + }], + showEditInChartStudio: true, + plotlyServerURL: "https://chart-studio.plotly.com", + modeBarButtonsToRemove:['toImage', 'sendDataToCloud', 'hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines'], + displaylogo: false +} + +cofactor1_dict = {} +ranked_cofactor1_dict = {} +//cofactor1_values = [] +//ranked_cofactor1_values = [] +cofactor2_dict = {} +ranked_cofactor2_dict = {} +//cofactor2_values = [] +//ranked_cofactor2_values = [] +cofactor3_dict = {} +ranked_cofactor3_dict = {} + +function drawg() { + x_values = [] + y_values = [] + sample_names = [] + for (j = 0; j < js_data.data[0].length; j++) { + x_values.push(js_data.data[0][j]) + y_values.push(js_data.data[1][j]) + sample_names.push(js_data.indIDs[j]) + } + + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: sample_names, + hoverinfo: "text+x+y" + } + + var trace2 = { + x: [js_data.intercept_coords[0][0], js_data.intercept_coords[1][0]], + y: [js_data.intercept_coords[0][1], js_data.intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + Plotly.newPlot('scatterplot2', [trace2, trace1], layout, modebar_options) + +} + +function srdrawg() { + x_values = [] + y_values = [] + sample_names = [] + for (j = 0; j < js_data.rdata[0].length; j++) { + x_values.push(js_data.rdata[0][j]) + y_values.push(js_data.rdata[1][j]) + sample_names.push(js_data.indIDs[j]) + } + + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: sample_names, + hoverinfo: "text+x+y" + } + + Plotly.newPlot('srscatterplot2', [trace1], sr_layout, modebar_options) +} + +function getdata() { + var data = []; + data.push({ + values: [], + slope: js_data.slope, + intercept: js_data.intercept + }); + + sizemin = 8; + sizemax = 30; + + samples1 = []; + samples2 = []; + samples3 = []; + + if ($('input[name=cofactor1_vals]').val()){ + vals1 = [] + val_sample_dict = {} + val_sample_pairs = $('input[name=cofactor1_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples1.push(val_sample_pairs[i].split(":")[0]) + vals1.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1]) + } + datamin1 = d3.min(vals1); + datamax1 = d3.max(vals1); + + cofactor1_dict = val_sample_dict + cofactor1_values = vals1 + } + + if ($('input[name=cofactor2_vals]').val()){ + vals2 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=cofactor2_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples2.push(val_sample_pairs[i].split(":")[0]) + vals2.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + datamin2 = d3.min(vals2); + datamax2 = d3.max(vals2); + + cofactor2_dict = val_sample_dict + cofactor2_values = vals2 + } + + if ($('input[name=cofactor3_vals]').val()){ + vals3 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=cofactor3_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples3.push(val_sample_pairs[i].split(":")[0]) + vals3.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + + datamin3 = d3.min(vals3); + datamax3 = d3.max(vals3); + + cofactor3_dict = val_sample_dict + cofactor3_values = vals3 + } + + x_values = [] + y_values = [] + sample_names = [] + sizes = [] + + size_cofactor_vals = [] + if ($('#cofactor1_type option:selected').val() == "size" && $('input[name=cofactor1_vals]').val()){ + size_cofactor_vals = cofactor1_values + cofactor_samples = samples1 + datamin = datamin1 + datamax = datamax1 + } else if ($('#cofactor2_type option:selected').val() == "size" && $('input[name=cofactor2_vals]').val()) { + size_cofactor_vals = cofactor2_values + cofactor_samples = samples2 + datamin = datamin2 + datamax = datamax2 + } else if ($('#cofactor3_type option:selected').val() == "size" && $('input[name=cofactor3_vals]').val()) { + size_cofactor_vals = cofactor3_values + cofactor_samples = samples3 + datamin = datamin3 + datamax = datamax3 + } + + unique_vals = [] + symbol_cofactor_vals = [] + if ($('#cofactor1_type option:selected').val() == "symbol" && $('input[name=cofactor1_vals]').val()){ + symbol_cofactor_vals = cofactor1_values + cofactor_samples = samples1 + } else if ($('#cofactor2_type option:selected').val() == "symbol" && $('input[name=cofactor2_vals]').val()) { + symbol_cofactor_vals = cofactor2_values + cofactor_samples = samples2 + } else if ($('#cofactor3_type option:selected').val() == "symbol" && $('input[name=cofactor3_vals]').val()) { + symbol_cofactor_vals = cofactor3_values + cofactor_samples = samples3 + } + + symbol_list = [] + if (symbol_cofactor_vals.length > 0) { + unique_vals = [...new Set(symbol_cofactor_vals)] + for (i=0; i<symbol_cofactor_vals.length; i++){ + val_pos = unique_vals.indexOf(symbol_cofactor_vals[i]) + if (val_pos != "-1") { + symbol_list.push(val_pos) + } else { + symbol_list.push(0) + } + } + } + + //This is needed to calculate samples shared by cofactors + cofactor_samples_array = [] + if (samples1.length > 0){ + cofactor_samples_array.push(samples1) + } + if (samples2.length > 0){ + cofactor_samples_array.push(samples2) + } + if (samples3.length > 0){ + cofactor_samples_array.push(samples3) + } + if (cofactor_samples_array.length > 0){ + shared_samples = _.intersection.apply(_, cofactor_samples_array) + } else { + shared_samples = js_data.indIDs + } + + for (j = 0; j < js_data.data[0].length; j++) { + + if (shared_samples.indexOf(js_data.indIDs[j]) == -1) { + continue + } + + sizev = 10; + datav = 0; + if (size_cofactor_vals.length > 0){ + if (cofactor_samples.indexOf(js_data.indIDs[j])) { + datav = size_cofactor_vals[j] + sizev = map1to2(datamin, datamax, sizemin, sizemax, datav); + } + } + + x_values.push(js_data.data[0][j]) + y_values.push(js_data.data[1][j]) + sample_names.push(js_data.indIDs[j]) + sizes.push(sizev) + + data[0].values.push({ + type: "normal", + x: js_data.data[0][j], + y: js_data.data[1][j], + name: js_data.indIDs[j], + size: sizev, + v3: datav + }); + } + + point_text = [] + for (j = 0; j < sample_names.length; j++) { + this_text = "" + this_text += sample_names[j] + if (sample_names[j] in cofactor1_dict){ + this_text += "<br>Cofactor 1: " + cofactor1_dict[sample_names[j]] + } + if (sample_names[j] in cofactor2_dict){ + this_text += "<br>Cofactor 2: " + cofactor2_dict[sample_names[j]] + } + if (sample_names[j] in cofactor3_dict){ + this_text += "<br>Cofactor 3: " + cofactor3_dict[sample_names[j]] + } + point_text.push(this_text) + } + + if (symbol_list.length > 0) { + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: point_text, + hoverinfo: "text+x+y", + marker: { + color: 'rgb(66, 66, 245)', + symbol: symbol_list, + size: sizes + } + } + } else { + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: point_text, + hoverinfo: "text+x+y", + marker: { + color: 'rgb(66, 66, 245)', + size: sizes + } + } + } + + var trace2 = { + x: [js_data.intercept_coords[0][0], js_data.intercept_coords[1][0]], + y: [js_data.intercept_coords[0][1], js_data.intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + return [trace2, trace1]; +} + +function map1to2 (min1, max1, min2, max2, v1) { + v2 = (v1 - min1) * (max2 - min2) / (max1 - min1) + min2; + return v2; +} + +function srgetdata() { + var data = []; + data.push({ + values: [], + slope: js_data.srslope, + intercept: js_data.srintercept + }); + + sizemin = 8; + sizemax = 30; + + ranked_cofactor_vals = "" + + samples1 = []; + samples2 = []; + samples3 = []; + + if ($('input[name=ranked_cofactor1_vals]').val()){ + vals1 = [] + val_sample_dict = {} + val_sample_pairs = $('input[name=ranked_cofactor1_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples1.push(val_sample_pairs[i].split(":")[0]) + vals1.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = parseFloat(val_sample_pairs[i].split(":")[1]) + } + datamin1 = d3.min(vals1); + datamax1 = d3.max(vals1); + + ranked_cofactor1_dict = val_sample_dict + ranked_cofactor1_values = vals1 + } + + if ($('input[name=ranked_cofactor2_vals]').val()){ + vals2 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=ranked_cofactor2_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples2.push(val_sample_pairs[i].split(":")[0]) + vals2.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + datamin2 = d3.min(vals2); + datamax2 = d3.max(vals2); + + ranked_cofactor2_dict = val_sample_dict + ranked_cofactor2_values = vals2 + } + + if ($('input[name=ranked_cofactor3_vals]').val()){ + vals3 = []; + val_sample_dict = {} + val_sample_pairs = $('input[name=ranked_cofactor3_vals]').val().split(",") + for (i=0; i < val_sample_pairs.length; i++) { + samples3.push(val_sample_pairs[i].split(":")[0]) + vals3.push(parseFloat(val_sample_pairs[i].split(":")[1])) + val_sample_dict[val_sample_pairs[i].split(":")[0]] = val_sample_pairs[i].split(":")[1] + } + + datamin3 = d3.min(vals3); + datamax3 = d3.max(vals3); + + ranked_cofactor3_dict = val_sample_dict + ranked_cofactor3_values = vals3 + } + + x_values = [] + y_values = [] + sample_names = [] + sizes = [] + + if ($('#cofactor1_type option:selected').val() == "size" && $('input[name=ranked_cofactor1_vals]').val()){ + size_cofactor_vals = ranked_cofactor1_values + cofactor_samples = samples1 + datamin = datamin1 + datamax = datamax1 + } else if ($('#cofactor2_type option:selected').val() == "size" && $('input[name=ranked_cofactor2_vals]').val()) { + size_cofactor_vals = ranked_cofactor2_values + cofactor_samples = samples2 + datamin = datamin2 + datamax = datamax2 + } else if ($('#cofactor3_type option:selected').val() == "size" && $('input[name=ranked_cofactor3_vals]').val()) { + size_cofactor_vals = ranked_cofactor3_values + cofactor_samples = samples3 + datamin = datamin3 + datamax = datamax3 + } + + unique_vals = [] + symbol_cofactor_vals = [] + if ($('#cofactor1_type option:selected').val() == "symbol" && $('input[name=ranked_cofactor1_vals]').val()){ + symbol_cofactor_vals = cofactor1_values + cofactor_samples = samples1 + } else if ($('#cofactor2_type option:selected').val() == "symbol" && $('input[name=ranked_cofactor2_vals]').val()) { + symbol_cofactor_vals = cofactor2_values + cofactor_samples = samples2 + } else if ($('#cofactor3_type option:selected').val() == "symbol" && $('input[name=ranked_cofactor3_vals]').val()) { + symbol_cofactor_vals = cofactor3_values + cofactor_samples = samples3 + } + + symbol_list = [] + if (symbol_cofactor_vals.length > 0) { + unique_vals = [...new Set(symbol_cofactor_vals)] + for (i=0; i<symbol_cofactor_vals.length; i++){ + val_pos = unique_vals.indexOf(symbol_cofactor_vals[i]) + if (val_pos != "-1") { + symbol_list.push(val_pos) + } else { + symbol_list.push(0) + } + } + } + + //This is needed to calculate samples shared by cofactors + cofactor_samples_array = [] + if (samples1.length > 0){ + cofactor_samples_array.push(samples1) + } + if (samples2.length > 0){ + cofactor_samples_array.push(samples2) + } + if (samples3.length > 0){ + cofactor_samples_array.push(samples3) + } + if (cofactor_samples_array.length > 0){ + shared_samples = _.intersection.apply(_, cofactor_samples_array) + } else { + shared_samples = js_data.indIDs + } + + for (j = 0; j < js_data.rdata[0].length; j++) { + + if (shared_samples.indexOf(js_data.indIDs[j]) == -1) { + continue + } + + if (size_cofactor_vals.length > 0){ + if (cofactor_samples.indexOf(js_data.indIDs[j])) { + datav = size_cofactor_vals[j] + sizev = map1to2(datamin, datamax, sizemin, sizemax, datav); + } + } else { + sizev = 10; + } + + x_values.push(js_data.rdata[0][j]) + y_values.push(js_data.rdata[1][j]) + sample_names.push(js_data.indIDs[j]) + sizes.push(sizev) + + data[0].values.push({ + type: "ranked", + x: js_data.rdata[0][j], + y: js_data.rdata[1][j], + name: js_data.indIDs[j], + size: sizev, + }); + } + + point_text = [] + for (j = 0; j < sample_names.length; j++) { + this_text = "" + this_text += sample_names[j] + if (sample_names[j] in ranked_cofactor1_dict){ + this_text += "<br>Cofactor 1: " + ranked_cofactor1_dict[sample_names[j]] + } + if (sample_names[j] in ranked_cofactor2_dict){ + this_text += "<br>Cofactor 2: " + ranked_cofactor2_dict[sample_names[j]] + } + if (sample_names[j] in cofactor3_dict){ + this_text += "<br>Cofactor 3: " + ranked_cofactor3_dict[sample_names[j]] + } + point_text.push(this_text) + } + + var trace1 = { + x: x_values, + y: y_values, + mode: 'markers', + text: point_text, + hoverinfo: "text+x+y", + marker: { + color: 'rgb(66, 66, 245)', + symbol: symbol_list, + size: sizes + } + } + + var trace2 = { + x: [js_data.sr_intercept_coords[0][0], js_data.sr_intercept_coords[1][0]], + y: [js_data.sr_intercept_coords[0][1], js_data.sr_intercept_coords[1][1]], + mode: 'lines', + line: { + color: 'rgb(250, 60, 73)' + } + } + + return [trace2, trace1]; +} + +function chartupdatewh() { + var width = $("#width").val(); + var height = $("#height").val(); + + width_height_update = { + height: height, + width: width + } + + Plotly.newPlot('scatterplot2', getdata(), layout, modebar_options) + Plotly.relayout('scatterplot2', width_height_update) + + Plotly.newPlot('srscatterplot2', srgetdata(), sr_layout, modebar_options) + Plotly.relayout('srscatterplot2', width_height_update) +} + +function colorer(d) { + if ($('#cofactor1_type option:selected').val() == "color"){ + datamin = d3.min(cofactor1_values); + datamax = d3.max(cofactor1_values); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + datamin = d3.min(cofactor2_values); + datamax = d3.max(cofactor2_values); + } else { + datamin = d3.min(cofactor3_values); + datamax = d3.max(cofactor3_values); + } + colormin = $("#cocolorfrom").val(); + colormax = $("#cocolorto").val(); + + compute = d3.interpolate("#"+colormin, "#"+colormax); + linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]); + + this_sample = d.tx.split("<br>")[0] + + if ($('#cofactor1_type option:selected').val() == "color"){ + c= compute(linear(cofactor1_dict[this_sample])); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + c= compute(linear(cofactor2_dict[this_sample])); + } else { + c= compute(linear(cofactor3_dict[this_sample])); + } + + return c; +} + +function ranked_colorer(d) { + if ($('#cofactor1_type option:selected').val() == "color"){ + datamin = d3.min(ranked_cofactor1_values); + datamax = d3.max(ranked_cofactor1_values); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + datamin = d3.min(ranked_cofactor2_values); + datamax = d3.max(ranked_cofactor2_values); + } else { + datamin = d3.min(ranked_cofactor3_values); + datamax = d3.max(ranked_cofactor3_values); + } + colormin = $("#cocolorfrom").val(); + colormax = $("#cocolorto").val(); + + compute = d3.interpolate("#"+colormin, "#"+colormax); + linear = d3.scale.linear().domain([datamin, datamax]).range([0,1]); + + this_sample = d.tx.split("<br>")[0] + + if ($('#cofactor1_type option:selected').val() == "color"){ + c= compute(linear(ranked_cofactor1_dict[this_sample])); + } else if ($('#cofactor2_type option:selected').val() == "color"){ + c= compute(linear(ranked_cofactor2_dict[this_sample])); + } else { + c= compute(linear(ranked_cofactor3_dict[this_sample])); + } + + return c; +} + +function chartupdatedata() { + var size = $("#marksize").val(); + var shape = $("#markshape").val(); + + var pearson_title_update = { + title: "Pearson Correlation Scatterplot" + } + var spearman_title_update = { + title: "Spearman Rank Correlation Scatterplot" + } + + Plotly.newPlot('scatterplot2', getdata(), layout, modebar_options) + Plotly.relayout('scatterplot2', pearson_title_update) + Plotly.newPlot('srscatterplot2', srgetdata(), sr_layout, modebar_options) + Plotly.relayout('srscatterplot2', spearman_title_update) + + if ($('#cofactor1_type option:selected').val() == "color"){ + $('#cofactor_color_selector').css("display", "inline") + if ($('input[name=cofactor1_vals]').val()){ + d3.select('#scatterplot2 svg').selectAll('.point') + .style({ + 'stroke': colorer, + 'fill': colorer + }); + d3.select('#srscatterplot2 svg').selectAll('.point') + .style({ + 'stroke': ranked_colorer, + 'fill': ranked_colorer + }); + } + } else if ($('#cofactor2_type option:selected').val() == "color"){ + $('#cofactor_color_selector').css("display", "inline") + if ($('input[name=cofactor2_vals]').val()){ + d3.select('#scatterplot2 svg').selectAll('.point') + .style({ + 'stroke': colorer, + 'fill': colorer + }); + d3.select('#srscatterplot2 svg').selectAll('.point') + .style({ + 'stroke': ranked_colorer, + 'fill': ranked_colorer + }); + } + } else { + $('#cofactor_color_selector').css("display", "inline") + if ($('input[name=cofactor3_vals]').val()){ + d3.select('#scatterplot2 svg').selectAll('.point') + .style({ + 'stroke': colorer, + 'fill': colorer + }); + d3.select('#srscatterplot2 svg').selectAll('.point') + .style({ + 'stroke': ranked_colorer, + 'fill': ranked_colorer + }); + } + } +} + +drawg(); +srdrawg(); + +$(".chartupdatewh").change(function () { + chartupdatewh(); +}); + +$(".chartupdatedata").change(function () { + chartupdatedata(); +}); + +$("#cofactor1_type").change(function () { + + the_types = ["color", "size", "symbol"] + + cofactor1_type = $(this).val() + cofactor2_type = $("#cofactor2_type option:selected").val() + cofactor3_type = $("#cofactor3_type option:selected").val() + + if (cofactor2_type == cofactor1_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor1_type && the_types[i] != cofactor3_type) { + $("#cofactor2_type").val(the_types[i]); + } + } + } + else if (cofactor3_type == cofactor1_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor1_type && the_types[i] != cofactor2_type) { + $("#cofactor3_type").val(the_types[i]); + } + } + } + + chartupdatedata(); +}); + +$("#cofactor2_type").change(function () { + + the_types = ["color", "size", "symbol"] + + cofactor2_type = $(this).val() + cofactor1_type = $("#cofactor1_type option:selected").val() + cofactor3_type = $("#cofactor3_type option:selected").val() + + if (cofactor1_type == cofactor2_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor3_type){ + $("#cofactor1_type").val(the_types[i]); + } + } + } + else if (cofactor3_type == cofactor2_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor1_type){ + $("#cofactor3_type").val(the_types[i]); + } + } + } + + chartupdatedata(); +}); + +$("#cofactor3_type").change(function () { + + the_types = ["color", "size", "symbol"] + + cofactor3_type = $(this).val() + cofactor1_type = $("#cofactor1_type option:selected").val() + cofactor2_type = $("#cofactor2_type option:selected").val() + + if (cofactor1_type == cofactor3_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor3_type){ + $("#cofactor1_type").val(the_types[i]); + } + } + } + else if (cofactor2_type == cofactor3_type){ + for (i=0; i<3; i++){ + if (the_types[i] != cofactor2_type && the_types[i] != cofactor1_type){ + $("#cofactor3_type").val(the_types[i]); + } + } + } +}); + +open_covariate_selection = function() { + return $('#collections_holder').load('/collections/list #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)); +}; + +remove_cofactors = function() { + $('input[name=cofactor1_vals]').val(""); + $('input[name=ranked_cofactor1_vals]').val(""); + $('input[name=cofactor2_vals]').val(""); + $('input[name=ranked_cofactor2_vals]').val(""); + $('input[name=cofactor3_vals]').val(""); + $('input[name=ranked_cofactor3_vals]').val(""); + + $('#select_cofactor1').text("Select Cofactor 1"); + $('#cofactor2_button').css("display", "none"); + $('#cofactor3_button').css("display", "none"); + + $('#cofactor_color_select').css("display", "none"); + + $('#cofactor1_info_container').css("display", "none"); + $('#cofactor2_info_container').css("display", "none"); + $('#cofactor3_info_container').css("display", "none"); + + chartupdatedata(); +}; + +$(document).ready(function(){ + chartupdatedata(); + + $('#select_cofactor1').click(function () { + $('input[name=selecting_which_cofactor]').val("1"); + open_covariate_selection(); + }); + + $('#select_cofactor2').click(function () { + $('input[name=selecting_which_cofactor]').val("2"); + open_covariate_selection(); + }); + + $('#select_cofactor3').click(function () { + $('input[name=selecting_which_cofactor]').val("3"); + open_covariate_selection(); + }); + + $('#remove_cofactors').click(function () { + remove_cofactors(); + }); + + $('#invert_axes').click(function () { + var [dataset_1, trait_1] = js_data.trait_2.split(": ") + var [dataset_2, trait_2] = js_data.trait_1.split(": ") + window.location.replace("/corr_scatter_plot?method=pearson&dataset_1=" + dataset_1 + "&dataset_2=" + dataset_2 + "&trait_1=" + trait_1 + "&trait_2=" + trait_2) + }); + +}); diff --git a/gn2/wqflask/static/new/javascript/draw_probability_plot.js b/gn2/wqflask/static/new/javascript/draw_probability_plot.js new file mode 100644 index 00000000..1b944d4f --- /dev/null +++ b/gn2/wqflask/static/new/javascript/draw_probability_plot.js @@ -0,0 +1,136 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var get_z_scores, redraw_prob_plot, root; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + get_z_scores = function(n) { + var i, j, osm_uniform, ref, x; + osm_uniform = new Array(n); + osm_uniform[n - 1] = Math.pow(0.5, 1.0 / n); + osm_uniform[0] = 1 - osm_uniform[n - 1]; + for (i = j = 1, ref = n - 2; 1 <= ref ? j <= ref : j >= ref; i = 1 <= ref ? ++j : --j) { + osm_uniform[i] = (i + 1 - 0.3175) / (n + 0.365); + } + return (function() { + var k, len, results; + results = []; + for (k = 0, len = osm_uniform.length; k < len; k++) { + x = osm_uniform[k]; + results.push(jStat.normal.inv(x, 0, 1)); + } + return results; + })(); + }; + + redraw_prob_plot = function(samples, sample_group) { + var container, h, margin, totalh, totalw, w; + h = 600; + w = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + totalh = h + margin.top + margin.bottom; + totalw = w + margin.left + margin.right; + container = $("#prob_plot_container"); + container.width(totalw); + container.height(totalh); + return nv.addGraph((function(_this) { + return function() { + var W, all_samples, chart, data, intercept, make_data, names, pvalue, pvalue_str, slope, sorted_names, sorted_values, sw_result, test_str, x, z_scores; + chart = nv.models.scatterChart().width(w).height(h).showLegend(true).color(d3.scale.category10().range()); + chart.pointRange([50, 50]); + chart.legend.updateState(false); + chart.xAxis.axisLabel("Expected Z score").axisLabelDistance(20).tickFormat(d3.format('.02f')); + chart.tooltipContent(function(obj) { + return '<b style="font-size: 20px">' + obj.point.name + '</b>'; + }); + all_samples = samples[sample_group]; + names = (function() { + var j, len, ref, results; + ref = _.keys(all_samples); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + if (all_samples[x] !== null) { + results.push(x); + } + } + return results; + })(); + sorted_names = names.sort(function(x, y) { + return all_samples[x].value - all_samples[y].value; + }); + max_decimals = 0 + sorted_values = (function() { + var j, len, results; + results = []; + for (j = 0, len = sorted_names.length; j < len; j++) { + x = sorted_names[j]; + results.push(all_samples[x].value); + if (all_samples[x].value.countDecimals() > max_decimals) { + max_decimals = all_samples[x].value.countDecimals()-1 + } + } + return results; + })(); + //ZS: 0.1 indicates buffer, increase to increase buffer + y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1] + chart.yDomain(y_domain) + chart.yAxis.axisLabel("Trait value").axisLabelDistance(10).tickFormat(d3.format('.0'+max_decimals.toString()+'f')); + sw_result = ShapiroWilkW(sorted_values); + W = sw_result.w.toFixed(3); + pvalue = sw_result.p.toFixed(3); + pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>"; + test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")"; + z_scores = get_z_scores(sorted_values.length); + //ZS: 0.1 indicates buffer, increase to increase buffer + x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1] + chart.xDomain(x_domain) + slope = jStat.stdev(sorted_values); + intercept = jStat.mean(sorted_values); + make_data = function(group_name) { + var sample, value, z_score; + return { + key: js_data.sample_group_types[group_name], + slope: slope, + intercept: intercept, + values: (function() { + var j, len, ref, ref1, results; + ref = _.zip(get_z_scores(sorted_values.length), sorted_values, sorted_names); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + ref1 = ref[j], z_score = ref1[0], value = ref1[1], sample = ref1[2]; + if (sample in samples[group_name]) { + results.push({ + x: z_score, + y: value, + name: sample + }); + } + } + return results; + })() + }; + }; + data = [make_data('samples_primary'), make_data('samples_other')]; + d3.select("#prob_plot_container svg").datum(data).call(chart); + if (js_data.trait_symbol != null) { + $("#prob_plot_title").html("<h3>" + js_data.trait_symbol + ": " + js_data.trait_id + "</h3>"); + } else { + $("#prob_plot_title").html("<h3>" + js_data.trait_id + "</h3>"); + } + $("#shapiro_wilk_text").html(test_str) + $("#prob_plot_container .nv-legendWrap").toggle(sample_group === "samples_all"); + return chart; + }; + })(this)); + }; + + root.redraw_prob_plot_impl = redraw_prob_plot; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/get_covariates_from_collection.js b/gn2/wqflask/static/new/javascript/get_covariates_from_collection.js new file mode 100644 index 00000000..ba8fa8b0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/get_covariates_from_collection.js @@ -0,0 +1,248 @@ +// Generated by CoffeeScript 1.8.0 +var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + +this_trait_data = null; + +selected_traits = {}; + +$('#collections_list').attr("style", "width: 100%;"); +$('#trait_table').dataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + }, + "columns": [ + { "type": "natural", "width": "3%" }, + { "type": "natural", "width": "8%" }, + { "type": "natural", "width": "20%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "15%" } + ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true +} ); + +if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { + $('#collection_table').dataTable( { + "createdRow": function ( row, data, index ) { + if ($('td', row).eq(2).text().length > 40) { + $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40)); + $('td', row).eq(2).text($('td', row).eq(2).text() + '...') + } + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + }, + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "ZRtr", + "iDisplayLength": -1, + "autoWidth": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); +} + +collection_click = function() { + var this_collection_url; + this_collection_url = $(this).find('.collection_name').prop("href"); + this_collection_url += "&json"; + collection_list = $("#collections_holder").html(); + return $.ajax({ + dataType: "json", + url: this_collection_url, + success: process_traits + }); +}; + +submit_click = function() { + var covariates_string = ""; + var covariates_as_set = new Set(); + $(".selected-covariates:first option").each(function() { + if ($(this).val() != ""){ + covariates_as_set.add($(this).val() + "," + $(this).text()); + } + }); + $('#collections_holder').find('input[type=checkbox]:checked').each(function() { + var this_dataset, this_trait; + this_trait = $(this).parents('tr').find('.trait').text(); + this_trait_display = $(this).parents('tr').find('.trait').data("display_name"); + this_description = $(this).parents('tr').find('.description').text(); + this_dataset = $(this).parents('tr').find('.dataset').data("dataset"); + this_covariate_display_string = this_trait_display + if (this_covariate_display_string.length > 50) { + this_covariate_display_string = this_covariate_display_string.substring(0, 45) + "..." + } + covariates_as_set.add(this_trait + ":" + this_dataset + "," + this_covariate_display_string) + }); + + covariates_as_list = Array.from(covariates_as_set) + + // Removed the starting "No covariates selected" option before adding options for each covariate + if (covariates_as_list.length > 0){ + $(".selected-covariates option[value='']").each(function() { + $(this).remove(); + }); + } + + $(".selected-covariates option").each(function() { + $(this).remove(); + }); + + covariate_list_for_form = [] + $.each(covariates_as_list, function (index, value) { + option_value = value.split(",")[0] + option_text = value.split(",")[1] + $(".selected-covariates").append($("<option/>", { + value: option_value, + text: option_text + })) + covariate_list_for_form.push(option_value) + }); + + $("input[name=covariates]").val(covariate_list_for_form.join(",")); + + cofactor_count = $(".selected-covariates:first option").length; + if (cofactor_count > 10){ + $(".selected-covariates").attr("size", 10); + } else { + $(".selected-covariates").attr("size", cofactor_count); + } + + return $.colorbox.close(); +}; + +trait_click = function() { + var dataset, this_trait_url, trait; + trait = $(this).parent().find('.trait').text(); + dataset = $(this).parent().find('.dataset').data("dataset"); + $("input[name=covariates]").val(trait + ":" + dataset) + $(".selected-covariates").text(trait) + return $.colorbox.close(); +}; + +add_trait_data = function(trait_data, textStatus, jqXHR) { + var trait_name, trait_sample_data; + trait_name = trait_data[0]; + trait_sample_data = trait_data[1]; + selected_traits[trait_name] = trait_sample_data; + return console.log("selected_traits:", selected_traits); +}; + +get_trait_data = function(trait_data, textStatus, jqXHR) { + var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len; + trait_sample_data = trait_data[1]; + samples = $('input[name=allsamples]').val().split(" "); + vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + if (__indexOf.call(Object.keys(trait_sample_data), sample) >= 0) { + vals.push(parseFloat(trait_sample_data[sample])); + } else { + vals.push(null); + } + } + if ($('input[name=samples]').length < 1) { + $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />'); + } + $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />'); + this_trait_vals = get_this_trait_vals(samples); + return color_by_trait(trait_sample_data); +}; + +get_this_trait_vals = function(samples) { + var sample, this_trait_vals, this_val, this_vals_json, _i, _len; + this_trait_vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + this_val = parseFloat($("input[name='value:" + sample + "']").val()); + if (!isNaN(this_val)) { + this_trait_vals.push(this_val); + } else { + this_trait_vals.push(null); + } + } + this_vals_json = '[' + this_trait_vals.toString() + ']'; + return this_trait_vals; +}; + +assemble_into_json = function(this_trait_vals) { + var json_data, json_ids, num_traits, samples; + num_traits = $('input[name=vals]').length; + samples = $('input[name=samples]').val(); + json_ids = samples; + json_data = '[' + this_trait_vals; + $('input[name=vals]').each((function(_this) { + return function(index, element) { + return json_data += ',' + $(element).val(); + }; + })(this)); + json_data += ']'; + return [json_ids, json_data]; +}; + +color_by_trait = function(trait_sample_data, textStatus, jqXHR) { + console.log('in color_by_trait:', trait_sample_data); + return root.bar_chart.color_by_trait(trait_sample_data); +}; + +process_traits = function(trait_data, textStatus, jqXHR) { + var the_html, trait, _i, _len; + the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; + the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; + the_html += " <button id='submit_cofactors' class='btn btn-primary btn-small submit'> Submit </button>"; + the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; + the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; + the_html += "<tbody>"; + for (_i = 0, _len = trait_data.length; _i < _len; _i++) { + trait = trait_data[_i]; + the_html += "<tr class='trait_line'>"; + the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>"; + if ("abbreviation" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>"; + } else if ("symbol" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>"; + } else { + the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>"; + } + the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>"; + the_html += "<td class='description'>" + trait.description + "</td>"; + } + the_html += "</tbody>"; + the_html += "</table>"; + the_html += "<script type='text/javascript' src='/static/new/javascript/get_covariates_from_collection.js'></script>" + $("#collections_holder").html(the_html); + return $('#collections_holder').colorbox.resize(); +}; + +back_to_collections = function() { + console.log("collection_list:", collection_list); + $("#collections_holder").html(collection_list); + $(document).on("click", ".collection_line", collection_click); + return $('#collections_holder').colorbox.resize(); +}; + +$(".collection_line").on("click", collection_click); +$(".submit").on("click", submit_click); +$(".trait").on("click", trait_click); +$("#back_to_collections").on("click", back_to_collections); diff --git a/gn2/wqflask/static/new/javascript/get_traits_from_collection.js b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js new file mode 100644 index 00000000..c115f3b0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/get_traits_from_collection.js @@ -0,0 +1,414 @@ +// Generated by CoffeeScript 1.8.0 +var add_trait_data, assemble_into_json, back_to_collections, collection_click, collection_list, color_by_trait, create_trait_data_csv, get_this_trait_vals, get_trait_data, process_traits, selected_traits, submit_click, this_trait_data, trait_click, + __indexOf = [].indexOf || function(item) { for (var i = 0, l = this.length; i < l; i++) { if (i in this && this[i] === item) return i; } return -1; }; + +this_trait_data = null; + +selected_traits = {}; + +$('#collections_list').attr("style", "width: 100%;"); +$('#trait_table').dataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').click(function(event) { + if (event.target.type !== 'checkbox') { + $(':checkbox', this).trigger('click'); + } + }); + }, + "columns": [ + { "type": "natural", "width": "3%" }, + { "type": "natural", "width": "8%" }, + { "type": "natural", "width": "20%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "25%" }, + { "type": "natural", "width": "15%" } + ], + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "RZtr", + "iDisplayLength": -1, + "autoWidth": true, + "bDeferRender": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true +} ); + +if ( ! $.fn.DataTable.isDataTable( '#collection_table' ) ) { + $('#collection_table').dataTable( { + "createdRow": function ( row, data, index ) { + if ($('td', row).eq(2).text().length > 40) { + $('td', row).eq(2).text($('td', row).eq(2).text().substring(0, 40)); + $('td', row).eq(2).text($('td', row).eq(2).text() + '...') + } + if ($('td', row).eq(4).text().length > 50) { + $('td', row).eq(4).text($('td', row).eq(4).text().substring(0, 50)); + $('td', row).eq(4).text($('td', row).eq(4).text() + '...') + } + }, + "columnDefs": [ { + "targets": 0, + "orderable": false + } ], + "order": [[1, "asc" ]], + "sDom": "ZRtr", + "iDisplayLength": -1, + "autoWidth": true, + "bSortClasses": false, + "paging": false, + "orderClasses": true + } ); +} + +collection_click = function() { + var this_collection_url; + + this_collection_url = $(this).find('.collection_name').prop("href"); + this_collection_url += "&json"; + collection_list = $("#collections_holder").html(); + return $.ajax({ + dataType: "json", + url: this_collection_url, + success: process_traits + }); +}; + +submit_click = function() { + var all_vals, sample, samples, scatter_matrix, this_trait_vals, trait, trait_names, trait_vals_csv, traits, _i, _j, _len, _len1, _ref; + selected_traits = {}; + traits = []; + $('#collections_holder').find('input[type=checkbox]:checked').each(function() { + var this_dataset, this_trait, this_trait_url; + this_trait = $(this).parents('tr').find('.trait').text(); + this_dataset = $(this).parents('tr').find('.dataset').text(); + this_trait_url = "/trait/get_sample_data?trait=" + this_trait + "&dataset=" + this_dataset; + return $.ajax({ + dataType: "json", + url: this_trait_url, + async: false, + success: add_trait_data + }); + }); + trait_names = []; + samples = $('input[name=allsamples]').val().split(" "); + all_vals = []; + this_trait_vals = get_this_trait_vals(samples); + all_vals.push(this_trait_vals); + _ref = Object.keys(selected_traits); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + trait = _ref[_i]; + trait_names.push(trait); + this_trait_vals = []; + for (_j = 0, _len1 = samples.length; _j < _len1; _j++) { + sample = samples[_j]; + if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) { + this_trait_vals.push(parseFloat(selected_traits[trait][sample])); + } else { + this_trait_vals.push(null); + } + } + all_vals.push(this_trait_vals); + } + trait_vals_csv = create_trait_data_csv(selected_traits); + scatter_matrix = new ScatterMatrix(trait_vals_csv); + scatter_matrix.render(); + return $.colorbox.close(); +}; + +create_trait_data_csv = function(selected_traits) { + var all_vals, index, sample, sample_vals, samples, this_trait_vals, trait, trait_names, trait_vals_csv, _i, _j, _k, _l, _len, _len1, _len2, _len3, _ref; + trait_names = []; + trait_names.push($('input[name=trait_id]').val()); + samples = $('input[name=allsamples]').val().split(" "); + all_vals = []; + this_trait_vals = get_this_trait_vals(samples); + all_vals.push(this_trait_vals); + _ref = Object.keys(selected_traits); + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + trait = _ref[_i]; + trait_names.push(trait); + this_trait_vals = []; + for (_j = 0, _len1 = samples.length; _j < _len1; _j++) { + sample = samples[_j]; + if (__indexOf.call(Object.keys(selected_traits[trait]), sample) >= 0) { + this_trait_vals.push(parseFloat(selected_traits[trait][sample])); + } else { + this_trait_vals.push(null); + } + } + all_vals.push(this_trait_vals); + } + + trait_vals_csv = trait_names.join(","); + trait_vals_csv += "\n"; + for (index = _k = 0, _len2 = samples.length; _k < _len2; index = ++_k) { + sample = samples[index]; + if (all_vals[0][index] === null) { + continue; + } + sample_vals = []; + for (_l = 0, _len3 = all_vals.length; _l < _len3; _l++) { + trait = all_vals[_l]; + sample_vals.push(trait[index]); + } + trait_vals_csv += sample_vals.join(","); + trait_vals_csv += "\n"; + } + return trait_vals_csv; +}; + +trait_click = function() { + var dataset, this_trait_url, trait; + + trait = $(this).parent().find('.trait').text(); + dataset = $(this).parent().find('.dataset').text(); + this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset; + $.ajax({ + dataType: "json", + url: this_trait_url, + success: get_trait_data + }); + return $.colorbox.close(); +}; + +trait_row_click = function() { + var dataset, this_trait_url, trait; + trait = $(this).find('.trait').text(); + dataset = $(this).find('.dataset').data("dataset"); + this_trait_url = "/trait/get_sample_data?trait=" + trait + "&dataset=" + dataset; + $.ajax({ + dataType: "json", + url: this_trait_url, + success: get_trait_data + }); + return $.colorbox.close(); +}; + +add_trait_data = function(trait_data, textStatus, jqXHR) { + var trait_name, trait_sample_data; + trait_name = trait_data[0]; + trait_sample_data = trait_data[1]; + selected_traits[trait_name] = trait_sample_data; + return console.log("selected_traits:", selected_traits); +}; + +populate_cofactor_info = function(trait_info) { + if ($('input[name=selecting_which_cofactor]').val() == "1"){ + $('#cofactor1_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor1_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor1_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor1_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor1').text("Change Cofactor 1"); + $('#cofactor1_info_container').css("display", "inline"); + $('#cofactor2_button').css("display", "inline-block"); + } else if ($('input[name=selecting_which_cofactor]').val() == "2"){ + $('#cofactor2_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor2_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor2_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor2_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor2').text("Change Cofactor 2"); + $('#cofactor2_info_container').css("display", "inline"); + $('#cofactor3_button').css("display", "inline-block"); + } else { + $('#cofactor3_trait_link').attr("href", trait_info['url']) + if (trait_info['type'] == "ProbeSet"){ + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['tissue'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['symbol'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } else if (trait_info['type'] == "Publish") { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + if ('pubmed_link' in trait_info) { + $('#cofactor3_description').html('<a href=\"' + trait_info['pubmed_link'] + '\">PubMed: ' + trait_info['pubmed_text'] + '</a><br>' + trait_info['description']) + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n" + trait_info['description']) + } + } else { + $('#cofactor3_trait_link').text(trait_info['species'] + " " + trait_info['group'] + " " + trait_info['db'] + ": " + trait_info['name']) + $('#cofactor3_description').text("[" + trait_info['name'] + " on " + trait_info['location'] + " Mb]\n") + } + $('#select_cofactor3').text("Change Cofactor 3"); + $('#cofactor3_info_container').css("display", "inline"); + } +} + +get_trait_data = function(trait_data, textStatus, jqXHR) { + var sample, samples, this_trait_vals, trait_sample_data, vals, _i, _len; + trait_sample_data = trait_data[1]; + if ( $('input[name=allsamples]').length ) { + samples = $('input[name=allsamples]').val().split(" "); + } else { + samples = js_data.indIDs + } + sample_vals = []; + vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + if (sample in trait_sample_data) { + sample_vals.push(sample + ":" + parseFloat(trait_sample_data[sample])) + vals.push(parseFloat(trait_sample_data[sample])) + } else { + sample_vals.push(null) + vals.push(null) + } + } + if ( $('input[name=allsamples]').length ) { + if ($('input[name=samples]').length < 1) { + $('#hidden_inputs').append('<input type="hidden" name="samples" value="[' + samples.toString() + ']" />'); + } + $('#hidden_inputs').append('<input type="hidden" name="vals" value="[' + vals.toString() + ']" />'); + this_trait_vals = get_this_trait_vals(samples); + return color_by_trait(trait_sample_data); + } else{ + sorted = vals.slice().sort(function(a,b){return a-b}) + ranks = vals.slice().map(function(v){ return sorted.indexOf(v)+1 }); + sample_ranks = [] + for (_i = 0; _i < samples.length; _i++){ + if (samples[_i] in trait_sample_data){ + sample_ranks.push(samples[_i] + ":" + ranks[_i]) + } else { + sample_ranks.push(null) + } + } + + if ($('input[name=selecting_which_cofactor]').val() == "1"){ + if ($('#cofactor1_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor1_vals]').val(sample_vals) + $('input[name=ranked_cofactor1_vals]').val(sample_ranks) + } else if ($('input[name=selecting_which_cofactor]').val() == "2"){ + if ($('#cofactor2_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor2_vals]').val(sample_vals) + $('input[name=ranked_cofactor2_vals]').val(sample_ranks) + } else{ + if ($('#cofactor3_type option:selected').val() == "symbol") { + unique_vals = [...new Set(vals)] + if (unique_vals.length > 45) { + alert("If displaying cofactor as symbol, please choose a trait with 45 or fewer distinct sample values."); + return false; + } + } + $('input[name=cofactor3_vals]').val(sample_vals) + $('input[name=ranked_cofactor3_vals]').val(sample_ranks) + } + populate_cofactor_info(trait_data[0]) + chartupdatedata(); + return false + } +}; + +get_this_trait_vals = function(samples) { + var sample, this_trait_vals, this_val, this_vals_json, _i, _len; + this_trait_vals = []; + for (_i = 0, _len = samples.length; _i < _len; _i++) { + sample = samples[_i]; + this_val = parseFloat($("input[name='value:" + sample + "']").val()); + if (!isNaN(this_val)) { + this_trait_vals.push(this_val); + } else { + this_trait_vals.push(null); + } + } + this_vals_json = '[' + this_trait_vals.toString() + ']'; + return this_trait_vals; +}; + +assemble_into_json = function(this_trait_vals) { + var json_data, json_ids, num_traits, samples; + num_traits = $('input[name=vals]').length; + samples = $('input[name=samples]').val(); + json_ids = samples; + json_data = '[' + this_trait_vals; + $('input[name=vals]').each((function(_this) { + return function(index, element) { + return json_data += ',' + $(element).val(); + }; + })(this)); + json_data += ']'; + return [json_ids, json_data]; +}; + +color_by_trait = function(trait_sample_data, textStatus, jqXHR) { + return root.bar_chart.color_by_trait(trait_sample_data); +}; + +process_traits = function(trait_data, textStatus, jqXHR) { + var the_html, trait, _i, _len; + the_html = "<button id='back_to_collections' class='btn btn-inverse btn-small'>"; + the_html += "<i class='icon-white icon-arrow-left'></i> Back </button>"; + the_html += " <button id='submit_cofactors' class='btn btn-primary btn-small submit'> Submit </button>"; + the_html += "<table id='collection_table' style='padding-top: 10px;' class='table table-hover'>"; + the_html += "<thead><tr><th></th><th>Record</th><th>Data Set</th><th>Description</th></tr></thead>"; + the_html += "<tbody>"; + for (_i = 0, _len = trait_data.length; _i < _len; _i++) { + trait = trait_data[_i]; + the_html += "<tr class='trait_line'>"; + the_html += "<td class='select_trait'><input type='checkbox' name='selectCheck' class='checkbox edit_sample_checkbox'></td>"; + if ("abbreviation" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.abbreviation + "'>" + trait.name + "</td>"; + } else if ("symbol" in trait) { + the_html += "<td class='trait' data-display_name='" + trait.name + " - " + trait.symbol + "'>" + trait.name + "</td>"; + } else { + the_html += "<td class='trait' data-display_name='" + trait.name + "'>" + trait.name + "</td>"; + } + the_html += "<td class='dataset' data-dataset='" + trait.dataset + "'>" + trait.dataset_name + "</td>"; + the_html += "<td class='description'>" + trait.description + "</td>"; + } + the_html += "</tbody>"; + the_html += "</table>"; + the_html += "<script type='text/javascript' src='/static/new/javascript/get_traits_from_collection.js'></script>" + $("#collections_holder").html(the_html); + return $('#collections_holder').colorbox.resize(); +}; + +back_to_collections = function() { + $("#collections_holder").html(collection_list); + $(document).on("click", ".collection_line", collection_click); + return $('#collections_holder').colorbox.resize(); +}; + +$(".collection_line").on("click", collection_click); +$("#submit_cofactors").on("click", submit_click); +if ($('#scatterplot2').length){ + $(".trait_line").on("click", trait_row_click); +} else { + $(".trait").on("click", trait_click); +} +$("#back_to_collections").on("click", back_to_collections); diff --git a/gn2/wqflask/static/new/javascript/group_manager.js b/gn2/wqflask/static/new/javascript/group_manager.js new file mode 100644 index 00000000..cd56133a --- /dev/null +++ b/gn2/wqflask/static/new/javascript/group_manager.js @@ -0,0 +1,37 @@ +$('#add_to_admins').click(function() { + add_emails('admin') +}) + +$('#add_to_members').click(function() { + add_emails('member') +}) + +$('#clear_admins').click(function(){ + clear_emails('admin') +}) + +$('#clear_members').click(function(){ + clear_emails('member') +}) + + +function add_emails(user_type){ + let email_address = $('input[name=user_email]').val(); + let email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim() + if (email_list_string == ""){ + let email_set = new Set(); + } else { + let email_set = new Set(email_list_string.split(",")) + } + email_set.add(email_address) + + $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(',')) + + let emails_display_string = Array.from(email_set).join('\n') + $('.added_' + user_type + 's').val(emails_display_string) +} + +function clear_emails(user_type){ + $('input[name=' + user_type + '_emails_to_add]').val("") + $('.added_' + user_type + 's').val("") +} diff --git a/gn2/wqflask/static/new/javascript/histogram.js b/gn2/wqflask/static/new/javascript/histogram.js new file mode 100644 index 00000000..f71080e8 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/histogram.js @@ -0,0 +1,134 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var Histogram, root; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + Histogram = (function() { + function Histogram(sample_list1, sample_group) { + this.sample_list = sample_list1; + this.sample_group = sample_group; + this.sort_by = "name"; + this.format_count = d3.format(",.0f"); + this.margin = { + top: 10, + right: 30, + bottom: 30, + left: 30 + }; + this.plot_width = 960 - this.margin.left - this.margin.right; + this.plot_height = 500 - this.margin.top - this.margin.bottom; + this.x_buffer = this.plot_width / 20; + this.y_buffer = this.plot_height / 20; + this.plot_height -= this.y_buffer; + this.get_sample_vals(this.sample_list); + this.redraw(this.sample_vals); + } + + Histogram.prototype.redraw = function(sample_vals) { + this.sample_vals = sample_vals; + this.y_min = d3.min(this.sample_vals); + this.y_max = d3.max(this.sample_vals) * 1.1; + this.create_x_scale(); + this.get_histogram_data(); + this.create_y_scale(); + $("#histogram").empty(); + this.svg = this.create_svg(); + return this.create_graph(); + }; + + Histogram.prototype.get_sample_vals = 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; + })(); + }; + + Histogram.prototype.create_svg = function() { + var svg; + svg = d3.select("#histogram").append("svg").attr("class", "histogram").attr("width", this.plot_width + this.margin.left + this.margin.right).attr("height", this.plot_height + this.margin.top + this.margin.bottom).append("g").attr("transform", "translate(" + this.margin.left + "," + this.margin.top + ")"); + return svg; + }; + + Histogram.prototype.create_x_scale = function() { + var x0; + console.log("min/max:", d3.min(this.sample_vals) + "," + d3.max(this.sample_vals)); + x0 = Math.max(-d3.min(this.sample_vals), d3.max(this.sample_vals)); + return this.x_scale = d3.scale.linear().domain([d3.min(this.sample_vals), d3.max(this.sample_vals)]).range([0, this.plot_width]).nice(); + }; + + Histogram.prototype.get_histogram_data = function() { + var n_bins; + console.log("sample_vals:", this.sample_vals); + n_bins = 2*Math.sqrt(this.sample_vals.length); //Was originally just the square root, but increased to 2*; ideally would be a GUI for changing this + this.histogram_data = d3.layout.histogram().bins(this.x_scale.ticks(n_bins))(this.sample_vals); + return console.log("histogram_data:", this.histogram_data[0]); + }; + + Histogram.prototype.create_y_scale = function() { + return this.y_scale = d3.scale.linear().domain([ + 0, d3.max(this.histogram_data, (function(_this) { + return function(d) { + return d.y; + }; + })(this)) + ]).range([this.plot_height, 0]); + }; + + Histogram.prototype.create_graph = function() { + this.add_x_axis(); + this.add_y_axis(); + return this.add_bars(); + }; + + Histogram.prototype.add_x_axis = function() { + var x_axis; + x_axis = d3.svg.axis().scale(this.x_scale).orient("bottom"); + return this.svg.append("g").attr("class", "x axis").attr("transform", "translate(0," + this.plot_height + ")").call(x_axis); + }; + + Histogram.prototype.add_y_axis = function() { + var yAxis; + yAxis = d3.svg.axis().scale(this.y_scale).orient("left").ticks(5); + return this.svg.append("g").attr("class", "y axis").call(yAxis).append("text").attr("transform", "rotate(-90)").attr("y", 6).attr("dy", ".71em").style("text-anchor", "end"); + }; + + Histogram.prototype.add_bars = function() { + var bar, rect_width; + bar = this.svg.selectAll(".bar").data(this.histogram_data).enter().append("g").attr("class", "bar").attr("transform", (function(_this) { + return function(d) { + return "translate(" + _this.x_scale(d.x) + "," + _this.y_scale(d.y) + ")"; + }; + })(this)); + rect_width = this.x_scale(this.histogram_data[0].x + this.histogram_data[0].dx) - this.x_scale(this.histogram_data[0].x); + bar.append("rect").attr("x", 1).attr("width", rect_width - 1).attr("height", (function(_this) { + return function(d) { + return _this.plot_height - _this.y_scale(d.y); + }; + })(this)); + return bar.append("text").attr("dy", ".75em").attr("y", 6).attr("x", rect_width / 2).attr("text-anchor", "middle").style("fill", "#fff").text((function(_this) { + return function(d) { + var bar_height; + bar_height = _this.plot_height - _this.y_scale(d.y); + if (bar_height > 20) { + return _this.format_count(d.y); + } + }; + })(this)); + }; + + return Histogram; + + })(); + + root.Histogram = Histogram; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/init_genome_browser.js b/gn2/wqflask/static/new/javascript/init_genome_browser.js new file mode 100644 index 00000000..508f5bf2 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/init_genome_browser.js @@ -0,0 +1,82 @@ +snps_filename = "/browser_input?filename=" + js_data.browser_files[0] +annot_filename = "/browser_input?filename=" + js_data.browser_files[1] + +localUrls = +{ + snps: snps_filename, + annotations: annot_filename +}; + +var coordinateSystem = js_data.chr_lengths + +var vscaleWidth = 90.0; +var legendWidth = 150.0; + +if ('significant' in js_data) { + var significant_score = parseFloat(js_data.significant) +} else { + var significant_score = js_data.max_score * 0.75 +} +var score = { min: 0.0, max: js_data.max_score, sig: significant_score }; +var gwasPadding = { top: 35.0, + bottom: 35.0, + left: vscaleWidth, + right: legendWidth }; +var gwasHeight = 500.0; +var config = +{ score: score, + urls: localUrls, + tracks: { + gwas: { + trackHeight: gwasHeight, + padding: gwasPadding, + snps: { + radius: 3.75, + lineWidth: 1.0, + color: { outline: "#FFFFFF", + fill: "#00008B" }, + pixelOffset: {x: 0.0, y: 0.0} + }, + annotations: { + urls: { + url: "GeneNetwork" + }, + radius: 5.5, + outline: "#000000", + snpColor: "#0074D9", + geneColor: "#FF4136" + }, + score: score, + legend: { + fontSize: 14, + hPad: 0.1, + vPad: 0.2 + }, + vscale: { + color: "#000000", + hPad: 0.125, + numSteps: 3, + fonts: { labelSize: 18, scaleSize: 16 } + }, + }, + }, + chrs: { + chrBG1: "#FFFFFF", + chrBG2: "#EEEEEE", + chrLabels: { fontSize: 16 }, + }, + // initialChrs: { left: "1", right: "5" } + coordinateSystem: coordinateSystem, +}; + +if (js_data.selected_chr != -1) { + config['initialChrs'] = {left: js_data.selected_chr, right: js_data.selected_chr} +} + +$('#browser_tab').click(function() { + if ($('#gwas').length == 0){ + GenomeBrowser.main(config)(); + } +}); + +document.getElementById("controls").style.visibility = "visible";
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js new file mode 100644 index 00000000..44076c17 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/initialize_show_trait_tables.js @@ -0,0 +1,246 @@ +// This file initializes the tables for the show_trait page + +// This variable is just created to get the column position of the first case attribute (if case attributes exist), since it's needed to set the row classes in createdRow for the DataTable +var attributeStartPos = 3; +if (js_data.se_exists) { + attributeStartPos += 2; +} +if (js_data.has_num_cases === true) { + attributeStartPos += 1; +} + +buildColumns = function() { + let columnList = [ + { + 'data': null, + 'orderDataType': "dom-checkbox", + 'searchable' : false, + 'targets': 0, + 'width': "25px", + 'render': function() { + return '<input type="checkbox" name="searchResult" class="checkbox edit_sample_checkbox" value="">' + } + }, + { + 'title': "ID", + 'type': "natural", + 'searchable' : false, + 'targets': 1, + 'width': "35px", + 'data': "this_id" + }, + { + 'title': "Sample", + 'type': "natural", + 'data': null, + 'targets': 2, + 'width': "60px", + 'render': function(data) { + return '<span class="edit_sample_sample_name">' + data.name + '</span>' + } + }, + { + 'title': "<div style='text-align: right;'>Value</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 3, + 'width': "60px", + 'render': function(data) { + if (data.value == null) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" style="text-align: right;" class="trait_value_input edit_sample_value" value="x" size=' + js_data.max_digits[0] + '>' + } else { + if (js_data.no_decimal_place == false) { + return '<input type="text" data-value="' + data.value.toFixed(3) + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value.toFixed(3) + '" size=' + js_data.max_digits[0] + '>' + } else { + return '<input type="text" data-value="' + data.value + '" data-qnorm="' + js_data['qnorm_values'][0][parseInt(data.this_id) - 1] + '" data-zscore="' + js_data['zscore_values'][0][parseInt(data.this_id) - 1] + '" name="value:' + data.name + '" class="trait_value_input edit_sample_value" value="' + data.value + '" size=' + js_data.max_digits[0] + '>' + } + } + } + } + ]; + + attrStart = 4 + if (js_data.se_exists) { + attrStart += 2 + columnList.push( + { + 'bSortable': false, + 'type': "natural", + 'data': null, + 'targets': 4, + 'searchable' : false, + 'width': "25px", + 'render': function() { + return '±' + } + }, + { + 'title': "<div style='text-align: right;'>SE</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 5, + 'width': "60px", + 'render': function(data) { + if (data.variance == null) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="x" size=6>' + } else { + return '<input type="text" data-value="' + data.variance.toFixed(3) + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_se" value="' + data.variance.toFixed(3) + '" size=6>' + } + } + } + ); + + if (js_data.has_num_cases === true) { + attrStart += 1 + columnList.push( + { + 'title': "<div style='text-align: right;'>N</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 6, + 'width': "60px", + 'render': function(data) { + if (data.num_cases == null || data.num_cases == undefined) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' + } else { + return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' + } + } + } + ); + } + } + else { + if (js_data.has_num_cases === true) { + attrStart += 1 + columnList.push( + { + 'title': "<div style='text-align: right;'>N</div>", + 'orderDataType': "dom-input", + 'type': "cust-txt", + 'data': null, + 'targets': 4, + 'width': "60px", + 'render': function(data) { + if (data.num_cases == null || data.num_cases == undefined) { + return '<input type="text" data-value="x" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="x" size=4 maxlength=4>' + } else { + return '<input type="text" data-value="' + data.num_cases + '" data-qnorm="x" data-zscore="x" name="value:' + data.name + '" class="trait_value_input edit_sample_num_cases" value="' + data.num_cases + '" size=4 maxlength=4>' + } + } + } + ); + } + } + + attrKeys = Object.keys(js_data.attributes).sort((a, b) => (js_data.attributes[a].id > js_data.attributes[b].id) ? 1 : -1) + for (i = 0; i < attrKeys.length; i++){ + columnList.push( + { + 'title': "<div title='" + js_data.attributes[attrKeys[i]].description + "' style='text-align: " + js_data.attributes[attrKeys[i]].alignment + "'>" + js_data.attributes[attrKeys[i]].name + "</div>", + 'type': "natural", + 'data': null, + 'targets': attrStart + i, + 'render': function(data, type, row, meta) { + attr_name = Object.keys(data.extra_attributes).sort((a, b) => (parseInt(a) > parseInt(b)) ? 1 : -1)[meta.col - data.first_attr_col] + + if (attr_name != null && attr_name != undefined){ + if (Array.isArray(data.extra_attributes[attr_name])){ + return '<a href="' + data.extra_attributes[attr_name][1] + '">' + data.extra_attributes[attr_name][0] + '</a>' + } else { + return data.extra_attributes[attr_name] + } + } else { + return "" + } + } + } + ) + } + return columnList +} + +columnDefs = buildColumns(); + +tableIds = ["samples_primary"] +if (js_data.sample_lists.length > 1) { + tableIds.push("samples_other") +} + +for (var i = 0; i < tableIds.length; i++) { + tableId = tableIds[i] + + if (tableId == "samples_primary"){ + tableType = "Primary" + } else { + tableType = "Other" + } + + tableSettings = { + "drawCallback": function( settings ) { + $('#' + tableId + ' tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(this).find('input'); + obj.prop('checked', !obj.is(':checked')); + } + if ($(this).hasClass("selected") && event.target.tagName.toLowerCase() !== 'a'){ + $(this).removeClass("selected") + } else if (event.target.tagName.toLowerCase() !== 'a') { + $(this).addClass("selected") + } + }); + }, + 'createdRow': function ( row, data, index ) { + $(row).attr('id', tableType + "_" + data.this_id) + $(row).addClass("value_se"); + if (data.outlier) { + $(row).addClass("outlier"); + $(row).attr("style", "background-color: orange;"); + } + $('td', row).eq(1).addClass("column_name-Index") + $('td', row).eq(2).addClass("column_name-Sample") + $('td', row).eq(3).addClass("column_name-Value") + if (js_data.se_exists) { + $('td', row).eq(5).addClass("column_name-SE") + if (js_data.has_num_cases === true) { + $('td', row).eq(6).addClass("column_name-num_cases") + } else { + if (js_data.has_num_cases === true) { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + } else { + if (js_data.has_num_cases === true) { + $('td', row).eq(4).addClass("column_name-num_cases") + } + } + + for (j=0; j < attrKeys.length; j++) { + $('td', row).eq(attributeStartPos + j + 1).addClass("column_name-" + js_data.attributes[attrKeys[j]].name) + $('td', row).eq(attributeStartPos + j + 1).attr("style", "text-align: " + js_data.attributes[attrKeys[j]].alignment + "; padding-top: 2px; padding-bottom: 0px;") + } + } + } + + create_table(tableId, js_data['sample_lists'][i], columnDefs, tableSettings); + + // Enable mapping compute buttons and replace their text only after table has loaded + // This is because submitting the form prior to the table loading causes an error + $('button.submit_special').html('<span class="glyphicon glyphicon-play-circle"></span> Compute'); + $('button.submit_special').prop('disabled', false); +} + +primary_table = $('#samples_primary').DataTable(); +$('#primary_searchbox').on( 'keyup', function () { + primary_table.search($(this).val()).draw(); +} ); + +if ($('#samples_other').length) { + other_table = $('#samples_other').DataTable(); + $('#other_searchbox').on( 'keyup', function () { + other_table.search($(this).val()).draw(); + } ); +} diff --git a/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js b/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js new file mode 100644 index 00000000..5ecf46e1 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/iplotMScanone_noeff.js @@ -0,0 +1,114 @@ +// Generated by CoffeeScript 1.8.0 +var iplotMScanone_noeff, lod_data; + +iplotMScanone_noeff = function(lod_data, times, chartOpts) { + var axispos, chartdivid, chrGap, colors, darkrect, extra_digits, g_heatmap, g_lodchart, hbot, htop, i, lightrect, linecolor, linewidth, lod4curves, lod_labels, lod_ylab, lodchart_curves, lodcolumn, lodcurve, margin, mylodchart, mylodheatmap, nullcolor, nxticks, plotLodCurve, pos, svg, titlepos, totalh, totalw, wleft, wright, x, xticks, y, zlim, zthresh, _ref, _ref1, _ref10, _ref11, _ref12, _ref13, _ref14, _ref15, _ref16, _ref17, _ref18, _ref19, _ref2, _ref20, _ref3, _ref4, _ref5, _ref6, _ref7, _ref8, _ref9; + wleft = (_ref = chartOpts != null ? chartOpts.wleft : void 0) != null ? _ref : 1000; + wright = (_ref1 = chartOpts != null ? chartOpts.wright : void 0) != null ? _ref1 : 500; + htop = (_ref2 = chartOpts != null ? chartOpts.htop : void 0) != null ? _ref2 : 350; + hbot = (_ref3 = chartOpts != null ? chartOpts.hbot : void 0) != null ? _ref3 : 350; + margin = (_ref4 = chartOpts != null ? chartOpts.margin : void 0) != null ? _ref4 : { + left: 100, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = (_ref5 = chartOpts != null ? chartOpts.axispos : void 0) != null ? _ref5 : { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = (_ref6 = chartOpts != null ? chartOpts.titlepos : void 0) != null ? _ref6 : 20; + chrGap = (_ref7 = chartOpts != null ? chartOpts.chrGap : void 0) != null ? _ref7 : 8; + darkrect = (_ref8 = chartOpts != null ? chartOpts.darkrect : void 0) != null ? _ref8 : "#C8C8C8"; + lightrect = (_ref9 = chartOpts != null ? chartOpts.lightrect : void 0) != null ? _ref9 : "#E6E6E6"; + nullcolor = (_ref10 = chartOpts != null ? chartOpts.nullcolor : void 0) != null ? _ref10 : "#E6E6E6"; + colors = (_ref11 = chartOpts != null ? chartOpts.colors : void 0) != null ? _ref11 : ["slateblue", "white", "crimson"]; + zlim = (_ref12 = chartOpts != null ? chartOpts.zlim : void 0) != null ? _ref12 : null; + zthresh = (_ref13 = chartOpts != null ? chartOpts.zthresh : void 0) != null ? _ref13 : null; + lod_ylab = (_ref14 = chartOpts != null ? chartOpts.lod_ylab : void 0) != null ? _ref14 : ""; + linecolor = (_ref15 = chartOpts != null ? chartOpts.linecolor : void 0) != null ? _ref15 : "darkslateblue"; + linewidth = (_ref16 = chartOpts != null ? chartOpts.linewidth : void 0) != null ? _ref16 : 2; + nxticks = (_ref17 = chartOpts != null ? chartOpts.nxticks : void 0) != null ? _ref17 : 5; + xticks = (_ref18 = chartOpts != null ? chartOpts.xticks : void 0) != null ? _ref18 : null; + lod_labels = (_ref19 = chartOpts != null ? chartOpts.lod_labels : void 0) != null ? _ref19 : null; + chartdivid = (_ref20 = chartOpts != null ? chartOpts.chartdivid : void 0) != null ? _ref20 : 'chart'; + totalh = htop + hbot + 2 * (margin.top + margin.bottom); + totalw = wleft + wright + 2 * (margin.left + margin.right); + if (lod_labels == null) { + lod_labels = times != null ? (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = times.length; _i < _len; _i++) { + x = times[_i]; + _results.push(formatAxis(times, extra_digits = 1)(x)); + } + return _results; + })() : lod_data.lodnames; + } + mylodheatmap = lodheatmap().height(htop).width(wleft).margin(margin).axispos(axispos); + svg = d3.select("div#" + chartdivid).append("svg").attr("height", totalh).attr("width", totalw); + g_heatmap = svg.append("g").attr("id", "heatmap").datum(lod_data).call(mylodheatmap); + mylodchart = lodchart().height(hbot).width(wleft).margin(margin).axispos(axispos).titlepos(titlepos).chrGap(chrGap).linecolor("none").pad4heatmap(true).darkrect(darkrect).lightrect(lightrect).ylim([0, d3.max(mylodheatmap.zlim())]).pointsAtMarkers(false); + g_lodchart = svg.append("g").attr("transform", "translate(0," + (htop + margin.top + margin.bottom) + ")").attr("id", "lodchart").datum(lod_data).call(mylodchart); + lodcurve = function(chr, lodcolumn) { + return d3.svg.line().x(function(d) { + return mylodchart.xscale()[chr](d); + }).y(function(d, i) { + return mylodchart.yscale()(Math.abs(lod_data.lodByChr[chr][i][lodcolumn])); + }); + }; + lodchart_curves = null; + plotLodCurve = function(lodcolumn) { + var chr, _i, _len, _ref21, _results; + g_lodchart.selectAll("g#curves").remove(); + lodchart_curves = g_lodchart.append("g").attr("id", "lodcurves"); + _ref21 = lod_data.chrnames; + _results = []; + for (_i = 0, _len = _ref21.length; _i < _len; _i++) { + chr = _ref21[_i]; + _results.push(lodchart_curves.append("path").datum(lod_data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodcolumn)).attr("stroke", linecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none")); + } + return _results; + }; + lod4curves = { + data: [] + }; + for (pos in lod_data.pos) { + y = (function() { + var _i, _len, _ref21, _results; + _ref21 = lod_data.lodnames; + _results = []; + for (_i = 0, _len = _ref21.length; _i < _len; _i++) { + lodcolumn = _ref21[_i]; + _results.push(Math.abs(lod_data[lodcolumn][pos])); + } + return _results; + })(); + x = (function() { + var _results; + _results = []; + for (i in lod_data.lodnames) { + _results.push(+i); + } + return _results; + })(); + lod4curves.data.push({ + x: x, + y: y + }); + } + return mylodheatmap.cellSelect().on("mouseover", function(d) { + var p; + plotLodCurve(d.lodindex); + g_lodchart.select("g.title text").text("" + lod_labels[d.lodindex]); + return p = d3.format(".1f")(d.pos); + }).on("mouseout", function(d) { + lodchart_curves.remove(); + return g_lodchart.select("g.title text").text(""); + }); +}; + +iplotMScanone_noeff(lod_data = js_data.json_data); diff --git a/gn2/wqflask/static/new/javascript/loadings_plot.js b/gn2/wqflask/static/new/javascript/loadings_plot.js new file mode 100644 index 00000000..c44288c0 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/loadings_plot.js @@ -0,0 +1,109 @@ +var margin = {top: 20, right: 70, bottom: 60, left: 60} + , width = 960 - margin.left - margin.right + , height = 500 - margin.top - margin.bottom; + +var x = d3.scale.linear() + .domain([d3.min(loadings, function(d) { return d[0]; }) + 0.1*d3.min(loadings, function(d) { return d[0]; }), d3.max(loadings, function(d) { return d[0]; })]) + .range([ 0, width ]); + +var y = d3.scale.linear() + .domain([d3.min(loadings, function(d) { return d[1]; }) + 0.1*d3.min(loadings, function(d) { return d[1]; }), d3.max(loadings, function(d) { return d[1]; })]) + .range([ height, 0 ]); + +var chart = d3.select('#loadings_plot') + .append('svg:svg') + .attr('width', width + margin.right + margin.left) + .attr('height', height + margin.top + margin.bottom) + .attr('class', 'chart') + +var main = chart.append('g') + .attr('transform', 'translate(' + margin.left + ',' + margin.top + ')') + .attr('width', width) + .attr('height', height) + .attr('class', 'main') + +// draw the x axis +var xAxis = d3.svg.axis() + .scale(x) + .orient('bottom'); + +main.append('g') + .attr('transform', 'translate(0,' + height + ')') + .attr('class', 'x axis') + .call(xAxis); + +chart.append("text") + .attr("class", "x label") + .attr("text-anchor", "end") + .attr("x", 550) + .attr("y", 480) + .style("font-size", 14) + .style("fill", "blue") + .text("Factor (1)"); + +chart.append("text") + .attr("class", "y label") + .attr("text-anchor", "end") + .attr("x", -200) + .attr("y", 5) + .attr("dy", ".75em") + .attr("transform", "rotate(-90)") + .style("font-size", 14) + .style("fill", "blue") + .text("Factor (2)"); + +// draw the y axis +var yAxis = d3.svg.axis() + .scale(y) + .orient('left'); + +main.append('g') + .attr('transform', 'translate(0,0)') + .attr('class', 'y axis') + .call(yAxis); + +chart.select('.x.axis') + .selectAll("text") + .style("font-size","14px"); + +chart.select('.y.axis') + .selectAll("text") + .style("font-size","14px"); + +var g = main.append("svg:g"); + +g.selectAll("scatter-dots") + .data(loadings) + .enter().append("svg:circle") + .attr("cx", function (d,i) { return x(d[0]); } ) + .attr("cy", function (d) { return y(d[1]); } ) + .attr("r", 4) + .style("fill", "blue"); + +traits_and_loadings = [] +for (i = 0; i < js_data.traits.length; i++) { + this_trait_loadings = [] + this_trait_loadings[0] = js_data.traits[i] + this_trait_loadings[1] = [loadings[i][0], loadings[i][1]] + traits_and_loadings[i] = this_trait_loadings +} + +g.selectAll("scatter-dots") + .data(traits_and_loadings) + .enter().append("text") + .attr("x", function(d, i) { return x(d[1][0]); }) + .attr("y", function(d) { return y(d[1][1]); }) + .text(function(d) { return d[0]; }) + .style("font-size", 12) + .style("fill", "blue"); + +g.selectAll("scatter-lines") + .data(loadings) + .enter().append("svg:line") + .attr("x1", x(0)) + .attr("y1", y(0)) + .attr("x2", function (d,i) {return x(d[0]); } ) + .attr("y2", function (d) { return y(d[1]); } ) + .attr("stroke-width", 1) + .attr("stroke", "red"); +
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/lod_chart.js b/gn2/wqflask/static/new/javascript/lod_chart.js new file mode 100644 index 00000000..014bf59b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/lod_chart.js @@ -0,0 +1,473 @@ +// Generated by CoffeeScript 1.9.2 +var lodchart; + +lodchart = function() { + var additive, additive_ylab, additive_ylim, additive_yscale, additive_yticks, additivelinecolor, axispos, chart, chrGap, chrSelect, darkrect, height, lightrect, linewidth, lodcurve, lodlinecolor, lodvarname, manhattanPlot, mappingScale, margin, markerSelect, nyticks, pad4heatmap, pointcolor, pointsAtMarkers, pointsize, pointstroke, rotate_ylab, significantcolor, suggestivecolor, title, titlepos, width, xlab, xscale, ylab, ylim, yscale, yticks; + width = 800; + height = 500; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + manhattanPlot = false; + ylim = null; + additive_ylim = null; + nyticks = 5; + yticks = null; + additive_yticks = null; + chrGap = 8; + darkrect = "#F1F1F9"; + lightrect = "#FBFBFF"; + lodlinecolor = "darkslateblue"; + additivelinecolor_plus = "red"; + additivelinecolor_negative = "green"; + linewidth = 2; + suggestivecolor = "gainsboro"; + significantcolor = "#EBC7C7"; + pointcolor = "#E9CFEC"; + pointsize = 0; + pointstroke = "black"; + title = ""; + xlab = "Chromosome"; + ylab = "LRS score"; + additive_ylab = "Additive Effect"; + rotate_ylab = null; + yscale = d3.scale.linear(); + additive_yscale = d3.scale.linear(); + xscale = null; + pad4heatmap = false; + lodcurve = null; + lodvarname = null; + markerSelect = null; + chrSelect = null; + pointsAtMarkers = true; + chart = function(selection) { + return selection.each(function(data) { + var additive_yaxis, additivecurve, chr, curves, g, gEnter, hiddenpoints, j, k, len, len1, lodvarnum, markerpoints, markertip, redraw_plot, ref, ref1, rotate_additive_ylab, suggestive_bar, svg, titlegrp, x, xaxis, yaxis; + if (manhattanPlot === true) { + pointcolor = "darkslateblue"; + pointsize = 2; + } + lodvarname = lodvarname != null ? lodvarname : data.lodnames[0]; + data[lodvarname] = (function() { + var j, len, ref, results; + ref = data[lodvarname]; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + results.push(Math.abs(x)); + } + return results; + })(); + ylim = ylim != null ? ylim : [0, d3.max(data[lodvarname])]; + + if ('additive' in data) { + data['additive'] = (function() { + var j, len, ref, results; + ref = data['additive']; + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + results.push(x); + } + return results; + })(); + additive_ylim = additive_ylim != null ? additive_ylim : [0, d3.max(data['additive'])]; + } + lodvarnum = data.lodnames.indexOf(lodvarname); + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", width).attr("fill", darkrect).attr("stroke", "none"); + yscale.domain(ylim).range([height + margin.top, margin.top + margin.inner]); + yticks = yticks != null ? yticks : yscale.ticks(nyticks); + if ('additive' in data) { + additive_yscale.domain(additive_ylim).range([height + margin.top, margin.top + margin.inner + height / 2]); + additive_yticks = additive_yticks != null ? additive_yticks : additive_yscale.ticks(nyticks); + } + reorgLodData(data, lodvarname); + data = chrscales(data, width, chrGap, margin.left, pad4heatmap, mappingScale); + xscale = data.xscale; + chrSelect = g.append("g").attr("class", "chrRect").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { + return "chrrect" + d[0]; + }).attr("x", function(d, i) { + if (i === 0 && pad4heatmap) { + return data.chrStart[i]; + } + return data.chrStart[i] - chrGap / 2; + }).attr("width", function(d, i) { + if ((i === 0 || i + 1 === data.chrnames.length) && pad4heatmap) { + return data.chrEnd[i] - data.chrStart[i] + chrGap / 2; + } + return data.chrEnd[i] - data.chrStart[i] + chrGap; + }).attr("y", margin.top).attr("height", height).attr("fill", function(d, i) { + if (i % 2) { + return darkrect; + } + return lightrect; + }).attr("stroke", "none").on("click", function(d) { + console.log("d is:", d); + return redraw_plot(d); + }); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(data.chrnames).enter().append("text").text(function(d) { + return d[0]; + }).attr("x", function(d, i) { + return (data.chrStart[i] + data.chrEnd[i]) / 2; + }).attr("y", margin.top + height + axispos.xlabel).attr("dominant-baseline", "hanging").attr("text-anchor", "middle").attr("cursor", "pointer").on("click", function(d) { + return redraw_plot(d); + }); + xaxis.append("text").attr("class", "title").attr("y", margin.top + height + axispos.xtitle).attr("x", margin.left + width / 2).attr("fill", "slateblue").text(xlab); + redraw_plot = function(chr_ob) { + var chr_plot; + $('#topchart').remove(); + $('#chart_container').append('<div class="qtlcharts" id="topchart"></div>'); + return chr_plot = new Chr_Lod_Chart(600, 1200, chr_ob, manhattanPlot, mappingScale); + }; + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).attr("fill", "blue").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : "").attr("text-anchor", "middle").attr("fill", "slateblue"); + if ('additive' in data) { + rotate_additive_ylab = rotate_additive_ylab != null ? rotate_additive_ylab : additive_ylab.length > 1; + additive_yaxis = g.append("g").attr("class", "y axis"); + additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("line").attr("y1", function(d) { + return additive_yscale(d); + }).attr("y2", function(d) { + return additive_yscale(d); + }).attr("x1", margin.left + width).attr("x2", margin.left + width - 7).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + additive_yaxis.selectAll("empty").data(additive_yticks).enter().append("text").attr("y", function(d) { + return additive_yscale(d); + }).attr("x", function(d) { + return margin.left + width + axispos.ylabel + 20; + }).attr("fill", "green").attr("dominant-baseline", "middle").attr("text-anchor", "end").text(function(d) { + return formatAxis(additive_yticks)(d); + }); + additive_yaxis.append("text").attr("class", "title").attr("y", margin.top + 1.5 * height).attr("x", margin.left + width + axispos.ytitle).text(additive_ylab).attr("transform", rotate_additive_ylab ? "rotate(270," + (margin.left + width + axispos.ytitle) + ", " + (margin.top + height * 1.5) + ")" : "").attr("text-anchor", "middle").attr("fill", "green"); + } + if ('suggestive' in data) { + suggestive_bar = g.append("g").attr("class", "suggestive"); + suggestive_bar.selectAll("empty").data([data.suggestive]).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", suggestivecolor).attr("stroke-width", 5).style("pointer-events", "none"); + suggestive_bar = g.append("g").attr("class", "significant"); + suggestive_bar.selectAll("empty").data([data.significant]).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", significantcolor).attr("stroke-width", 5).style("pointer-events", "none"); + } + if (manhattanPlot === false) { + lodcurve = function(chr, lodcolumn) { + return d3.svg.line().x(function(d) { + return xscale[chr](d); + }).y(function(d, i) { + return yscale(data.lodByChr[chr][i][lodcolumn]); + }); + }; + if ('additive' in data) { + additivecurve = function(chr, lodcolumn) { + if (data.additiveByChr[chr][0] < 0) { + pos_neg = "negative" + } + else { + pos_neg = "positive" + } + return [pos_neg, d3.svg.line().x(function(d) { + return xscale[chr](d); + }).y(function(d, i) { + return additive_yscale(Math.abs(data.additiveByChr[chr][i])); + })]; + }; + } + curves = g.append("g").attr("id", "curves"); + ref = data.chrnames; + for (j = 0, len = ref.length; j < len; j++) { + chr = ref[j]; + if (chr.indexOf(data['chr'])) { + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", lodcurve(chr[0], lodvarnum)).attr("stroke", lodlinecolor).attr("fill", "none").attr("stroke-width", linewidth).style("pointer-events", "none"); + } + } + if ('additive' in data) { + ref1 = data.chrnames; + for (k = 0, len1 = ref1.length; k < len1; k++) { + chr = ref1[k]; + if (chr.indexOf(data['chr'])) { + if (additivecurve(chr[0], lodvarnum)[0] == "negative") { + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_negative).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); + } + else { + curves.append("path").datum(data.posByChr[chr[0]]).attr("d", additivecurve(chr[0], lodvarnum)[1]).attr("stroke", additivelinecolor_plus).attr("fill", "none").attr("stroke-width", 1).style("pointer-events", "none"); + } + } + } + } + } + console.log("before pointsize"); + if (pointsize > 0) { + console.log("pointsize > 0 !!!"); + } + markerpoints = g.append("g").attr("id", "markerpoints_visible"); + markerpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) { + return xscale[d.chr](d.pos); + }).attr("cy", function(d) { + return yscale(d.lod); + }).attr("r", pointsize).attr("fill", pointcolor).attr("stroke", pointstroke).attr("pointer-events", "hidden"); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", height).attr("width", function() { + if (pad4heatmap) { + return data.chrEnd.slice(-1)[0] - margin.left; + } + return data.chrEnd.slice(-1)[0] - margin.left + chrGap / 2; + }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + if (pointsAtMarkers) { + hiddenpoints = g.append("g").attr("id", "markerpoints_hidden"); + markertip = d3.tip().attr('class', 'd3-tip').html(function(d) { + return [d.name, " LRS = " + (d3.format('.2f')(d.lod))]; + }).direction("e").offset([0, 10]); + svg.call(markertip); + return markerSelect = hiddenpoints.selectAll("empty").data(data.markers).enter().append("circle").attr("cx", function(d) { + return xscale[d.chr](d.pos); + }).attr("cy", function(d) { + return yscale(d.lod); + }).attr("id", function(d) { + return d.name; + }).attr("r", d3.max([pointsize * 2, 3])).attr("opacity", 0).attr("fill", pointcolor).attr("stroke", pointstroke).attr("stroke-width", "1").on("mouseover.paneltip", function(d) { + d3.select(this).attr("opacity", 1); + return markertip.show(d); + }).on("mouseout.paneltip", function() { + return d3.select(this).attr("opacity", 0).call(markertip.hide); + }); + } + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.manhattanPlot = function(value) { + if (!arguments.length) { + return manhattanPlot; + } + manhattanPlot = value; + return chart; + }; + chart.mappingScale = function(value) { + if (!arguments.length) { + return mappingScale; + } + mappingScale = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.additive_ylim = function(value) { + if (!arguments.length) { + return additive_ylim; + } + additive_ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.chrGap = function(value) { + if (!arguments.length) { + return chrGap; + } + chrGap = value; + return chart; + }; + chart.darkrect = function(value) { + if (!arguments.length) { + return darkrect; + } + darkrect = value; + return chart; + }; + chart.lightrect = function(value) { + if (!arguments.length) { + return lightrect; + } + lightrect = value; + return chart; + }; + chart.linecolor = function(value) { + var linecolor; + if (!arguments.length) { + return linecolor; + } + linecolor = value; + return chart; + }; + chart.linewidth = function(value) { + if (!arguments.length) { + return linewidth; + } + linewidth = value; + return chart; + }; + chart.pointcolor = function(value) { + if (!arguments.length) { + return pointcolor; + } + pointcolor = value; + return chart; + }; + chart.pointsize = function(value) { + if (!arguments.length) { + return pointsize; + } + pointsize = value; + return chart; + }; + chart.pointstroke = function(value) { + if (!arguments.length) { + return pointstroke; + } + pointstroke = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.lodvarname = function(value) { + if (!arguments.length) { + return lodvarname; + } + lodvarname = value; + return chart; + }; + chart.pad4heatmap = function(value) { + if (!arguments.length) { + return pad4heatmap; + } + pad4heatmap = value; + return chart; + }; + chart.pointsAtMarkers = function(value) { + if (!arguments.length) { + return pointsAtMarkers; + } + pointsAtMarkers = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.additive_yscale = function() { + return additive_yscale; + }; + chart.xscale = function() { + return xscale; + }; + if (manhattanPlot === false) { + chart.lodcurve = function() { + return lodcurve; + }; + } + chart.additivecurve = function() { + return additivecurve; + }; + chart.markerSelect = function() { + return markerSelect; + }; + chart.chrSelect = function() { + return chrSelect; + }; + return chart; +};
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/lodheatmap.js b/gn2/wqflask/static/new/javascript/lodheatmap.js new file mode 100644 index 00000000..b82c95ad --- /dev/null +++ b/gn2/wqflask/static/new/javascript/lodheatmap.js @@ -0,0 +1,277 @@ +// Generated by CoffeeScript 1.8.0 +var lodheatmap; + +lodheatmap = function() { + var axispos, cellSelect, chart, chrGap, colors, height, margin, rectcolor, rotate_ylab, title, titlepos, width, xlab, xscale, ylab, yscale, zlim, zscale, zthresh; + width = 1200; + height = 600; + margin = { + left: 100, + top: 40, + right: 40, + bottom: 40 + }; + axispos = { + xtitle: 25, + ytitle: 30, + xlabel: 5, + ylabel: 5 + }; + chrGap = 8; + titlepos = 20; + rectcolor = d3.rgb(230, 230, 230); + colors = ["slateblue", "white", "red"]; + title = ""; + xlab = "Chromosome"; + ylab = ""; + rotate_ylab = null; + zlim = null; + zthresh = null; + xscale = d3.scale.linear(); + yscale = d3.scale.linear(); + zscale = d3.scale.linear(); + cellSelect = null; + chart = function(selection) { + return selection.each(function(data) { + var cells, celltip, chr, chr_ob, extent, g, gEnter, i, j, lod, lodcol, nlod, pos, rectHeight, svg, titlegrp, xLR, xaxis, yaxis, zmax, zmin, _i, _j, _k, _l, _len, _len1, _len2, _len3, _len4, _m, _ref, _ref1, _ref2, _ref3, _ref4; + data = reorgLodData(data); + data = chrscales(data, width, chrGap, margin.left, true); + xscale = data.xscale; + nlod = data.lodnames.length; + yscale.domain([-0.5, nlod - 0.5]).range([margin.top + height, margin.top]); + rectHeight = yscale(0) - yscale(1); + xLR = {}; + _ref = data.chrnames; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + chr = _ref[_i]; + if (data.posByChr[chr[0]].length > 0){ + xLR[chr[0]] = getLeftRight(data.posByChr[chr[0]]); + } + } + zmin = 0; + zmax = 0; + _ref1 = data.lodnames; + for (_j = 0, _len1 = _ref1.length; _j < _len1; _j++) { + lodcol = _ref1[_j]; + extent = d3.extent(data[lodcol]); + if (extent[0] < zmin) { + zmin = extent[0]; + } + if (extent[1] > zmax) { + zmax = extent[1]; + } + } + if (-zmin > zmax) { + zmax = -zmin; + } + zlim = zlim != null ? zlim : [-zmax, 0, zmax]; + if (zlim.length !== colors.length) { + console.log("zlim.length (" + zlim.length + ") != colors.length (" + colors.length + ")"); + } + zscale.domain(zlim).range(colors); + zthresh = zthresh != null ? zthresh : zmin - 1; + data.cells = []; + _ref2 = data.chrnames; + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + chr_ob = _ref2[_k]; + chr = chr_ob[0]; + _ref3 = data.posByChr[chr]; + for (i = _l = 0, _len3 = _ref3.length; _l < _len3; i = ++_l) { + pos = _ref3[i]; + _ref4 = data.lodByChr[chr][i]; + for (j = _m = 0, _len4 = _ref4.length; _m < _len4; j = ++_m) { + lod = _ref4[j]; + if (lod >= zthresh || lod <= -zthresh) { + data.cells.push({ + z: lod, + left: (xscale[chr](pos) + xscale[chr](xLR[chr][pos].left)) / 2, + right: (xscale[chr](pos) + xscale[chr](xLR[chr][pos].right)) / 2, + lodindex: j, + chr: chr, + pos: pos + }); + } + } + } + } + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { + return "box" + d[0]; + }).attr("x", function(d, i) { + return data.chrStart[i]; + }).attr("y", function(d) { + return margin.top; + }).attr("height", height).attr("width", function(d, i) { + return data.chrEnd[i] - data.chrStart[i]; + }).attr("fill", rectcolor).attr("stroke", "none"); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(data.chrnames).enter().append("text").attr("x", function(d, i) { + return (data.chrStart[i] + data.chrEnd[i]) / 2; + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return d[0]; + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).text(xlab); + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + yaxis.selectAll("empty").data(data.lodnames).enter().append("text").attr("id", function(d, i) { + return "yaxis" + i; + }).attr("y", function(d, i) { + return yscale(i); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return d; + }).attr("opacity", 0); + celltip = d3.tip().attr('class', 'd3-tip').html(function(d) { + var p, z; + z = d3.format(".2f")(Math.abs(d.z)); + p = d3.format(".1f")(d.pos); + return "" + d.chr + "@" + p + " → " + z; + }).direction('e').offset([0, 10]); + svg.call(celltip); + cells = g.append("g").attr("id", "cells"); + cellSelect = cells.selectAll("empty").data(data.cells).enter().append("rect").attr("x", function(d) { + return d.left; + }).attr("y", function(d) { + return yscale(d.lodindex) - rectHeight / 2; + }).attr("width", function(d) { + return d.right - d.left; + }).attr("height", rectHeight).attr("class", function(d, i) { + return "cell" + i; + }).attr("fill", function(d) { + return zscale(d.z); + }).attr("stroke", "none").attr("stroke-width", "1").on("mouseover.paneltip", function(d) { + yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 1); + d3.select(this).attr("stroke", "black"); + return celltip.show(d, this); + }).on("mouseout.paneltip", function(d) { + yaxis.select("text#yaxis" + d.lodindex).attr("opacity", 0); + d3.select(this).attr("stroke", "none"); + return celltip.hide(); + }); + return g.append("g").attr("id", "boxes").selectAll("empty").data(data.chrnames).enter().append("rect").attr("id", function(d) { + return "box" + d; + }).attr("x", function(d, i) { + return data.chrStart[i]; + }).attr("y", function(d) { + return margin.top; + }).attr("height", height).attr("width", function(d, i) { + return data.chrEnd[i] - data.chrStart[i]; + }).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.colors = function(value) { + if (!arguments.length) { + return colors; + } + colors = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.zthresh = function(value) { + if (!arguments.length) { + return zthresh; + } + zthresh = value; + return chart; + }; + chart.zlim = function(value) { + if (!arguments.length) { + return zlim; + } + zlim = value; + return chart; + }; + chart.chrGap = function(value) { + if (!arguments.length) { + return chrGap; + } + chrGap = value; + return chart; + }; + chart.xscale = function() { + return xscale; + }; + chart.yscale = function() { + return yscale; + }; + chart.zscale = function() { + return zscale; + }; + chart.cellSelect = function() { + return cellSelect; + }; + return chart; +}; diff --git a/gn2/wqflask/static/new/javascript/login.js b/gn2/wqflask/static/new/javascript/login.js new file mode 100644 index 00000000..2fe9ba3c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/login.js @@ -0,0 +1,41 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + var form_success, modalize, submit_form; + modalize = function(event) { + event.preventDefault(); + console.log("in modal_replace:", $(this).attr("href")); + return $.colorbox({ + open: true, + href: this.href, + onComplete: function() { + return $(".focused").focus(); + } + }); + }; + $(document).one("click", ".modalize", modalize); + console.log("Modalized click!!!"); + form_success = function(data) { + return $.colorbox({ + open: true, + html: data, + onComplete: function() { + return $("form").on("submit", submit_form); + } + }); + }; + submit_form = function(event) { + var data, submit_to; + event.preventDefault(); + submit_to = $(this).attr('action'); + data = $(this).serialize(); + console.log("submit_to is:", submit_to); + return $.ajax({ + type: "POST", + url: submit_to, + data: data, + dataType: "html", + success: form_success + }); + }; + return $("#colorbox form").on("submit", submit_form); +}); diff --git a/gn2/wqflask/static/new/javascript/network_graph.js b/gn2/wqflask/static/new/javascript/network_graph.js new file mode 100644 index 00000000..480443ee --- /dev/null +++ b/gn2/wqflask/static/new/javascript/network_graph.js @@ -0,0 +1,259 @@ +var default_style = [ // the stylesheet for the graph + { + selector: 'node', + style: { + 'background-color': '#666', + 'label': 'data(label)', + 'font-size': 10 + } + }, + + { + selector: 'edge', + style: { + 'width': 'data(width)', + 'line-color': 'data(color)', + 'target-arrow-color': '#ccc', + 'target-arrow-shape': 'triangle', + 'font-size': 8 + } + } + ] + +var default_layout = { name: 'circle', + fit: true, // whether to fit the viewport to the graph + padding: 30 // the padding on fit + //idealEdgeLength: function( edge ){ return edge.data['correlation']*10; }, + } + +window.onload=function() { + // id of Cytoscape Web container div + //var div_id = "cytoscapeweb"; + + var cy = cytoscape({ + container: $('#cytoscapeweb'), // container to render in + + elements: elements_list, + + style: default_style, + + zoom: 12, + layout: default_layout, + + zoomingEnabled: true, + userZoomingEnabled: true, + panningEnabled: true, + userPanningEnabled: true, + boxSelectionEnabled: false, + selectionType: 'single', + + // rendering options: + styleEnabled: true + }); + + var eles = cy.$() // var containing all elements, so elements can be restored after being removed + + var defaults = { + zoomFactor: 0.05, // zoom factor per zoom tick + zoomDelay: 45, // how many ms between zoom ticks + minZoom: 0.1, // min zoom level + maxZoom: 10, // max zoom level + fitPadding: 30, // padding when fitting + panSpeed: 10, // how many ms in between pan ticks + panDistance: 10, // max pan distance per tick + panDragAreaSize: 75, // the length of the pan drag box in which the vector for panning is calculated (bigger = finer control of pan speed and direction) + panMinPercentSpeed: 0.25, // the slowest speed we can pan by (as a percent of panSpeed) + panInactiveArea: 8, // radius of inactive area in pan drag box + panIndicatorMinOpacity: 0.5, // min opacity of pan indicator (the draggable nib); scales from this to 1.0 + zoomOnly: false, // a minimal version of the ui only with zooming (useful on systems with bad mousewheel resolution) + fitSelector: undefined, // selector of elements to fit + animateOnFit: function(){ // whether to animate on fit + return false; + }, + fitAnimationDuration: 1000, // duration of animation on fit + + // icon class names + sliderHandleIcon: 'fa fa-minus', + zoomInIcon: 'fa fa-plus', + zoomOutIcon: 'fa fa-minus', + resetIcon: 'fa fa-expand' + }; + + cy.panzoom( defaults ); + + function create_qtips(cy){ + cy.nodes().qtip({ + content: function(){ + qtip_content = '' + gn_link = '<b>'+'<a href="' + gn2_url + '/show_trait?trait_id=' + this.data().id.split(":")[0] + '&dataset=' + this.data().id.split(":")[1] + '" >'+this.data().id +'</a>'+'</b><br>' + qtip_content += gn_link + if (typeof(this.data().geneid) !== 'undefined'){ + ncbi_link = '<a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=Graphics&list_uids=' + this.data().geneid + '" >NCBI<a>'+'<br>' + qtip_content += ncbi_link + } + if (typeof(this.data().omim) !== 'undefined'){ + omim_link = '<a href="http://www.ncbi.nlm.nih.gov/omim/' + this.data().omim + '" >OMIM<a>'+'<br>' + qtip_content += omim_link + } + return qtip_content + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + + cy.edges().qtip({ + content: function(){ + correlation_line = '<b>Sample r: ' + this.data().correlation + '</b><br>' + p_value_line = 'Sample p(r): ' + this.data().p_value + '<br>' + overlap_line = 'Overlap: ' + this.data().overlap + '<br>' + scatter_plot = '<a href="' + gn2_url + '/corr_scatter_plot?method=pearson&dataset_1=' + this.data().source.split(":")[1] + '&dataset_2=' + this.data().target.split(":")[1] + '&trait_1=' + this.data().source.split(":")[0] + '&trait_2=' + this.data().target.split(":")[0] + '" >View Scatterplot</a>' + return correlation_line + p_value_line + overlap_line + scatter_plot + }, + position: { + my: 'top center', + at: 'bottom center' + }, + style: { + classes: 'qtip-bootstrap', + tip: { + width: 16, + height: 8 + } + } + }); + } + + create_qtips(cy) + + $('#neg_slide').change(function() { + eles.restore() + + pos_slide_val = $('#pos_slide').val(); + cy.$("node[max_corr > " + $(this).val() + "][max_corr < " + pos_slide_val + "]").remove(); + cy.$("edge[correlation > " + $(this).val() + "][correlation < " + pos_slide_val + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + + }); + $('#pos_slide').change(function() { + eles.restore() + + neg_slide_val = $('#neg_slide').val(); + cy.$("node[max_corr > " + neg_slide_val +"][max_corr < " + $(this).val() + "]").remove(); + cy.$("edge[correlation > " + neg_slide_val +"][correlation < " + $(this).val() + "]").remove(); + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + + }); + + $('#reset_graph').click(function() { + eles.restore() + $('#pos_slide').val(0) + $('#neg_slide').val(0) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=focus_select]').change(function() { + focus_trait = $(this).val() + + eles.restore() + cy.$('edge[source != "' + focus_trait + '"][target != "' + focus_trait + '"]').remove() + + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=layout_select]').change(function() { + layout_type = $(this).val() + cy.layout({ name: layout_type, + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=font_size]').change(function() { + font_size = $(this).val() + + new_style = default_style + new_style[0]['style']['font-size'] = parseInt(font_size) + cy.style().fromJson(new_style).update() + }); + $('select[name=edge_width]').change(function() { + //eles.restore() + + //ZS: This is needed, or else it alters the original object + orig_elements = JSON.parse(JSON.stringify(elements_list)); + + width_multiplier = $(this).val() + updated_elements = [] + for (i=0; i < orig_elements.length; i++){ + this_element = orig_elements[i] + if ('source' in this_element['data']) { + orig_width = this_element['data']['width'] + this_element['data']['width'] = orig_width * width_multiplier + } + updated_elements.push(this_element) + } + cy.remove(eles) + cy.add(updated_elements) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $('select[name=edge_width]').change(function() { + //eles.restore() + + //ZS: This is needed, or else it alters the original object + orig_elements = JSON.parse(JSON.stringify(elements_list)); + + width_multiplier = $(this).val() + updated_elements = [] + for (i=0; i < orig_elements.length; i++){ + this_element = orig_elements[i] + if ('source' in this_element['data']) { + orig_width = this_element['data']['width'] + this_element['data']['width'] = orig_width * width_multiplier + } + updated_elements.push(this_element) + } + cy.remove(eles) + cy.add(updated_elements) + cy.layout({ name: $('select[name=layout_select]').val(), + fit: true, // whether to fit the viewport to the graph + padding: 25 // the padding on fit + }).run(); + }); + + $("a#image_link").click(function(e) { + var pngData = cy.png(); + + $(this).attr('href', pngData); + $(this).attr('download', 'network_graph.png'); + }); + + +}; + + diff --git a/gn2/wqflask/static/new/javascript/panelutil.js b/gn2/wqflask/static/new/javascript/panelutil.js new file mode 100644 index 00000000..ea55a7cf --- /dev/null +++ b/gn2/wqflask/static/new/javascript/panelutil.js @@ -0,0 +1,462 @@ +// Generated by CoffeeScript 1.8.0 +var abs, calc_crosstab, chrscales, colSums, displayError, expand2vector, forceAsArray, formatAxis, getLeftRight, log10, log2, matrixExtent, matrixMax, matrixMaxAbs, matrixMin, maxdiff, median, missing2null, pullVarAsArray, reorgLodData, rowSums, selectGroupColors, sumArray, transpose, unique; + +formatAxis = function(d, extra_digits) { + var ndig; + if (extra_digits == null) { + extra_digits = 0; + } + d = d[1] - d[0]; + ndig = Math.floor(Math.log(d % 10) / Math.log(10)); + if (ndig > 0) { + ndig = 0; + } + ndig = Math.abs(ndig) + extra_digits; + return d3.format("." + ndig + "f"); +}; + +unique = function(x) { + var output, v, _i, _len, _results; + output = {}; + for (_i = 0, _len = x.length; _i < _len; _i++) { + v = x[_i]; + if (v) { + output[v] = v; + } + } + _results = []; + for (v in output) { + _results.push(output[v]); + } + return _results; +}; + +pullVarAsArray = function(data, variable) { + var i, v; + v = []; + for (i in data) { + v = v.concat(data[i][variable]); + } + return v; +}; + +reorgLodData = function(data, lodvarname) { + var chr, i, j, lodcolumn, lodval, marker, pos, _i, _j, _k, _len, _len1, _len2, _ref, _ref1, _ref2; + if (lodvarname == null) { + lodvarname = null; + } + data.posByChr = {}; + data.lodByChr = {}; + if ('additive' in data){ + data.additiveByChr = {}; + } + _ref = data.chrnames; + for (i = _i = 0, _len = _ref.length; _i < _len; i = ++_i) { + chr = _ref[i]; + data.posByChr[chr[0]] = []; + data.lodByChr[chr[0]] = []; + if ('additive' in data){ + data.additiveByChr[chr[0]] = []; + } + _ref1 = data.pos; + + for (j = _j = 0, _len1 = _ref1.length; _j < _len1; j = ++_j) { + pos = _ref1[j]; + if (data.chr[j].toString() === chr[0]) { + data.posByChr[chr[0]].push(pos); + if (!Array.isArray(data.lodnames)) { + data.lodnames = [data.lodnames]; + } + lodval = (function() { + var _k, _len2, _ref2, _results; + _ref2 = data.lodnames; + _results = []; + for (_k = 0, _len2 = _ref2.length; _k < _len2; _k++) { + lodcolumn = _ref2[_k]; + _results.push(data[lodcolumn][j]); + } + return _results; + })(); + data.lodByChr[chr[0]].push(lodval); + + if ('additive' in data){ + addval = data['additive'][j] + data.additiveByChr[chr[0]].push(addval); + } + + } + } + } + if (lodvarname != null) { + data.markers = []; + _ref2 = data.markernames; + for (i = _k = 0, _len2 = _ref2.length; _k < _len2; i = ++_k) { + marker = _ref2[i]; + if (marker !== "") { + data.markers.push({ + name: marker, + chr: data.chr[i], + pos: data.pos[i], + lod: data[lodvarname][i] + }); + } + } + } + return data; +}; + +chrscales = function(data, width, chrGap, leftMargin, pad4heatmap, mappingScale) { + var L, chr, chrEnd, chrLength, chrStart, cur, d, i, maxd, rng, totalChrLength, w, _i, _j, _len, _len1, _ref, _ref1; + chrStart = []; + chrEnd = []; + chrLength = []; + totalChrLength = 0; + maxd = 0; + _ref = data.chrnames; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + chr = _ref[_i]; + d = maxdiff(data.posByChr[chr[0]]); + if (d > maxd) { + maxd = d; + } + //rng = d3.extent(data.posByChr[chr[0]]); + //chrStart.push(rng[0]); + //chrEnd.push(rng[1]); + //L = rng[1] - rng[0]; + chrStart.push(0); + chrEnd.push(chr[1]); + L = chr[1] + chrLength.push(L); + totalChrLength += L; + } + if (pad4heatmap) { + data.recwidth = maxd; + chrStart = chrStart.map(function(x) { + return x - maxd / 2; + }); + chrEnd = chrEnd.map(function(x) { + return x + maxd / 2; + }); + chrLength = chrLength.map(function(x) { + return x + maxd; + }); + totalChrLength += chrLength.length * maxd; + } + data.chrStart = []; + data.chrEnd = []; + cur = leftMargin; + if (!pad4heatmap) { + cur += chrGap / 2; + } + data.xscale = {}; + _ref1 = data.chrnames; + for (i = _j = 0, _len1 = _ref1.length; _j < _len1; i = ++_j) { + chr = _ref1[i]; + data.chrStart.push(cur); + w = Math.round((width - chrGap * (data.chrnames.length - pad4heatmap)) / totalChrLength * chrLength[i]); + data.chrEnd.push(cur + w); + cur = data.chrEnd[i] + chrGap; + + if (mappingScale == "morgan") { + max_pos = d3.max(data.posByChr[chr[0]]) + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], max_pos]).range([data.chrStart[i], data.chrEnd[i]]); + } + else { + data.xscale[chr[0]] = d3.scale.linear().domain([chrStart[i], chrEnd[i]]).range([data.chrStart[i], data.chrEnd[i]]); + } + } + return data; +}; + +selectGroupColors = function(ngroup, palette) { + if (ngroup === 0) { + return []; + } + if (palette === "dark") { + if (ngroup === 1) { + return ["slateblue"]; + } + if (ngroup === 2) { + return ["MediumVioletRed", "slateblue"]; + } + if (ngroup <= 9) { + return colorbrewer.Set1[ngroup]; + } + return d3.scale.category20().range().slice(0, ngroup); + } else { + if (ngroup === 1) { + return ["#bebebe"]; + } + if (ngroup === 2) { + return ["lightpink", "lightblue"]; + } + if (ngroup <= 9) { + return colorbrewer.Pastel1[ngroup]; + } + return ["#8fc7f4", "#fed7f8", "#ffbf8e", "#fffbb8", "#8ce08c", "#d8ffca", "#f68788", "#ffd8d6", "#d4a7fd", "#f5f0f5", "#cc968b", "#f4dcd4", "#f3b7f2", "#f7f6f2", "#bfbfbf", "#f7f7f7", "#fcfd82", "#fbfbcd", "#87feff", "#defaf5"].slice(0, ngroup); + } +}; + +expand2vector = function(input, n) { + var i; + if (input == null) { + return input; + } + if (Array.isArray(input) && input.length >= n) { + return input; + } + if (!Array.isArray(input)) { + input = [input]; + } + if (input.length === 1 && n > 1) { + input = (function() { + var _results; + _results = []; + for (i in d3.range(n)) { + _results.push(input[0]); + } + return _results; + })(); + } + return input; +}; + +median = function(x) { + var n; + if (x == null) { + return null; + } + n = x.length; + x.sort(function(a, b) { + return a - b; + }); + if (n % 2 === 1) { + return x[(n - 1) / 2]; + } + return (x[n / 2] + x[(n / 2) - 1]) / 2; +}; + +getLeftRight = function(x) { + var i, n, result, v, xdif, _i, _j, _k, _len, _ref; + n = x.length; + x.sort(function(a, b) { + return a - b; + }); + xdif = []; + result = {}; + for (_i = 0, _len = x.length; _i < _len; _i++) { + v = x[_i]; + result[v] = {}; + } + for (i = _j = 1; 1 <= n ? _j < n : _j > n; i = 1 <= n ? ++_j : --_j) { + xdif.push(x[i] - x[i - 1]); + result[x[i]].left = x[i - 1]; + } + for (i = _k = 0, _ref = n - 1; 0 <= _ref ? _k < _ref : _k > _ref; i = 0 <= _ref ? ++_k : --_k) { + result[x[i]].right = x[i + 1]; + } + xdif = median(xdif); + result.mediandiff = xdif; + result[x[0]].left = x[0] - xdif; + result[x[n - 1]].right = x[n - 1] + xdif; + result.extent = [x[0] - xdif / 2, x[n - 1] + xdif / 2]; + return result; +}; + +maxdiff = function(x) { + var d, i, result, _i, _ref; + if (x.length < 2) { + return null; + } + result = x[1] - x[0]; + if (x.length < 3) { + return result; + } + for (i = _i = 2, _ref = x.length; 2 <= _ref ? _i < _ref : _i > _ref; i = 2 <= _ref ? ++_i : --_i) { + d = x[i] - x[i - 1]; + if (d > result) { + result = d; + } + } + return result; +}; + +matrixMin = function(mat) { + var i, j, result; + result = mat[0][0]; + for (i in mat) { + for (j in mat[i]) { + if (result > mat[i][j]) { + result = mat[i][j]; + } + } + } + return result; +}; + +matrixMax = function(mat) { + var i, j, result; + result = mat[0][0]; + for (i in mat) { + for (j in mat[i]) { + if (result < mat[i][j]) { + result = mat[i][j]; + } + } + } + return result; +}; + +matrixMaxAbs = function(mat) { + var i, j, result; + result = Math.abs(mat[0][0]); + for (i in mat) { + for (j in mat[i]) { + if (result < mat[i][j]) { + result = Math.abs(mat[i][j]); + } + } + } + return result; +}; + +matrixExtent = function(mat) { + return [matrixMin(mat), matrixMax(mat)]; +}; + +d3.selection.prototype.moveToFront = function() { + return this.each(function() { + return this.parentNode.appendChild(this); + }); +}; + +d3.selection.prototype.moveToBack = function() { + return this.each(function() { + var firstChild; + firstChild = this.parentNode.firstchild; + if (firstChild) { + return this.parentNode.insertBefore(this, firstChild); + } + }); +}; + +forceAsArray = function(x) { + if (x == null) { + return x; + } + if (Array.isArray(x)) { + return x; + } + return [x]; +}; + +missing2null = function(vec, missingvalues) { + if (missingvalues == null) { + missingvalues = ['NA', '']; + } + return vec.map(function(value) { + if (missingvalues.indexOf(value) > -1) { + return null; + } else { + return value; + } + }); +}; + +displayError = function(message) { + if (d3.select("div.error").empty()) { + d3.select("body").insert("div", ":first-child").attr("class", "error"); + } + return d3.select("div.error").append("p").text(message); +}; + +sumArray = function(vec) { + return vec.reduce(function(a, b) { + return a + b; + }); +}; + +calc_crosstab = function(data) { + var col, cs, i, ncol, nrow, result, row, rs, _i, _j; + nrow = data.ycat.length; + ncol = data.xcat.length; + result = (function() { + var _i, _results; + _results = []; + for (row = _i = 0; 0 <= nrow ? _i <= nrow : _i >= nrow; row = 0 <= nrow ? ++_i : --_i) { + _results.push((function() { + var _j, _results1; + _results1 = []; + for (col = _j = 0; 0 <= ncol ? _j <= ncol : _j >= ncol; col = 0 <= ncol ? ++_j : --_j) { + _results1.push(0); + } + return _results1; + })()); + } + return _results; + })(); + for (i in data.x) { + result[data.y[i]][data.x[i]] += 1; + } + rs = rowSums(result); + cs = colSums(result); + for (i = _i = 0; 0 <= ncol ? _i < ncol : _i > ncol; i = 0 <= ncol ? ++_i : --_i) { + result[nrow][i] = cs[i]; + } + for (i = _j = 0; 0 <= nrow ? _j < nrow : _j > nrow; i = 0 <= nrow ? ++_j : --_j) { + result[i][ncol] = rs[i]; + } + result[nrow][ncol] = sumArray(rs); + return result; +}; + +rowSums = function(mat) { + var x, _i, _len, _results; + _results = []; + for (_i = 0, _len = mat.length; _i < _len; _i++) { + x = mat[_i]; + _results.push(sumArray(x)); + } + return _results; +}; + +transpose = function(mat) { + var i, j, _i, _ref, _results; + _results = []; + for (j = _i = 0, _ref = mat[0].length; 0 <= _ref ? _i < _ref : _i > _ref; j = 0 <= _ref ? ++_i : --_i) { + _results.push((function() { + var _j, _ref1, _results1; + _results1 = []; + for (i = _j = 0, _ref1 = mat.length; 0 <= _ref1 ? _j < _ref1 : _j > _ref1; i = 0 <= _ref1 ? ++_j : --_j) { + _results1.push(mat[i][j]); + } + return _results1; + })()); + } + return _results; +}; + +colSums = function(mat) { + return rowSums(transpose(mat)); +}; + +log2 = function(x) { + if (x == null) { + return x; + } + return Math.log(x) / Math.log(2.0); +}; + +log10 = function(x) { + if (x == null) { + return x; + } + return Math.log(x) / Math.log(10.0); +}; + +abs = function(x) { + if (x == null) { + return x; + } + return Math.abs(x); +};
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/partial_correlations.js b/gn2/wqflask/static/new/javascript/partial_correlations.js new file mode 100644 index 00000000..5de1204c --- /dev/null +++ b/gn2/wqflask/static/new/javascript/partial_correlations.js @@ -0,0 +1,26 @@ +function selected_traits() { + traits = $("#trait_table input:checked").map(function() { + return $(this).attr("data-trait-info"); + }).get(); + if (traits.length == 0){ + num_traits = $("#trait_table input").length + if (num_traits <= 100){ + traits = $("#trait_table input").map(function() { + return $(this).attr("data-trait-info"); + }).get(); + } + } + return traits +} + +$("#partial-correlations").on("click", function() { + // Submit the form to the `partial_correlations` endpoint + url = $(this).data("url") + traits = selected_traits(); + $("#trait_list").val(traits.reduce(function(acc, str) { + return acc.concat(";;;".concat(str)); + })); + $("input[name=tool_used]").val("Partial Correlation") + $("input[name=form_url]").val(url) + return submit_special(url) +}) diff --git a/gn2/wqflask/static/new/javascript/password_strength.js b/gn2/wqflask/static/new/javascript/password_strength.js new file mode 100644 index 00000000..a8a45f7d --- /dev/null +++ b/gn2/wqflask/static/new/javascript/password_strength.js @@ -0,0 +1,57 @@ +// Generated by CoffeeScript 1.8.0 + +$(function() { + var word_score; + $("#password").keyup(function() { + var crack_time, display, passtext, result, word; + passtext = $(this).val(); + result = zxcvbn(passtext); + if (passtext.length < 6) { + let error_message = `<strong style="color:red;">the password must have a length greater than six characters</strong>` + $("#password_strength").html(error_message); + return $("#password_alert").fadeIn(); + } else { + word = word_score(result.score); + crack_time = result.crack_times_display.online_throttling_100_per_hour; + if (crack_time === "instant") { + crack_time = "a second"; + } + display = `This is ${word} password.` + $("#password_strength").html(display); + return $("#password_alert").fadeIn(); + } + }); + return word_score = function(num_score) { + num_score = parseInt(num_score); + console.log("num_score is:", num_score); + + let passwordFeedback = { + 0:{ + color:"#cc1818", + feedback:"a weak" + }, + + 1:{ + color:"#cc1818", + feedback:"a bad" + }, + + 2:{ + color:"#f59105", + feedback:"a mediocre" + }, + + 3:{ + color:"#44ba34", + feedback:"a strong" + }, + 4:{ + color:"green", + feedback:"a stronger" + } + } + + let mappingResult = `<strong style="color:${passwordFeedback[num_score].color};">${passwordFeedback[num_score].feedback}</strong>` + return mappingResult; + }; +}); diff --git a/gn2/wqflask/static/new/javascript/plotly_probability_plot.js b/gn2/wqflask/static/new/javascript/plotly_probability_plot.js new file mode 100644 index 00000000..bc1e021b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/plotly_probability_plot.js @@ -0,0 +1,308 @@ +// Generated by CoffeeScript 1.9.2 +(function() { + var get_z_scores, redraw_prob_plot, root; + + root = typeof exports !== "undefined" && exports !== null ? exports : this; + + get_z_scores = function(n) { + var i, j, osm_uniform, ref, x; + osm_uniform = new Array(n); + osm_uniform[n - 1] = Math.pow(0.5, 1.0 / n); + osm_uniform[0] = 1 - osm_uniform[n - 1]; + for (i = j = 1, ref = n - 2; 1 <= ref ? j <= ref : j >= ref; i = 1 <= ref ? ++j : --j) { + osm_uniform[i] = (i + 1 - 0.3175) / (n + 0.365); + } + return (function() { + var k, len, results; + results = []; + for (k = 0, len = osm_uniform.length; k < len; k++) { + x = osm_uniform[k]; + results.push(jStat.normal.inv(x, 0, 1)); + } + return results; + })(); + }; + + redraw_prob_plot = function(samples, sample_group) { + var container, h, margin, totalh, totalw, w; + h = 550; + w = 600; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + totalh = h + margin.top + margin.bottom; + totalw = w + margin.left + margin.right; + container = $("#prob_plot_container"); + container.width(totalw); + container.height(totalh); + var W, all_samples, chart, data, intercept, make_data, names, pvalue, pvalue_str, slope, sorted_names, sorted_values, sw_result, test_str, x, z_scores; + all_samples = samples[sample_group]; + names = (function() { + var j, len, ref, results; + ref = _.keys(all_samples); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + x = ref[j]; + if (all_samples[x] !== null) { + results.push(x); + } + } + return results; + })(); + sorted_names = names.sort(function(x, y) { + return all_samples[x].value - all_samples[y].value; + }); + max_decimals = 0 + sorted_values = (function() { + var j, len, results; + results = []; + for (j = 0, len = sorted_names.length; j < len; j++) { + x = sorted_names[j]; + results.push(all_samples[x].value); + if (all_samples[x].value.countDecimals() > max_decimals) { + max_decimals = all_samples[x].value.countDecimals()-1 + } + } + return results; + })(); + //ZS: 0.1 indicates buffer, increase to increase buffer + y_domain = [sorted_values[0] - (sorted_values.slice(-1)[0] - sorted_values[0])*0.1, sorted_values.slice(-1)[0] + (sorted_values.slice(-1)[0] - sorted_values[0])*0.1] + //sw_result = ShapiroWilkW(sorted_values); + //W = sw_result.w.toFixed(3); + //pvalue = sw_result.p.toFixed(3); + //pvalue_str = pvalue > 0.05 ? pvalue.toString() : "<span style='color:red'>" + pvalue + "</span>"; + //test_str = "Shapiro-Wilk test statistic is " + W + " (p = " + pvalue_str + ")"; + z_scores = get_z_scores(sorted_values.length); + //ZS: 0.1 indicates buffer, increase to increase buffer + x_domain = [z_scores[0] - (z_scores.slice(-1)[0] - z_scores[0])*0.1, z_scores.slice(-1)[0] + (z_scores.slice(-1)[0] - z_scores[0])*0.1] + slope = jStat.stdev(sorted_values); + intercept = jStat.mean(sorted_values); + make_data = function(group_name) { + var sample, value, z_score; + return { + key: js_data.sample_group_types[group_name], + slope: slope, + intercept: intercept, + values: (function() { + var j, len, ref, ref1, results; + ref = _.zip(get_z_scores(sorted_values.length), sorted_values, sorted_names); + results = []; + for (j = 0, len = ref.length; j < len; j++) { + ref1 = ref[j], z_score = ref1[0], value = ref1[1], sample = ref1[2]; + if (sample in samples[group_name]) { + results.push({ + x: z_score, + y: value, + name: sample + }); + } + } + return results; + })() + }; + }; + data = [make_data('samples_primary'), make_data('samples_other'), make_data('samples_all')]; + x_values = {} + y_values = {} + point_names = {} + for (i = 0; i < 3; i++){ + these_x_values = [] + these_y_values = [] + these_names = [] + for (j = 0; j < data[i].values.length; j++){ + these_x_values.push(data[i].values[j].x) + these_y_values.push(data[i].values[j].y) + these_names.push(data[i].values[j].name) + } + if (i == 0){ + x_values['samples_primary'] = these_x_values + y_values['samples_primary'] = these_y_values + point_names['samples_primary'] = these_names + } else if (i == 1) { + x_values['samples_other'] = these_x_values + y_values['samples_other'] = these_y_values + point_names['samples_other'] = these_names + } else { + x_values['samples_all'] = these_x_values + y_values['samples_all'] = these_y_values + point_names['samples_all'] = these_names + } + } + + intercept_line = {} + + if (sample_group == "samples_primary"){ + first_x = Math.floor(x_values['samples_primary'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_primary'][x_values['samples_primary'].length - 1]) + last_x = last_x + last_x*0.1 + first_value = data[0].intercept + data[0].slope * first_x + last_value = data[0].intercept + data[0].slope * last_x + intercept_line['samples_primary'] = [[first_x, last_x], [first_value, last_value]] + } else if (sample_group == "samples_other") { + first_x = Math.floor(x_values['samples_other'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_other'][x_values['samples_other'].length - 1]) + last_x = last_x + last_x*0.1 + first_value = data[1].intercept + data[1].slope * first_x + last_value = data[1].intercept + data[1].slope * last_x + intercept_line['samples_other'] = [[first_x, last_x], [first_value, last_value]] + } else { + first_x = Math.floor(x_values['samples_all'][0]) + first_x = first_x - first_x*0.1 + last_x = Math.ceil(x_values['samples_all'][x_values['samples_all'].length - 1]) + first_value = data[2].intercept + data[2].slope * first_x + last_x = last_x + last_x*0.1 + last_value = data[2].intercept + data[2].slope * last_x + intercept_line['samples_all'] = [[first_x, last_x], [first_value, last_value]] + } + + val_range = Math.max(...y_values['samples_all']) - Math.min(...y_values['samples_all']) + if (val_range < 4){ + tick_digits = '.1f' + } else if (val_range < 0.4) { + tick_digits = '.2f' + } else { + tick_digits = 'f' + } + + var layout = { + title: { + x: 0, + y: 10, + xanchor: 'left', + text: "<b>Trait " + js_data.trait_id + ": " + js_data.short_description + "</b>", + }, + margin: { + l: 100, + r: 30, + t: 100, + b: 60 + }, + legend: { + x: 0.05, + y: 0.9, + xanchor: 'left' + }, + xaxis: { + title: "<b>normal quantiles</b>", + range: [first_x, last_x], + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + titlefont: { + family: "arial", + size: 16 + }, + ticklen: 4, + tickfont: { + size: 16 + } + }, + yaxis: { + zeroline: false, + visible: true, + linecolor: 'black', + linewidth: 1, + title: "<b>" + js_data.unit_type + "</b>", + titlefont: { + family: "arial", + size: 16 + }, + ticklen: 4, + tickfont: { + size: 16 + }, + tickformat: tick_digits, + automargin: true + }, + width: 600, + height: 600, + hovermode: "closest", + dragmode: false + } + + var primary_trace = { + x: x_values['samples_primary'], + y: y_values['samples_primary'], + mode: 'markers', + type: 'scatter', + name: 'Samples', + text: point_names['samples_primary'], + marker: { + color: 'blue', + width: 6 + } + } + if ("samples_other" in js_data.sample_group_types) { + var other_trace = { + x: x_values['samples_other'], + y: y_values['samples_other'], + mode: 'markers', + type: 'scatter', + name: js_data.sample_group_types['samples_other'], + text: point_names['samples_other'], + marker: { + color: 'blue', + width: 6 + } + } + } + + if (sample_group == "samples_primary"){ + var primary_intercept_trace = { + x: intercept_line['samples_primary'][0], + y: intercept_line['samples_primary'][1], + mode: 'lines', + type: 'scatter', + name: 'Normal Function', + line: { + color: 'black', + width: 1 + } + } + } else if (sample_group == "samples_other"){ + var other_intercept_trace = { + x: intercept_line['samples_other'][0], + y: intercept_line['samples_other'][1], + mode: 'lines', + type: 'scatter', + name: 'Normal Function', + line: { + color: 'black', + width: 1 + } + } + } else { + var all_intercept_trace = { + x: intercept_line['samples_all'][0], + y: intercept_line['samples_all'][1], + mode: 'lines', + type: 'scatter', + name: 'Normal Function', + line: { + color: 'black', + width: 1 + } + } + } + + if (sample_group == "samples_primary"){ + var data = [primary_intercept_trace, primary_trace] + } else if (sample_group == "samples_other"){ + var data = [other_intercept_trace, other_trace] + } else { + var data = [all_intercept_trace, primary_trace, other_trace] + } + + Plotly.newPlot('prob_plot_div', data, layout, root.modebar_options) + }; + + root.redraw_prob_plot_impl = redraw_prob_plot; + +}).call(this); diff --git a/gn2/wqflask/static/new/javascript/scatter-matrix.js b/gn2/wqflask/static/new/javascript/scatter-matrix.js new file mode 100644 index 00000000..31cb384b --- /dev/null +++ b/gn2/wqflask/static/new/javascript/scatter-matrix.js @@ -0,0 +1,551 @@ +// Heavily influenced by Mike Bostock's Scatter Matrix example +// http://mbostock.github.io/d3/talk/20111116/iris-splom.html +// + +/* +ScatterMatrix = function(url) { + this.__url = url; + this.__data = undefined; + this.__cell_size = 140; +}; +*/ + +ScatterMatrix = function(csv_string) { + this.__csv_string = csv_string; + this.__data = undefined; + this.__cell_size = 140; +}; + +ScatterMatrix.prototype.cellSize = function(n) { + this.__cell_size = n; + return this; +}; + +/* +ScatterMatrix.prototype.onData = function(cb) { + if (this.__data) { cb(); return; } + var self = this; + d3.csv(self.__url, function(data) { + self.__data = data; + cb(); + }); +}; +*/ + +ScatterMatrix.prototype.onData = function(cb) { + if (this.__data) { cb(); return; } + var self = this; + console.log("self.csv_string:", self.__csv_string) + + data = d3.csv.parse(self.__csv_string); + self.__data = data; + cb(); + +/* + d3.csv.parseRows(self.__csv_string, function(data) { + self.__data = data; + cb(); + }); +*/ + +}; + +ScatterMatrix.prototype.render = function () { + var self = this; + + var container = d3.select('#scatterplot_container').append('div') + .attr('class', 'scatter-matrix-container'); + var control = container.append('div') + .attr('class', 'scatter-matrix-control') + .style({'float':'left', 'margin-right':'50px'}) + var svg = container.append('div') + .attr('class', 'scatter-matrix-svg') + .style({'float':'left'}) + .html('<em>Loading data...</em>'); + + this.onData(function() { + var data = self.__data; + + // Fetch data and get all string variables + var string_variables = [undefined]; + var numeric_variables = []; + var numeric_variable_values = {}; + + for (k in data[0]) { + if (isNaN(+data[0][k])) { string_variables.push(k); } + else { numeric_variables.push(k); numeric_variable_values[k] = []; } + } + + console.log("data:", data) + + data.forEach(function(d) { + for (var j in numeric_variables) { + var k = numeric_variables[j]; + var value = d[k]; + if (numeric_variable_values[k].indexOf(value) < 0) { + numeric_variable_values[k].push(value); + } + } + }); + + var size_control = control.append('div').attr('class', 'scatter-matrix-size-control'); + var color_control = control.append('div').attr('class', 'scatter-matrix-color-control'); + var filter_control = control.append('div').attr('class', 'scatter-matrix-filter-control'); + var variable_control = control.append('div').attr('class', 'scatter-matrix-variable-control'); + var drill_control = control.append('div').attr('class', 'scatter-matrix-drill-control'); + + // shared control states + var to_include = []; + var color_variable = undefined; + var selected_colors = undefined; + for (var j in numeric_variables) { + var v = numeric_variables[j]; + to_include.push(v); + } + var drill_variables = []; + + function set_filter(variable) { + filter_control.selectAll('*').remove(); + if (variable) { + // Get unique values for this variable + var values = []; + data.forEach(function(d) { + var v = d[variable]; + if (values.indexOf(v) < 0) { values.push(v); } + }); + + selected_colors = []; + for (var j in values) { + var v = values[j]; + selected_colors.push(v); + } + + var filter_li = + filter_control + .append('p').text('Filter by '+variable+': ') + .append('ul') + .selectAll('li') + .data(values) + .enter().append('li'); + + filter_li.append('input') + .attr('type', 'checkbox') + .attr('checked', 'checked') + .on('click', function(d, i) { + var new_selected_colors = []; + for (var j in selected_colors) { + var v = selected_colors[j]; + if (v !== d || this.checked) { new_selected_colors.push(v); } + } + if (this.checked) { new_selected_colors.push(d); } + selected_colors = new_selected_colors; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + filter_li.append('label') + .html(function(d) { return d; }); + } + } + + size_a = size_control.append('p').text('Change cell size: '); + size_a.append('a') + .attr('href', '#') + .html('-') + .on('click', function() { + self.__cell_size *= 0.75; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + size_a.append('span').html(' '); + size_a.append('a') + .attr('href', '#') + .html('+') + .on('click', function() { + self.__cell_size *= 1.25; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + + color_control.append('p').text('Select a variable to color:') + color_control + .append('ul') + .selectAll('li') + .data(string_variables) + .enter().append('li') + .append('a') + .attr('href', '#') + .text(function(d) { return d ? d : 'None'; }) + .on('click', function(d, i) { + color_variable = d; + selected_colors = undefined; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + set_filter(d); + }); + + var variable_li = + variable_control + .append('p').text('Include variables: ') + .append('ul') + .selectAll('li') + .data(numeric_variables) + .enter().append('li'); + + variable_li.append('input') + .attr('type', 'checkbox') + .attr('checked', 'checked') + .on('click', function(d, i) { + var new_to_include = []; + for (var j in to_include) { + var v = to_include[j]; + if (v !== d || this.checked) { new_to_include.push(v); } + } + if (this.checked) { new_to_include.push(d); } + to_include = new_to_include; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + variable_li.append('label') + .html(function(d) { return d; }); + + drill_li = + drill_control + .append('p').text('Drill and Expand: ') + .append('ul') + .selectAll('li') + .data(numeric_variables) + .enter().append('li'); + + drill_li.append('input') + .attr('type', 'checkbox') + .on('click', function(d, i) { + var new_drill_variables = []; + for (var j in drill_variables) { + var v = drill_variables[j]; + if (v !== d || this.checked) { new_drill_variables.push(v); } + } + if (this.checked) { new_drill_variables.push(d); } + drill_variables = new_drill_variables; + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); + drill_li.append('label') + .html(function(d) { return d+' ('+numeric_variable_values[d].length+')'; }); + + self.__draw(self.__cell_size, svg, color_variable, selected_colors, to_include, drill_variables); + }); +}; + +ScatterMatrix.prototype.__draw = + function(cell_size, container_el, color_variable, selected_colors, to_include, drill_variables) { + var self = this; + this.onData(function() { + var data = self.__data; + + if (color_variable && selected_colors) { + data = []; + self.__data.forEach(function(d) { + if (selected_colors.indexOf(d[color_variable]) >= 0) { data.push(d); } + }); + } + + container_el.selectAll('*').remove(); + + // If no data, don't do anything + if (data.length == 0) { return; } + + // Parse headers from first row of data + var numeric_variables = []; + for (k in data[0]) { + if (!isNaN(+data[0][k]) && to_include.indexOf(k) >= 0) { numeric_variables.push(k); } + } + numeric_variables.sort(); + + // Get values of the string variable + var colors = []; + if (color_variable) { + // Using self.__data, instead of data, so our css classes are consistent when + // we filter by value. + self.__data.forEach(function(d) { + var s = d[color_variable]; + if (colors.indexOf(s) < 0) { colors.push(s); } + }); + } + + function color_class(d) { + var c = d; + if (color_variable && d[color_variable]) { c = d[color_variable]; } + return colors.length > 0 ? 'color-'+colors.indexOf(c) : 'color-2'; + } + + // Size parameters + var size = cell_size, padding = 10, + axis_width = 20, axis_height = 15, legend_width = 200, label_height = 15; + + // Get x and y scales for each numeric variable + var x = {}, y = {}; + numeric_variables.forEach(function(trait) { + // Coerce values to numbers. + data.forEach(function(d) { d[trait] = +d[trait]; }); + + var value = function(d) { return d[trait]; }, + domain = [d3.min(data, value), d3.max(data, value)], + range_x = [padding / 2, size - padding / 2], + range_y = [padding / 2, size - padding / 2]; + + x[trait] = d3.scale.linear().domain(domain).range(range_x); + y[trait] = d3.scale.linear().domain(domain).range(range_y.reverse()); + }); + + // When drilling, user select one or more variables. The first drilled + // variable becomes the x-axis variable for all columns, and each column + // contains only data points that match specific values for each of the + // drilled variables other than the first. + + var drill_values = []; + var drill_degrees = [] + drill_variables.forEach(function(variable) { + // Skip first one, since that's just the x axis + if (drill_values.length == 0) { + drill_values.push([]); + drill_degrees.push(1); + } + else { + var values = []; + data.forEach(function(d) { + var v = d[variable]; + if (v !== undefined && values.indexOf(v) < 0) { values.push(v); } + }); + values.sort(); + drill_values.push(values); + drill_degrees.push(values.length); + } + }); + var total_columns = 1; + drill_degrees.forEach(function(d) { total_columns *= d; }); + + // Pick out stuff to draw on horizontal and vertical dimensions + + if (drill_variables.length > 0) { + // First drill is now the x-axis variable for all columns + x_variables = []; + for (var i=0; i<total_columns; i++) { + x_variables.push(drill_variables[0]); + } + } + else { + x_variables = numeric_variables.slice(0); + } + + if (drill_variables.length > 0) { + // Don't draw any of the "drilled" variables in vertical dimension + y_variables = []; + numeric_variables.forEach(function(variable) { + if (drill_variables.indexOf(variable) < 0) { y_variables.push(variable); } + }); + } + else { + y_variables = numeric_variables.slice(0); + } + + var filter_descriptions = 0; + if (drill_variables.length > 1) { + filter_descriptions = drill_variables.length-1; + } + + // Axes + var x_axis = d3.svg.axis(); + var y_axis = d3.svg.axis(); + var intf = d3.format('d'); + var fltf = d3.format('.f'); + var scif = d3.format('e'); + + x_axis.ticks(5) + .tickSize(size * y_variables.length) + .tickFormat(function(d) { + if (Math.abs(+d) > 10000 || (Math.abs(d) < 0.001 && Math.abs(d) != 0)) { return scif(d); } + if (parseInt(d) == +d) { return intf(d); } + return fltf(d); + }); + + y_axis.ticks(5) + .tickSize(size * x_variables.length) + .tickFormat(function(d) { + if (Math.abs(+d) > 10000 || (Math.abs(d) < 0.001 && Math.abs(d) != 0)) { return scif(d); } + if (parseInt(d) == +d) { return intf(d); } + return fltf(d); + }); + + // Brush - for highlighting regions of data + var brush = d3.svg.brush() + .on("brushstart", brushstart) + .on("brush", brush) + .on("brushend", brushend); + + // Root panel + var svg = container_el.append("svg:svg") + .attr("width", label_height + size * x_variables.length + axis_width + padding + legend_width) + .attr("height", size * y_variables.length + axis_height + label_height + label_height*filter_descriptions) + .append("svg:g") + .attr("transform", "translate("+label_height+",0)"); + + // Push legend to the side + var legend = svg.selectAll("g.legend") + .data(colors) + .enter().append("svg:g") + .attr("class", "legend") + .attr("transform", function(d, i) { + return "translate(" + (label_height + size * x_variables.length + padding) + "," + (i*20+10) + ")"; + }); + + legend.append("svg:circle") + .attr("class", function(d, i) { return color_class(d); }) + .attr("r", 3); + + legend.append("svg:text") + .attr("x", 12) + .attr("dy", ".31em") + .text(function(d) { return d; }); + + // Draw X-axis + svg.selectAll("g.x.axis") + .data(x_variables) + .enter().append("svg:g") + .attr("class", "x axis") + .attr("transform", function(d, i) { return "translate(" + i * size + ",0)"; }) + .each(function(d) { d3.select(this).call(x_axis.scale(x[d]).orient("bottom")); }); + + // Draw Y-axis + svg.selectAll("g.y.axis") + .data(y_variables) + .enter().append("svg:g") + .attr("class", "y axis") + .attr("transform", function(d, i) { return "translate(0," + i * size + ")"; }) + .each(function(d) { d3.select(this).call(y_axis.scale(y[d]).orient("right")); }); + + // Draw scatter plot + var cell = svg.selectAll("g.cell") + .data(cross(x_variables, y_variables)) + .enter().append("svg:g") + .attr("class", "cell") + .attr("transform", function(d) { return "translate(" + d.i * size + "," + d.j * size + ")"; }) + .each(plot); + + // Add titles for y variables + cell.filter(function(d) { return d.i == 0; }).append("svg:text") + .attr("x", padding-size) + .attr("y", -label_height) + .attr("dy", ".71em") + .attr("transform", function(d) { return "rotate(-90)"; }) + .text(function(d) { return d.y; }); + + function plot(p) { + // console.log(p); + + var data_to_draw = data; + + // If drilling, compute what values of the drill variables correspond to + // this column. + // + var filter = {}; + if (drill_variables.length > 1) { + var column = p.i; + + var cap = 1; + for (var i=drill_variables.length-1; i > 0; i--) { + var var_name = drill_variables[i]; + var var_value = undefined; + + if (i == drill_variables.length-1) { + // for the last drill variable, we index by % + var_value = drill_values[i][column % drill_degrees[i]]; + } + else { + // otherwise divide by capacity of subsequent variables to get value array index + var_value = drill_values[i][parseInt(column/cap)]; + } + + filter[var_name] = var_value; + cap *= drill_degrees[i]; + } + + data_to_draw = []; + data.forEach(function(d) { + var pass = true; + for (k in filter) { if (d[k] != filter[k]) { pass = false; break; } } + if (pass === true) { data_to_draw.push(d); } + }); + } + + var cell = d3.select(this); + + // Frame + cell.append("svg:rect") + .attr("class", "frame") + .attr("x", padding / 2) + .attr("y", padding / 2) + .attr("width", size - padding) + .attr("height", size - padding); + + // Scatter plot dots + cell.selectAll("circle") + .data(data_to_draw) + .enter().append("svg:circle") + .attr("class", function(d) { return color_class(d); }) + .attr("cx", function(d) { return x[p.x](d[p.x]); }) + .attr("cy", function(d) { return y[p.y](d[p.y]); }) + .attr("r", 5); + + // Add titles for x variables and drill variable values + if (p.j == y_variables.length-1) { + cell.append("svg:text") + .attr("x", padding) + .attr("y", size+axis_height) + .attr("dy", ".71em") + .text(function(d) { return d.x; }); + + if (drill_variables.length > 1) { + var i = 0; + for (k in filter) { + i += 1; + cell.append("svg:text") + .attr("x", padding) + .attr("y", size+axis_height+label_height*i) + .attr("dy", ".71em") + .text(function(d) { return filter[k]+': '+k; }); + } + } + } + + // Brush + cell.call(brush.x(x[p.x]).y(y[p.y])); + } + + // Clear the previously-active brush, if any + function brushstart(p) { + if (brush.data !== p) { + cell.call(brush.clear()); + brush.x(x[p.x]).y(y[p.y]).data = p; + } + } + + // Highlight selected circles + function brush(p) { + var e = brush.extent(); + svg.selectAll(".cell circle").attr("class", function(d) { + return e[0][0] <= d[p.x] && d[p.x] <= e[1][0] + && e[0][1] <= d[p.y] && d[p.y] <= e[1][1] + ? color_class(d) : null; + }); + } + + // If brush is empty, select all circles + function brushend() { + if (brush.empty()) svg.selectAll(".cell circle").attr("class", function(d) { + return color_class(d); + }); + } + + function cross(a, b) { + var c = [], n = a.length, m = b.length, i, j; + for (i = -1; ++i < n;) for (j = -1; ++j < m;) c.push({x: a[i], i: i, y: b[j], j: j}); + return c; + } + }); + +}; + diff --git a/gn2/wqflask/static/new/javascript/scatterplot.js b/gn2/wqflask/static/new/javascript/scatterplot.js new file mode 100644 index 00000000..3fea0503 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/scatterplot.js @@ -0,0 +1,414 @@ +// Generated by CoffeeScript 1.8.0 +var root, scatterplot; + +root = typeof exports !== "undefined" && exports !== null ? exports : this; + +scatterplot = function() { + var axispos, chart, dataByInd, height, margin, nxticks, nyticks, pointcolor, pointsSelect, pointsize, pointstroke, rectcolor, rotate_ylab, title, titlepos, width, xNA, xlab, xlim, xscale, xticks, xvar, yNA, ylab, ylim, yscale, yticks, yvar; + width = 800; + height = 600; + margin = { + left: 60, + top: 40, + right: 40, + bottom: 40, + inner: 5 + }; + axispos = { + xtitle: 25, + ytitle: 45, + xlabel: 5, + ylabel: 5 + }; + titlepos = 20; + xNA = { + handle: true, + force: false, + width: 15, + gap: 10 + }; + yNA = { + handle: true, + force: false, + width: 15, + gap: 10 + }; + xlim = null; + ylim = null; + nxticks = 5; + xticks = null; + nyticks = 5; + yticks = null; + rectcolor = d3.rgb(230, 230, 230); + pointcolor = null; + pointstroke = "black"; + pointsize = 3; + title = "Correlation Scatterplot"; + xlab = "X"; + ylab = "Y"; + rotate_ylab = null; + yscale = d3.scale.linear(); + xscale = d3.scale.linear(); + xvar = 0; + yvar = 1; + pointsSelect = null; + dataByInd = false; + chart = function(selection) { + return selection.each(function(data) { + var g, gEnter, group, i, indID, indtip, maxx, minx, na_value, ngroup, panelheight, paneloffset, panelwidth, points, svg, titlegrp, x, xaxis, xrange, xs, y, yaxis, yrange, ys, _i, _ref, _ref1, _ref2, _results; + if (dataByInd) { + x = data.data.map(function(d) { + return d[xvar]; + }); + y = data.data.map(function(d) { + return d[yvar]; + }); + } else { + x = data.data[xvar]; + y = data.data[yvar]; + } + + indID = (_ref = data != null ? data.indID : void 0) != null ? _ref : null; + indID = indID != null ? indID : (function() { + _results = []; + for (var _i = 1, _ref1 = x.length; 1 <= _ref1 ? _i <= _ref1 : _i >= _ref1; 1 <= _ref1 ? _i++ : _i--){ _results.push(_i); } + return _results; + }).apply(this); + + group = (_ref2 = data != null ? data.group : void 0) != null ? _ref2 : (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = x.length; _j < _len; _j++) { + i = x[_j]; + _results1.push(1); + } + return _results1; + })(); + ngroup = d3.max(group); + group = (function() { + var _j, _len, _results1; + _results1 = []; + for (_j = 0, _len = group.length; _j < _len; _j++) { + g = group[_j]; + _results1.push(g - 1); + } + return _results1; + })(); + pointcolor = pointcolor != null ? pointcolor : selectGroupColors(ngroup, "dark"); + pointcolor = expand2vector(pointcolor, ngroup); + if (x.every(function(v) { + return (v != null) && !xNA.force; + })) { + xNA.handle = false; + } + if (y.every(function(v) { + return (v != null) && !yNA.force; + })) { + yNA.handle = false; + } + if (xNA.handle) { + paneloffset = xNA.width + xNA.gap; + panelwidth = width - paneloffset; + } else { + paneloffset = 0; + panelwidth = width; + } + if (yNA.handle) { + panelheight = height - (yNA.width + yNA.gap); + } else { + panelheight = height; + } + xlim = xlim != null ? xlim : d3.extent(x); + ylim = ylim != null ? ylim : d3.extent(y); + na_value = d3.min(x.concat(y)) - 100; + svg = d3.select(this).selectAll("svg").data([data]); + gEnter = svg.enter().append("svg").append("g"); + svg.attr("width", width + margin.left + margin.right).attr("height", height + margin.top + margin.bottom); + g = svg.select("g"); + g.append("rect").attr("x", paneloffset + margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none"); + if (xNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none"); + } + if (xNA.handle && yNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", rectcolor).attr("stroke", "none"); + } + if (yNA.handle) { + g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", rectcolor).attr("stroke", "none"); + } + xrange = [margin.left + paneloffset + margin.inner, margin.left + paneloffset + panelwidth - margin.inner]; + yrange = [margin.top + panelheight - margin.inner, margin.top + margin.inner]; + xscale.domain(xlim).range(xrange); + yscale.domain(ylim).range(yrange); + xs = d3.scale.linear().domain(xlim).range(xrange); + ys = d3.scale.linear().domain(ylim).range(yrange); + if (xNA.handle) { + xscale.domain([na_value].concat(xlim)).range([margin.left + xNA.width / 2].concat(xrange)); + x = x.map(function(e) { + if (e != null) { + return e; + } else { + return na_value; + } + }); + } + if (yNA.handle) { + yscale.domain([na_value].concat(ylim)).range([height + margin.top - yNA.width / 2].concat(yrange)); + y = y.map(function(e) { + if (e != null) { + return e; + } else { + return na_value; + } + }); + } + minx = xlim[0]; + maxx = xlim[1]; + yticks = yticks != null ? yticks : ys.ticks(nyticks); + xticks = xticks != null ? xticks : xs.ticks(nxticks); + titlegrp = g.append("g").attr("class", "title").append("text").attr("x", margin.left + width / 2).attr("y", margin.top - titlepos).style("fill", "black").style("font-size", "24px").text(title); + xaxis = g.append("g").attr("class", "x axis"); + xaxis.selectAll("empty").data(xticks).enter().append("line").attr("x1", function(d) { + return xscale(d); + }).attr("x2", function(d) { + return xscale(d); + }).attr("y1", margin.top).attr("y2", margin.top + height).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + xaxis.selectAll("empty").data(xticks).enter().append("text").attr("x", function(d) { + return xscale(d); + }).attr("y", margin.top + height + axispos.xlabel).text(function(d) { + return formatAxis(xticks)(d); + }); + xaxis.append("text").attr("class", "title").attr("x", margin.left + width / 2).attr("y", margin.top + height + axispos.xtitle).style("fill", "black").text(xlab); + if (xNA.handle) { + xaxis.append("text").attr("x", margin.left + xNA.width / 2).attr("y", margin.top + height + axispos.xlabel).text("N/A"); + } + rotate_ylab = rotate_ylab != null ? rotate_ylab : ylab.length > 1; + yaxis = g.append("g").attr("class", "y axis"); + yaxis.selectAll("empty").data(yticks).enter().append("line").attr("y1", function(d) { + return yscale(d); + }).attr("y2", function(d) { + return yscale(d); + }).attr("x1", margin.left).attr("x2", margin.left + width).attr("fill", "none").attr("stroke", "white").attr("stroke-width", 1).style("pointer-events", "none"); + yaxis.selectAll("empty").data(yticks).enter().append("text").attr("y", function(d) { + return yscale(d); + }).attr("x", margin.left - axispos.ylabel).text(function(d) { + return formatAxis(yticks)(d); + }); + yaxis.append("text").attr("class", "title").attr("y", margin.top + height / 2).attr("x", margin.left - axispos.ytitle).style("fill", "black").text(ylab).attr("transform", rotate_ylab ? "rotate(270," + (margin.left - axispos.ytitle) + "," + (margin.top + height / 2) + ")" : ""); + if (yNA.handle) { + yaxis.append("text").attr("x", margin.left - axispos.ylabel).attr("y", margin.top + height - yNA.width / 2).text("N/A"); + } + indtip = d3.tip().attr('class', 'd3-tip').html(function(d, i) { + return indID[i]; + }).direction('e').offset([0, 10]); + svg.call(indtip); + if (js_data.slope && js_data.intercept) { + g.append("line").attr("x1", xscale(minx) - margin.inner).attr('y1', yscale(js_data.slope * minx + js_data.intercept)).attr("x2", xscale(maxx * 1) + margin.inner).attr("y2", yscale(slope * maxx * 1 + intercept)).style("stroke", "black").style("stroke-width", 2); + } + points = g.append("g").attr("id", "points"); + pointsSelect = points.selectAll("empty").data(d3.range(x.length)).enter().append("circle").attr("cx", function(d, i) { + return xscale(x[i]); + }).attr("cy", function(d, i) { + return yscale(y[i]); + }).attr("class", function(d, i) { + return "pt" + i; + }).attr("r", pointsize).attr("fill", function(d, i) { + return pointcolor[group[i]]; + }).attr("stroke", pointstroke).attr("stroke-width", "1").attr("opacity", function(d, i) { + if (((x[i] != null) || xNA.handle) && ((y[i] != null) || yNA.handle)) { + return 1; + } + return 0; + }).on("mouseover.paneltip", indtip.show).on("mouseout.paneltip", indtip.hide); + g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top).attr("height", panelheight).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + if (xNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top).attr("height", panelheight).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + } + if (xNA.handle && yNA.handle) { + g.append("rect").attr("x", margin.left).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", xNA.width).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + } + if (yNA.handle) { + return g.append("rect").attr("x", margin.left + paneloffset).attr("y", margin.top + height - yNA.width).attr("height", yNA.width).attr("width", panelwidth).attr("fill", "none").attr("stroke", "black").attr("stroke-width", "none"); + } + }); + }; + chart.width = function(value) { + if (!arguments.length) { + return width; + } + width = value; + return chart; + }; + chart.height = function(value) { + if (!arguments.length) { + return height; + } + height = value; + return chart; + }; + chart.margin = function(value) { + if (!arguments.length) { + return margin; + } + margin = value; + return chart; + }; + chart.axispos = function(value) { + if (!arguments.length) { + return axispos; + } + axispos = value; + return chart; + }; + chart.titlepos = function(value) { + if (!arguments.length) { + return titlepos; + } + titlepos; + return chart; + }; + chart.xlim = function(value) { + if (!arguments.length) { + return xlim; + } + xlim = value; + return chart; + }; + chart.nxticks = function(value) { + if (!arguments.length) { + return nxticks; + } + nxticks = value; + return chart; + }; + chart.xticks = function(value) { + if (!arguments.length) { + return xticks; + } + xticks = value; + return chart; + }; + chart.ylim = function(value) { + if (!arguments.length) { + return ylim; + } + ylim = value; + return chart; + }; + chart.nyticks = function(value) { + if (!arguments.length) { + return nyticks; + } + nyticks = value; + return chart; + }; + chart.yticks = function(value) { + if (!arguments.length) { + return yticks; + } + yticks = value; + return chart; + }; + chart.rectcolor = function(value) { + if (!arguments.length) { + return rectcolor; + } + rectcolor = value; + return chart; + }; + chart.pointcolor = function(value) { + if (!arguments.length) { + return pointcolor; + } + pointcolor = value; + return chart; + }; + chart.pointsize = function(value) { + if (!arguments.length) { + return pointsize; + } + pointsize = value; + return chart; + }; + chart.pointstroke = function(value) { + if (!arguments.length) { + return pointstroke; + } + pointstroke = value; + return chart; + }; + chart.dataByInd = function(value) { + if (!arguments.length) { + return dataByInd; + } + dataByInd = value; + return chart; + }; + chart.title = function(value) { + if (!arguments.length) { + return title; + } + title = value; + return chart; + }; + chart.xlab = function(value) { + if (!arguments.length) { + return xlab; + } + xlab = value; + return chart; + }; + chart.ylab = function(value) { + if (!arguments.length) { + return ylab; + } + ylab = value; + return chart; + }; + chart.rotate_ylab = function(value) { + if (!arguments.length) { + return rotate_ylab; + } + rotate_ylab = value; + return chart; + }; + chart.xvar = function(value) { + if (!arguments.length) { + return xvar; + } + xvar = value; + return chart; + }; + chart.yvar = function(value) { + if (!arguments.length) { + return yvar; + } + yvar = value; + return chart; + }; + chart.xNA = function(value) { + if (!arguments.length) { + return xNA; + } + xNA = value; + return chart; + }; + chart.yNA = function(value) { + if (!arguments.length) { + return yNA; + } + yNA = value; + return chart; + }; + chart.yscale = function() { + return yscale; + }; + chart.xscale = function() { + return xscale; + }; + chart.pointsSelect = function() { + return pointsSelect; + }; + return chart; +}; + +root.scatterplot = scatterplot; diff --git a/gn2/wqflask/static/new/javascript/search_autocomplete.js b/gn2/wqflask/static/new/javascript/search_autocomplete.js new file mode 100644 index 00000000..10c22c95 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/search_autocomplete.js @@ -0,0 +1,173 @@ + //replace with gn search hints + + + + + + function autocomplete(inp, arr) { + /*the autocomplete function takes two arguments, + the text field element and an array of possible autocompleted values:*/ + var currentFocus; + /*execute a function when someone writes in the text field:*/ + + inp.addEventListener("focus", function(e) { + + + var a, b, i, val = this.value; + closeAllLists(); + currentFocus = -1; + a = document.createElement("DIV"); + a.setAttribute("id", this.id + "autocomplete-list"); + a.setAttribute("class", "autocomplete-items"); + this.parentNode.appendChild(a); + let historySearch = retrieveSearchHistory().splice(0, 5) + let text_title = document.createElement("DIV") + text_title.innerHTML = "<strong>RECENT SEARCH</strong><input id='clear_all' type='button' value='clear_all'>"; + text_title.setAttribute("class", "recent-search-title") + text_title.setAttribute('disabled', true); + + a.appendChild(text_title); + for (i = 0; i < historySearch.length; i++) { + b = document.createElement("DIV"); + b.innerHTML = "<span>" + historySearch[i].substr(0, val.length) + "</span>"; + b.style.color = "blue"; + b.innerHTML += historySearch[i].substr(val.length); + b.innerHTML += "<input type='hidden' value='" + historySearch[i] + "'>"; + b.addEventListener("click", function(e) { + inp.value = this.getElementsByTagName("input")[0].value; + closeAllLists(); + }); + a.appendChild(b); + + } + document.getElementById("clear_all").addEventListener("click",(event)=>{ + + + deleteSearchHistory() + }) + + }); + + + + inp.addEventListener("input", function(e) { + var a, b, i, val = this.value; + /*close any already open lists of autocompleted values*/ + closeAllLists(); + if (!val) { return false; } + currentFocus = -1; + /*create a DIV element that will contain the items (values):*/ + a = document.createElement("DIV"); + a.setAttribute("id", this.id + "autocomplete-list"); + a.setAttribute("class", "autocomplete-items"); + /*append the DIV element as a child of the autocomplete container:*/ + this.parentNode.appendChild(a); + /*for each item in the array...*/ + for (i = 0; i < arr.length; i++) { + /*check if the item starts with the same letters as the text field value:*/ + if (arr[i].substr(0, val.length).toUpperCase() == val.toUpperCase()) { + /*create a DIV element for each matching element:*/ + b = document.createElement("DIV"); + /*make the matching letters bold:*/ + b.innerHTML = "<strong>" + arr[i].substr(0, val.length) + "</strong>"; + b.innerHTML += arr[i].substr(val.length); + /*insert a input field that will hold the current array item's value:*/ + b.innerHTML += "<input type='hidden' value='" + arr[i] + "'>"; + /*execute a function when someone clicks on the item value (DIV element):*/ + b.addEventListener("click", function(e) { + /*insert the value for the autocomplete text field:*/ + inp.value = this.getElementsByTagName("input")[0].value; + /*close the list of autocompleted values, + (or any other open lists of autocompleted values:*/ + closeAllLists(); + }); + a.appendChild(b); + } + } + }); + /*execute a function presses a key on the keyboard:*/ + inp.addEventListener("keydown", function(e) { + var x = document.getElementById(this.id + "autocomplete-list"); + if (x) x = x.getElementsByTagName("div"); + if (e.keyCode == 40) { + /*If the arrow DOWN key is pressed, + increase the currentFocus variable:*/ + currentFocus++; + /*and and make the current item more visible:*/ + addActive(x); + } else if (e.keyCode == 38) { //up + /*If the arrow UP key is pressed, + decrease the currentFocus variable:*/ + currentFocus--; + /*and and make the current item more visible:*/ + addActive(x); + } else if (e.keyCode == 13) { + /*If the ENTER key is pressed, prevent the form from being submitted,*/ + e.preventDefault(); + if (currentFocus > -1) { + /*and simulate a click on the "active" item:*/ + if (x) x[currentFocus].click(); + } + } + }); + + function addActive(x) { + /*a function to classify an item as "active":*/ + if (!x) return false; + /*start by removing the "active" class on all items:*/ + removeActive(x); + if (currentFocus >= x.length) currentFocus = 0; + if (currentFocus < 0) currentFocus = (x.length - 1); + /*add class "autocomplete-active":*/ + x[currentFocus].classList.add("autocomplete-active"); + } + + function removeActive(x) { + /*a function to remove the "active" class from all autocomplete items:*/ + for (var i = 0; i < x.length; i++) { + x[i].classList.remove("autocomplete-active"); + } + } + + function closeAllLists(elmnt) { + /*close all autocomplete lists in the document, + except the one passed as an argument:*/ + var x = document.getElementsByClassName("autocomplete-items"); + for (var i = 0; i < x.length; i++) { + if (elmnt != x[i] && elmnt != inp) { + x[i].parentNode.removeChild(x[i]); + } + } + } + + + + /*execute a function when someone clicks in the document:*/ + document.addEventListener("click", function(e) { + closeAllLists(e.target); + }) + + } + + function retrieveSearchHistory() { + let results = localStorage.getItem("gn_search_history") + + return results ? JSON.parse(results) : [] + } + + + + + + function saveBeforeSubmit(new_search) { + + let search = retrieveSearchHistory() + search.unshift(new_search) + + localStorage.setItem("gn_search_history", JSON.stringify([...new Set(search)].splice(0,8))) + + } + + function deleteSearchHistory(){ + localStorage.setItem("gn_search_history", []) + }
\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/search_results.js b/gn2/wqflask/static/new/javascript/search_results.js new file mode 100644 index 00000000..c263ef49 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/search_results.js @@ -0,0 +1,386 @@ +change_buttons = function(check_node = 0) { + var button, buttons, item, num_checked, text, _i, _j, _k, _l, _len, _len2, _len3, _len4, _results, _results2; + buttons = ["#add", "#remove"]; + + num_checked = 0 + table_api = $('#trait_table').DataTable(); + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + if (check_cells[i].childNodes[check_node].checked){ + num_checked += 1 + } + } + + if (num_checked === 0) { + for (_i = 0, _len = buttons.length; _i < _len; _i++) { + button = buttons[_i]; + $(button).prop("disabled", true); + } + } else { + for (_j = 0, _len2 = buttons.length; _j < _len2; _j++) { + button = buttons[_j]; + $(button).prop("disabled", false); + } + } +}; + +$(function() { + let selectAll, deselectAll, invert; + + selectAll = function() { + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + check_cells[i].childNodes[0].checked = true; + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + check_rows[i].classList.add("selected"); + } + + change_buttons(); + }; + + deselectAll = function() { + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + check_cells[i].childNodes[0].checked = false; + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + check_rows[i].classList.remove("selected") + } + + change_buttons(); + }; + + invert = function() { + table_api = $('#trait_table').DataTable(); + + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + if (check_cells[i].childNodes[0].checked){ + check_cells[i].childNodes[0].checked = false; + } else { + check_cells[i].childNodes[0].checked = true; + } + } + + check_rows = table_api.rows().nodes(); + for (let i =0; i < check_rows.length; i++) { + if (check_rows[i].classList.contains("selected")){ + check_rows[i].classList.remove("selected") + } else { + check_rows[i].classList.add("selected") + } + } + + change_buttons(); + }; + + $('#searchbox').keyup(function(){ + if ($(this).val() != ""){ + $('#filter_term').val($(this).val()); + } else { + $('#filter_term').val("None"); + } + $('#trait_table').DataTable().search($(this).val()).draw(); + }); + + /** + * parseIndexString takes a string consisting of integers, + * hyphens, and/or commas to indicate range(s) of indices + * to select a rows and returns the corresponding set of indices + * For example - "1, 5-10, 15" would return a set of 8 rows + * @return {Set} The list of indices as a Set + */ + parseIndexString = function(idx_string) { + index_list = []; + + _ref = idx_string.split(","); + for (_i = 0; _i < _ref.length; _i++) { + index_set = _ref[_i]; + if (!/^ *([0-9]+$) *| *([0-9]+ *- *[0-9]+$) *|(^$)$/.test(index_set)) { + $('#select_samples_invalid').show(); + break + } else { + $('#select_samples_invalid').hide(); + } + if (index_set.indexOf('-') !== -1) { + start_index = parseInt(index_set.split("-")[0]); + end_index = parseInt(index_set.split("-")[1]); + + // If start index is higher than end index (for example is the string "10-5" exists) swap values so it'll be interpreted as "5-10" instead + if (start_index > end_index) { + [start_index, end_index] = [end_index, start_index] + } + + for (index = start_index; index <= end_index; index++) { + index_list.push(index); + } + } else { + index = parseInt(index_set); + index_list.push(index); + } + } + return new Set(index_list) + } + + filterByIndex = function() { + indexString = $('#select_top').val() + indexSet = parseIndexString(indexString) + + tableApi = $('#trait_table').DataTable(); + checkNodes = tableApi.column(0).nodes().to$(); + checkNodes.each(function(index) { + if (indexSet.has(index + 1)){ + $(this)[0].childNodes[0].checked = true + } + }) + + checkRows = tableApi.rows().nodes().to$(); + checkRows.each(function(index) { + if (indexSet.has(index + 1)){ + $(this)[0].classList.add("selected"); + } + }) + } + + $(window).keydown(function(event){ + if((event.keyCode == 13)) { + event.preventDefault(); + return false; + } + }); + + $('#select_top').keyup(function(event){ + if (event.keyCode === 13) { + filterByIndex() + } + }); + + $('#select_top').blur(function() { + filterByIndex() + }); + + addToCollection = function() { + var traits; + table_api = $('#trait_table').DataTable(); + check_nodes = table_api.column(0).nodes().to$(); + traits = Array.from(check_nodes.map(function() { + if ($(this)[0].childNodes[0].checked){ + return $(this)[0].childNodes[0].value + } + })) + + var traits_hash = md5(traits.toString()); + + $.ajax({ + type: "POST", + url: "/collections/store_trait_list", + data: { + hash: traits_hash, + traits: traits.toString() + } + }); + + return $.colorbox({ + href: "/collections/add", + data: { + "traits": traits.toString(), + "hash": traits_hash + } + }); + + }; + + submitBnw = function() { + trait_data = submitTraits("trait_table", "submit_bnw") + } + + exportTraits = function() { + trait_data = submitTraits("trait_table", "export_traits_csv") + }; + + exportCollection = function() { + trait_data = submitTraits("trait_table", "export_collection") + } + + fetchTraits = function(table_name){ + trait_table = $('#'+table_name); + table_dict = {}; + + headers = []; + trait_table.find('th').each(function () { + if ($(this).data('export')){ + headers.push($(this).data('export')) + } + }); + table_dict['headers'] = headers; + + selected_rows = []; + all_rows = []; // If no rows are checked, export all + table_api = $('#' + table_name).DataTable(); + check_cells = table_api.column(0).nodes().to$(); + for (let i = 0; i < check_cells.length; i++) { + this_node = check_cells[i].childNodes[0]; + all_rows.push(this_node.value) + if (this_node.checked){ + selected_rows.push(this_node.value) + } + } + + if (selected_rows.length > 0){ + table_dict['rows'] = selected_rows; + } else { + table_dict['rows'] = all_rows; + } + + json_table_dict = JSON.stringify(table_dict); + $('input[name=export_data]').val(json_table_dict); + } + + submitTraits = function(table_name, destination) { + fetchTraits(table_name); + $('#export_form').attr('action', '/' + destination); + $('#export_form').submit(); + }; + + getTraitsFromTable = function(){ + traits = $("#trait_table input:checked").map(function() { + return $(this).val(); + }).get(); + if (traits.length == 0){ + num_traits = $("#trait_table input").length + if (num_traits <= 100){ + traits = $("#trait_table input").map(function() { + return $(this).val(); + }).get(); + } + } + return traits + } + + $("#corr_matrix").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Correlation Matrix") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#network_graph").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Network Graph") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#wgcna_setup").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("WGCNA Setup") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#ctl_setup").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("CTL Setup") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#heatmap").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Heatmap") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + $("#comp_bar_chart").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + $("input[name=tool_used]").val("Comparison Bar Chart") + $("input[name=form_url]").val($(this).data("url")) + return submit_special("/loading") + }); + + $("#send_to_webgestalt, #send_to_bnw, #send_to_geneweaver").on("click", function() { + traits = getTraitsFromTable() + $("#trait_list").val(traits) + url = $(this).data("url") + return submit_special(url) + }); + + + $("#select_all").click(selectAll); + $("#deselect_all").click(deselectAll); + $("#invert").click(invert); + $("#add").click(addToCollection); + $("#submit_bnw").click(submitBnw); + $("#export_traits").click(exportTraits); + $("#export_collection").click(exportCollection); + + let naturalAsc = $.fn.dataTableExt.oSort["natural-ci-asc"] + let naturalDesc = $.fn.dataTableExt.oSort["natural-ci-desc"] + + let na_equivalent_vals = ["N/A", "--", ""]; //ZS: Since there are multiple values that should be treated the same as N/A + + function extractInnerText(the_string){ + var span = document.createElement('span'); + span.innerHTML = the_string; + return span.textContent || span.innerText; + } + + function sortNAs(a, b, sort_function){ + if ( na_equivalent_vals.includes(a) && na_equivalent_vals.includes(b)) { + return 0; + } + if (na_equivalent_vals.includes(a)){ + return 1 + } + if (na_equivalent_vals.includes(b)) { + return -1; + } + return sort_function(a, b) + } + + $.extend( $.fn.dataTableExt.oSort, { + "natural-minus-na-asc": function (a, b) { + return sortNAs(extractInnerText(a), extractInnerText(b), naturalAsc) + }, + "natural-minus-na-desc": function (a, b) { + return sortNAs(extractInnerText(a), extractInnerText(b), naturalDesc) + } + }); + + $.fn.dataTable.ext.order['dom-checkbox'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $('input', td).prop('checked') ? '1' : '0'; + } ); + }; + + $.fn.dataTable.ext.order['dom-inner-text'] = function ( settings, col ) + { + return this.api().column( col, {order:'index'} ).nodes().map( function ( td, i ) { + return $(td).text(); + } ); + } + + applyDefault = function() { + let default_collection_id = $.cookie('default_collection'); + if (default_collection_id) { + let the_option = $('[name=existing_collection] option').filter(function() { + return ($(this).text().split(":")[0] == default_collection_id); + }) + the_option.prop('selected', true); + } + } + applyDefault(); + +}); 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; +} diff --git a/gn2/wqflask/static/new/javascript/show_trait_mapping_tools.js b/gn2/wqflask/static/new/javascript/show_trait_mapping_tools.js new file mode 100644 index 00000000..a4e6dafc --- /dev/null +++ b/gn2/wqflask/static/new/javascript/show_trait_mapping_tools.js @@ -0,0 +1,329 @@ +var block_outliers, composite_mapping_fields, do_ajax_post, get_progress, mapping_method_fields, open_mapping_results, outlier_text, showalert, submit_special, toggle_enable_disable, update_time_remaining; + +update_time_remaining = function(percent_complete) { + var minutes_remaining, now, period, total_seconds_remaining; + now = new Date(); + period = now.getTime() - root.start_time; + console.log("period is:", period); + if (period > 8000) { + total_seconds_remaining = (period / percent_complete * (100 - percent_complete)) / 1000; + minutes_remaining = Math.round(total_seconds_remaining / 60); + if (minutes_remaining < 3) { + return $('#time_remaining').text(Math.round(total_seconds_remaining) + " seconds remaining"); + } else { + return $('#time_remaining').text(minutes_remaining + " minutes remaining"); + } + } +}; + +get_progress = function() { + var params, params_str, temp_uuid, url; + console.log("temp_uuid:", $("#temp_uuid").val()); + temp_uuid = $("#temp_uuid").val(); + params = { + key: temp_uuid + }; + params_str = $.param(params); + url = "/get_temp_data?" + params_str; + console.log("url:", url); + $.ajax({ + type: "GET", + url: url, + success: (function(_this) { + return function(progress_data) { + var percent_complete; + percent_complete = progress_data['percent_complete']; + console.log("in get_progress data:", progress_data); + $('#marker_regression_progress').css("width", percent_complete + "%"); + if (root.start_time) { + if (!isNaN(percent_complete)) { + return update_time_remaining(percent_complete); + } + } else { + return root.start_time = new Date().getTime(); + } + }; + })(this) + }); + return false; +}; + +block_outliers = function() { + return $('.outlier').each((function(_this) { + return function(_index, element) { + return $(element).find('.trait_value_input').val('x'); + }; + })(this)); +}; + +do_ajax_post = function(url, form_data) { + $.ajax({ + type: "POST", + url: url, + data: form_data, + error: (function(_this) { + return function(xhr, ajaxOptions, thrownError) { + alert("Sorry, an error occurred"); + console.log(xhr); + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return $("body").html("We got an error."); + }; + })(this), + success: (function(_this) { + return function(data) { + clearInterval(_this.my_timer); + $('#progress_bar_container').modal('hide'); + $('#static_progress_bar_container').modal('hide'); + return open_mapping_results(data); + }; + })(this) + }); + console.log("settingInterval"); + this.my_timer = setInterval(get_progress, 1000); + return false; +}; + +open_mapping_results = function(data) { + return $.colorbox({ + html: data, + href: "#mapping_results_holder", + height: "90%", + width: "90%", + onComplete: (function(_this) { + return function() { + var filename, getSvgXml; + root.create_lod_chart(); + filename = "lod_chart_" + js_data.this_trait; + getSvgXml = function() { + var svg; + svg = $("#topchart").find("svg")[0]; + return (new XMLSerializer).serializeToString(svg); + }; + $("#exportform > #export").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + return $("#exportpdfform > #export_pdf").click(function() { + var form, svg_xml; + svg_xml = getSvgXml(); + form = $("#exportpdfform"); + form.find("#data").val(svg_xml); + form.find("#filename").val(filename); + return form.submit(); + }); + }; + })(this) + }); +}; + +outlier_text = "One or more outliers exist in this data set. Please review values before mapping. Including outliers when mapping may lead to misleading results."; +showalert = function(message, alerttype) { + return $('#outlier_alert_placeholder').append('<div id="mapping_alert" class="alert ' + alerttype + '"><a class="close" data-dismiss="alert">�</a><span>' + message + '</span></div>'); +}; + +$('#suggestive').hide(); + +$('input[name=display_all]').change((function(_this) { + return function() { + if ($('input[name=display_all]:checked').val() === "False") { + return $('#suggestive').show(); + } else { + return $('#suggestive').hide(); + } + }; +})(this)); + +// This is a list of inputs to be passed to the loading page, since not all inputs on the trait page are relevant to mapping +var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', + 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', + 'sample_vals', 'vals_hash', 'score_type', 'suggestive', 'significant', + 'num_perm', 'permCheck', 'perm_output', 'perm_strata', 'categorical_vars', + 'num_bootstrap', 'bootCheck', 'bootstrap_results', 'LRSCheck', 'covariates', + 'maf', 'use_loco', 'manhattan_plot', 'control_marker', 'do_control', + 'genofile', 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', + 'additiveCheck', 'showSNP', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', + 'mapmethod_rqtl', 'mapmodel_rqtl', 'temp_trait', 'group', 'species', + 'reaper_version', 'primary_samples'] + +$(".rqtl-geno-tab, #rqtl_geno_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_geno_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=pair_scan]').val("false"); + $('input[name=selected_chr]').val($('#chr_rqtl_geno').val()); + $('input[name=mapping_scale]').val($('#scale_rqtl_geno').val()); + $('input[name=genofile]').val($('#genofile_rqtl_geno').val()); + $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_geno').val()); + $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_geno').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_geno]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_rqtl]:checked').val()); + $('input[name=control_marker]').val($('input[name=control_rqtl_geno]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl]:checked').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$(".rqtl-pair-tab, #rqtl_pair_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "rqtl_pair_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("rqtl_geno"); + $('input[name=pair_scan]').val("true"); + $('input[name=genofile]').val($('#genofile_rqtl_pair').val()); + $('input[name=mapmodel_rqtl]').val($('#mapmodel_rqtl_pair').val()); + $('input[name=mapmethod_rqtl]').val($('#mapmethod_rqtl_pair').val()); + $('input[name=num_perm]').val($('input[name=num_perm_rqtl_pair]').val()); + $('input[name=categorical_vars]').val(js_data.categorical_vars) + $('input[name=control_marker]').val($('input[name=control_rqtl_pair]').val()); + $('input[name=do_control]').val($('input[name=do_control_rqtl_pair]:checked').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$(".gemma-tab, #gemma_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "gemma_compute"){ + var form_data, url; + url = "/loading"; + $('input[name=method]').val("gemma"); + $('input[name=mapping_scale]').val('physic'); + $('input[name=selected_chr]').val($('#chr_gemma').val()); + $('input[name=num_perm]').val(0); + $('input[name=genofile]').val($('#genofile_gemma').val()); + $('input[name=maf]').val($('input[name=maf_gemma]').val()); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$(".reaper-tab, #interval_mapping_compute").on("click", (function(_this) { + return function() { + if ($(this).hasClass('active') || $(this).attr('id') == "interval_mapping_compute"){ + var form_data, url; + console.log("In interval mapping"); + url = "/loading"; + $('input[name=method]').val("reaper"); + $('input[name=selected_chr]').val($('#chr_reaper').val()); + $('input[name=mapping_scale]').val($('#scale_reaper').val()); + $('input[name=genofile]').val($('#genofile_reaper').val()); + $('input[name=num_perm]').val($('input[name=num_perm_reaper]').val()); + $('input[name=control_marker]').val($('input[name=control_reaper]').val()); + $('input[name=do_control]').val($('input[name=do_control_reaper]:checked').val()); + $('input[name=manhattan_plot]').val($('input[name=manhattan_plot_reaper]:checked').val()); + $('input[name=mapping_display_all]').val($('input[name=display_all_reaper]')); + $('input[name=suggestive]').val($('input[name=suggestive_reaper]')); + $('input[name=tool_used]').val("Mapping"); + $('input[name=form_url]').val("/run_mapping"); + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + return submit_special(url); + } else { + return true + } + }; +})(this)); + +$("#interval_mapping_compute, #gemma_compute, rqtl_geno_compute").on("mouseover", (function(_this) { + return function() { + if ($(".outlier").length && $(".outlier-alert").length < 1) { + return showalert(outlier_text, "alert-success outlier-alert"); + } + }; +})(this)); + +composite_mapping_fields = function() { + return $(".composite_fields").toggle(); +}; + +mapping_method_fields = function() { + return $(".mapping_method_fields").toggle(); +}; + +$("#use_composite_choice").change(composite_mapping_fields); + +$("#mapping_method_choice").change(mapping_method_fields); + +$("#mapmodel_rqtl_geno,#mapmodel_rqtl_pair").change(function() { + if ($(this).val() == "np"){ + $("#mapmethod_rqtl_geno").attr('disabled', 'disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#CCC'); + $("#missing_geno,#missing_geno_pair").attr('disabled', 'disabled'); + $("#missing_geno,#missing_geno_pair").css('background-color', '#CCC'); + } else { + $("#mapmethod_rqtl_geno").removeAttr('disabled'); + $("#mapmethod_rqtl_geno").css('background-color', '#FFF'); + $("#missing_geno,#missing_geno_pair").removeAttr('disabled'); + $("#missing_geno,#missing_geno_pair").css('background-color', '#FFF'); + } +}); + +$("#mapmethod_rqtl_geno,#mapmethod_rqtl_pair").change(function() { + if ($(this).val() == "mr"){ + $("#missing_geno_div,#missing_geno_pair_div").css('display', 'block'); + } else { + $("#missing_geno_div,#missing_geno_pair_div").css('display', 'none'); + } +}); + +$("li.mapping-tab").click(function() { + if ($(this).hasClass("rqtl")){ + $(".rqtl_description").css("display", "block"); + } else { + $(".rqtl_description").css("display", "none"); + } +}); + +toggle_enable_disable = function(elem) { + return $(elem).prop("disabled", !$(elem).prop("disabled")); +}; + +$("#choose_closet_control").change(function() { + return toggle_enable_disable("#control_locus"); +}); + +$("#display_all_lrs").change(function() { + return toggle_enable_disable("#suggestive_lrs"); +}); + +$('#genofile_rqtl_geno').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_rqtl_geno').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_rqtl_geno').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); +$('#genofile_reaper').change(function() { + geno_location = $(this).children("option:selected").val().split(":")[0] + $('#scale_reaper').empty() + the_scales = js_data.scales_in_geno[geno_location] + for (var i = 0; i < the_scales.length; i++){ + $('#scale_reaper').append($("<option></option>").attr("value", the_scales[i][0]).text(the_scales[i][1])); + } +}); diff --git a/gn2/wqflask/static/new/javascript/stats.js b/gn2/wqflask/static/new/javascript/stats.js new file mode 100644 index 00000000..6c443ab3 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/stats.js @@ -0,0 +1,176 @@ +// Generated by CoffeeScript 1.8.0 +var Stats, bxd_only; + +Stats = (function() { + function Stats(the_values) { + this.the_values = the_values; + } + + Stats.prototype.add_value = function(value) { + return this.the_values.push(value); + }; + + Stats.prototype.n_of_samples = function() { + return this.the_values.length; + }; + + Stats.prototype.sum = function() { + var total, value, _i, _len, _ref; + total = 0; + _ref = this.the_values; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + value = _ref[_i]; + total += value; + } + return total; + }; + + Stats.prototype.mean = function() { + return this.sum() / this.n_of_samples(); + }; + + Stats.prototype.median = function() { + var is_odd, median_position, the_values_sorted; + is_odd = this.the_values.length % 2; + median_position = Math.floor(this.the_values.length / 2); + the_values_sorted = this.the_values.sort(function(a, b) { + return a - b; + }); + if (is_odd) { + return the_values_sorted[median_position]; + } else { + return (the_values_sorted[median_position] + the_values_sorted[median_position - 1]) / 2; + } + }; + + Stats.prototype.std_dev = function() { + var step_a, step_b, sum, value, _i, _len, _ref; + sum = 0; + _ref = this.the_values; + for (_i = 0, _len = _ref.length; _i < _len; _i++) { + value = _ref[_i]; + step_a = Math.pow(value - this.mean(), 2); + sum += step_a; + } + step_b = sum / this.the_values.length; + return Math.sqrt(step_b); + }; + + Stats.prototype.std_error = function() { + return this.std_dev() / Math.sqrt(this.n_of_samples()); + }; + + Stats.prototype.min = function() { + return Math.min.apply(Math, this.the_values); + }; + + Stats.prototype.max = function() { + return Math.max.apply(Math, this.the_values); + }; + + Stats.prototype.range = function() { + if (js_data.dataset_type == "ProbeSet"){ + if (js_data.data_scale == "linear_positive"){ + return Math.log2(this.max()) - Math.log2(this.min()); + } else { + return this.max() - this.min() + } + } else { + return this.max() - this.min() + } + }; + + Stats.prototype.range_fold = function() { + if (js_data.dataset_type == "ProbeSet"){ + return Math.pow(2, this.range()); + } else { + return this.range() + } + }; + + Stats.prototype.interquartile = function() { + var iq, length, q1, q3; + length = this.the_values.length; + if (js_data.dataset_type == "ProbeSet" && js_data.data_scale == "linear_positive") { + q1 = Math.log2(this.the_values[Math.floor(length * .25)]); + q3 = Math.log2(this.the_values[Math.floor(length * .75)]); + } else { + q1 = this.the_values[Math.floor(length * .25)]; + q3 = this.the_values[Math.floor(length * .75)]; + } + iq = q3 - q1; + if (js_data.dataset_type == "ProbeSet") { + return Math.pow(2, iq); + } else { + return iq; + } + }; + + Stats.prototype.skewness = function() { + var len = this.the_values.length, + delta = 0, + delta_n = 0, + term1 = 0, + N = 0, + mean = 0, + M2 = 0, + M3 = 0, + g; + + for ( var i = 0; i < len; i++ ) { + N += 1; + + delta = this.the_values[ i ] - mean; + delta_n = delta / N; + + term1 = delta * delta_n * (N-1); + + M3 += term1*delta_n*(N-2) - 3*delta_n*M2; + M2 += term1; + mean += delta_n; + } + // Calculate the population skewness: + g = Math.sqrt( N )*M3 / Math.pow( M2, 3/2 ); + + // Return the corrected sample skewness: + return Math.sqrt( N*(N-1))*g / (N-2); + }; + + Stats.prototype.kurtosis = function() { + var len = this.the_values.length, + delta = 0, + delta_n = 0, + delta_n2 = 0, + term1 = 0, + N = 0, + mean = 0, + M2 = 0, + M3 = 0, + M4 = 0, + g; + + for ( var i = 0; i < len; i++ ) { + N += 1; + + delta = this.the_values[ i ] - mean; + delta_n = delta / N; + delta_n2 = delta_n * delta_n; + + term1 = delta * delta_n * (N-1); + + M4 += term1*delta_n2*(N*N - 3*N + 3) + 6*delta_n2*M2 - 4*delta_n*M3; + M3 += term1*delta_n*(N-2) - 3*delta_n*M2; + M2 += term1; + mean += delta_n; + } + // Calculate the population excess kurtosis: + g = N*M4 / (M2*M2) - 3; + //Return the corrected sample excess kurtosis: + return (N-1) / ( (N-2)*(N-3) ) * ( (N+1)*g + 6 ); + }; + + return Stats; + +})(); + +window.Stats = Stats; diff --git a/gn2/wqflask/static/new/javascript/table_functions.js b/gn2/wqflask/static/new/javascript/table_functions.js new file mode 100644 index 00000000..62888cd9 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/table_functions.js @@ -0,0 +1,90 @@ +recheckRows = function(theTable, checkedRows){ + // This is meant to recheck checkboxes after columns are resized + checkCells = theTable.column(0).nodes().to$(); + for (let i = 0; i < checkCells.length; i++) { + if (checkedRows.includes(i)){ + checkCells[i].childNodes[0].checked = true; + } + } + + checkRows = traitTable.rows().nodes(); + for (let i =0; i < checkRows.length; i++) { + if (checkedRows.includes(i)){ + checkRows[i].classList.add("selected") + } + } +} + +getCheckedRows = function(tableId){ + let checkedRows = [] + $("#" + tableId + " input.checkbox").each(function(index){ + if ($(this).prop("checked") == true){ + checkedRows.push(index); + } + }); + + return checkedRows +} + +function setUserColumnsDefWidths(tableId, columnDefs) { + var userColumnDef; + + // Get the settings for this table from localStorage + var userColumnDefs = JSON.parse(localStorage.getItem(tableId)) || []; + + if (userColumnDefs.length === 0 ) return; + + columnDefs.forEach( function(columnDef) { + // Check if there is a width specified for this column + userColumnDef = userColumnDefs.find( function(column) { + return column.targets === columnDef.targets; + }); + + // If there is, set the width of this columnDef in px + if ( userColumnDef ) { + + columnDef.sWidth = userColumnDef.width + 'px'; + columnDef.width = userColumnDef.width + 'px'; + + $('.toggle-vis').each(function(){ + if ($(this).attr('data-column') == columnDef.targets){ + if ($(this).hasClass("active")){ + columnDef.bVisible = false + } else { + columnDef.bVisible = true + } + } + }) + } + }); + + return columnDefs +} + +function saveColumnSettings(tableId, traitTable) { + var userColumnDefs = JSON.parse(localStorage.getItem(tableId)) || []; + var width, header, existingSetting; + + traitTable.columns().every( function ( targets ) { + // Check if there is a setting for this column in localStorage + existingSetting = userColumnDefs.findIndex( function(column) { return column.targets === targets;}); + + // Get the width of this column + header = this.header(); + width = $(header).width(); + + if ( existingSetting !== -1 ) { + // Update the width + userColumnDefs[existingSetting].width = width; + } else { + // Add the width for this column + userColumnDefs.push({ + targets: targets, + width: width, + }); + } + }); + + // Save (or update) the settings in localStorage + localStorage.setItem(tableId, JSON.stringify(userColumnDefs)); +} diff --git a/gn2/wqflask/static/new/javascript/thank_you.js b/gn2/wqflask/static/new/javascript/thank_you.js new file mode 100644 index 00000000..deb68211 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/thank_you.js @@ -0,0 +1,6 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + console.log("Starting transform"); + $('#login_out').text('Sign out').attr('href', '/logout').removeClass('modalize'); + return console.log("Transformed to sign out I hope"); +}); diff --git a/gn2/wqflask/static/new/javascript/typeahead_rn6.json b/gn2/wqflask/static/new/javascript/typeahead_rn6.json new file mode 100644 index 00000000..1889d8a2 --- /dev/null +++ b/gn2/wqflask/static/new/javascript/typeahead_rn6.json @@ -0,0 +1 @@ +var rat_genes = 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\ No newline at end of file diff --git a/gn2/wqflask/static/new/javascript/validation.js b/gn2/wqflask/static/new/javascript/validation.js new file mode 100644 index 00000000..2cacacfa --- /dev/null +++ b/gn2/wqflask/static/new/javascript/validation.js @@ -0,0 +1,42 @@ +// Generated by CoffeeScript 1.8.0 +$(function() { + var remove_samples_is_valid, validate_remove_samples; + remove_samples_is_valid = function(input) { + var new_splats, pattern, splat, splats, _i, _len; + if (_.trim(input).length === 0) { + return true; + } + splats = input.split(","); + new_splats = (function() { + var _i, _len, _results; + _results = []; + for (_i = 0, _len = splats.length; _i < _len; _i++) { + input = splats[_i]; + _results.push(_.trim(input)); + } + return _results; + })(); + pattern = /^\d+\s*(?:-\s*\d+)?\s*$/; + for (_i = 0, _len = new_splats.length; _i < _len; _i++) { + splat = new_splats[_i]; + if (!splat.match(pattern)) { + return false; + } + } + return true; + }; + validate_remove_samples = function() { + + /* + Check if input for the remove samples function is valid and notify the user if not + */ + var input; + input = $('#remove_samples_field').val(); + if (remove_samples_is_valid(input)) { + return $('#remove_samples_invalid').hide(); + } else { + return $('#remove_samples_invalid').show(); + } + }; + return $('#remove_samples_field').change(validate_remove_samples); +}); |