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Diffstat (limited to 'gn2/wqflask/templates/mapping_results.html')
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diff --git a/gn2/wqflask/templates/mapping_results.html b/gn2/wqflask/templates/mapping_results.html new file mode 100644 index 00000000..0e084ba7 --- /dev/null +++ b/gn2/wqflask/templates/mapping_results.html @@ -0,0 +1,698 @@ +{% extends "base.html" %} +{% block title %}Mapping Results{% endblock %} +{% block css %} + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" /> + + <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.3.1/css/all.css" integrity="sha384-mzrmE5qonljUremFsqc01SB46JvROS7bZs3IO2EmfFsd15uHvIt+Y8vEf7N7fWAU" crossorigin="anonymous"> + <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='purescript-genome-browser/css/purescript-genetics-browser.css') }}" /> + + <link rel="stylesheet" type="text/css" href="/static/new/css/marker_regression.css" /> + <link rel="stylesheet" type="text/css" href="static/new/css/show_trait.css" /> + +{% endblock %} +{% from "base_macro.html" import header %} +{% block content %} + <div class="container"> + <form method="post" target="_blank" action="/run_mapping" name="marker_regression" id="marker_regression_form"> + <input type="hidden" name="temp_uuid" value="{{ temp_uuid }}"> + {% if temp_trait is defined %} + <input type="hidden" name="temp_trait" value="{{ temp_trait }}"> + {% endif %} + <input type="hidden" name="inputs_hash" value="{{ hash_of_inputs }}"> + <input type="hidden" name="group" value="{{ dataset.group.name }}"> + <input type="hidden" name="species" value="{{ dataset.group.species }}"> + <input type="hidden" name="trait_id" value="{{ this_trait.name }}"> + <input type="hidden" name="dataset" value="{{ dataset.name }}"> + <input type="hidden" name="genofile" value="{{ genofile_string }}"> + <input type="hidden" name="geno_db_exists" value="{{ geno_db_exists }}"> + <input type="hidden" name="first_run" value="{{ first_run }}"> + {% if output_files is defined %} + <input type="hidden" name="output_files" value="{{ output_files }}"> + {% endif %} + {% if reaper_version is defined %} + <input type="hidden" name="reaper_version" value="{{ reaper_version }}"> + {% endif %} + <input type="hidden" name="results_path" value="{{ mapping_results_path }}"> + <input type="hidden" name="method" value="{{ mapping_method }}"> + <input type="hidden" name="sample_vals" value="{{ sample_vals }}"> + <input type="hidden" name="vals_hash" value="{{ vals_hash }}"> + <input type="hidden" name="n_samples" value="{{ n_samples }}"> + <input type="hidden" name="maf" value="{{ maf }}"> + <input type="hidden" name="use_loco" value="{{ use_loco }}"> + <input type="hidden" name="selected_chr" value="{{ selectedChr }}"> + <input type="hidden" name="mapping_scale" value="{{ plotScale }}"> + <input type="hidden" name="manhattan_plot" value="{{ manhattan_plot }}"> + {% if manhattan_plot == True %} + <input type="hidden" name="color_scheme" value="alternating"> + {% endif %} + <input type="hidden" name="num_perm" value="{{ nperm }}"> + <input type="hidden" name="perm_info" value=""> + {% if categorical_vars is defined %} + <input type="hidden" name="categorical_vars" value="{{ categorical_vars|join(',') }}"> + {% endif %} + {% if perm_strata is defined %} + <input type="hidden" name="perm_strata" value="True"> + {% endif %} + <input type="hidden" name="num_bootstrap" value="{{ nboot }}"> + <input type="hidden" name="do_control" value="{{ doControl }}"> + <input type="hidden" name="control_marker" value="{{ controlLocus }}"> + <input type="hidden" name="covariates" value="{{ covariates }}"> + <input type="hidden" name="mapmethod_rqtl_geno" value="{{ mapmethod_rqtl_geno }}"> + <input type="hidden" name="mapmodel_rqtl_geno" value="{{ mapmodel_rqtl_geno }}"> + <input type="hidden" name="pair_scan" value="{{ pair_scan }}"> + <input type="hidden" name="transform" value="{{ transform }}"> + <input type="hidden" name="tool_used" value="Mapping"> + <input type="hidden" name="wanted_inputs" value=""> + <input type="hidden" name="form_url" value="/run_mapping"> + + <div class="container" style="width: 1200px; float: left;"> + <div class="col-xs-4" style="word-wrap: normal;"> + <h2>Map Viewer: Whole Genome</h2><br> + <b>Population:</b> {{ dataset.group.species|capitalize }} {{ dataset.group.name }}<br> + <b>Database:</b> {{ dataset.fullname }}<br> + {% if dataset.type == "ProbeSet" %}<b>Trait ID:</b>{% else %}<b>Record ID:</b>{% endif %} <a href="/show_trait?trait_id={{ this_trait.name }}&dataset={{ dataset.name }}">{{ this_trait.display_name }}</a><br> + <b>Trait Hash: </b> {{ vals_hash }}<br> + {% if dataset.type == "ProbeSet" %} + <b>Gene Symbol:</b> <i>{{ this_trait.symbol }}</i><br> + <b>Location:</b> Chr {{ this_trait.chr }} @ {{ this_trait.mb }} Mb<br> + {% endif %} + {% if genofile_string != "" %} + <b>Genotypes:</b> {{ genofile_string.split(":")[1] }}<br> + {% endif %} + <b>Current Date/Time:</b> {{ current_datetime }}<br> + <br> + <button class="btn btn-default export_mapping_results"><span class="glyphicon glyphicon-download-alt"></span>Map Data</button> + <br><br> + <div class="input-group"> + <input type="text" class="form-control" name="mappingLink" size="75"></input> + <div class="input-group-btn"> + <button class="btn btn-default share-results" type="button">Copy and Share</button> + </div> + </div> + </div> + <div id="gn1_map_options" class="col-xs-6" style="outline: 3px double #AAAAAA; padding: 10px; margin: 10px;"> + <div class="col-xs-8" style="padding: 0px;"> + <table> + <tr> + <td><b>Chr: </b></td> + <td style="padding: 5px;"> + <select name="chromosomes" size="1"> + {% for chr in ChrList %} + <option value="{{ chr[1] }}" {% if (chr[1] + 1) == selectedChr %}selected{% endif %}>{{ chr[0] }}</option> + {% endfor %} + </select> + <button type="button" class="btn btn-primary" style="padding-bottom: 2px; padding-top: 2px;" onclick="javascript:remap();">Remap</button> + </td> + </tr> + <tr> + <td ><b>View: </b></td> + <td style="padding: 5px;"> + <input type="text" name="startMb" size="7" value="{% if startMb != -1 %}{{ startMb }}{% endif %}"> to <input type="text" name="endMb" size="7" value="{% if endMb != -1 %}{{ endMb }}{% endif %}"> + </td> + </tr> + <tr> + <td><b>Units: </b></td> + <td style="padding: 5px;"> + <label class="radio-inline"> + <input type="radio" name="LRSCheck" value="LRS" {% if LRS_LOD == "LRS" %}checked{% endif %}>LRS + </label> + <label class="radio-inline"> + <input type="radio" name="LRSCheck" value="{% if LRS_LOD == "-logP" %}-logP{% else %}LOD{% endif %}" {% if LRS_LOD == "LOD" or LRS_LOD == "-logP" %}checked{% endif %}>{% if LRS_LOD == "-logP" %}-logP{% else %}LOD{% endif %} + </label> + <a href="https://genenetwork.org/glossary.html#LOD" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + </td> + </tr> + <tr> + <td></td> + <td style="padding: 5px;"> + <input type="text" name="lrsMax" value="{{ '%0.1f' | format(lrsMax|float) }}" size="3"> <span style="font-size: 12px;">units on the y-axis (0 for default)</span> + </td> + </tr> + <tr> + <td><b>Width: </b></td> + <td style="padding: 5px;"> + <input type="text" name="graphWidth" value="{% if graphWidth is defined %}{{ graphWidth }}{% else %}1600{% endif %}" size="5"><span style="font-size: 12px;"> pixels (minimum=900)</span> + </td> + </tr> + </table> + {% if manhattan_plot == True and selectedChr == -1 %} + <table style="margin-top: 10px;"> + <tr> + <td> + <b>Manhattan Plot Color Scheme: </b> + </td> + <td> + <select id="color_scheme"> + <option value="alternating" {% if color_scheme == "alternating" %}selected{% endif %}>Alternating</option> + <option value="varied" {% if color_scheme == "varied" %}selected{% endif %}>Varied by Chr</option> + <option value="single" {% if color_scheme == "single" %}selected{% endif %}>Single Color</option> + </select> + </td> + <td> + <input name="manhattan_single_color" type="hidden" id="point_color" value={% if manhattan_single_color %}{{ manhattan_single_color }}{% else %}"#D9D9D9"{% endif %}> + <button style="display: none; margin-left: 5px;" id="point_color_picker" class="jscolor {valueElement: 'point_color'}">Choose Color</button> + </td> + </tr> + </table> + {% endif %} + </div> + <div class="col-xs-4" style="padding: 0px;"> + {% if (mapping_method == "reaper" or mapping_method == "rqtl_geno") and nperm > 0 %} + <input type="checkbox" name="permCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if permChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Permutation Test + <a href="http://genenetwork.org/glossary.html#Permutation" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <br> + {% endif %} + {% if mapping_method == "reaper" and nboot > 0 %} + <input type="checkbox" name="bootCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if bootChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Bootstrap Test + <a href="http://genenetwork.org/glossary.html#bootstrap" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <br> + {% endif %} + {% if mapping_method == "reaper" %} + <input type="checkbox" name="additiveCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if additiveChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Allele Effects + <a href="http://genenetwork.org/glossary.html#additive" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <br> + {% endif %} + <input type="checkbox" name="showSNP" class="checkbox" style="display: inline; margin-top: 0px;" {% if SNPChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">SNP Track </span> + <a href="http://genenetwork.org/glossary.html#snpSeismograph" target="_blank"> + <sup style="color:#f00"> ?</sup> + </a> + <span style="color:red;">*</span> + <br> + <input type="checkbox" name="showGenes" class="checkbox" style="display: inline; margin-top: 0px;" {% if geneChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Gene Track </span> <span style="color:red;">*</span><br> + {% if plotScale != "morgan" %} + <input type="checkbox" name="haplotypeAnalystCheck" class="checkbox" style="display: inline; margin-top: 0px;" {% if haplotypeAnalystChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Haplotype Tracks </span> <span style="color:red;">*</span><br> + {% endif %} + <input type="checkbox" name="viewLegend" class="checkbox" style="display: inline; margin-top: 0px;" {% if legendChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Legend </span><br> + <input type="checkbox" name="showHomology" class="checkbox" style="display: inline; margin-top: 0px;" {% if homologyChecked|upper == "ON" %}value="ON" checked{% endif %}> <span style="font-size: 12px;">Human Chromosomes <a href="http://hgdownload.cse.ucsc.edu/goldenpath/hg38/liftOver/"><sup style="color:#f00" title="Human Syntenic Chromosomes taken from HG38 (Human Genome 38)"> ?</sup></a></span> + <br> + <span style="color:red;">*</span> <span style="font-size: 12px;">only apply to single chromosome physical mapping</span> + </div> + </div> + </div> + + <div class="tabbable" style="width: 100%; overflow-x: auto; margin: 10px; float: left;"> + <ul class="nav nav-tabs"> + <li id="gn1_map_tab"> + <a href="#gn1_map" data-toggle="tab" aria-expanded="true">GN1 Map</a> + </li> + {% if mapping_method == "gemma" or mapping_method == "reaper" %} + <li id="browser_tab"> + <a href="#browser_holder" data-toggle="tab" aria-expanded="true">Genome Browser</a> + </li> + {% endif %} + </ul> + <div class="tab-content"> + <div class="tab-pane active" id="gn1_map"> + <div class="qtlcharts"> + {{ gifmap|safe }} + <img src="/generated/{{ filename }}.png" usemap="#WebQTLImageMap"> + {% if additiveChecked|upper == "ON" %} + <br> + <span style="white-space: nowrap;">A positive additive coefficient (green line) indicates that {{ dataset.group.parlist[1] }} alleles increase trait values. In contrast, a negative additive coefficient (orange line) indicates that {{ dataset.group.parlist[0] }} alleles increase trait values.</span> + {% endif %} + </div> + </div> + {% if mapping_method == "gemma" or mapping_method == "reaper" %} + <div class="tab-pane" id="browser_holder" style="height: 600px;"> + <div id="browser" style="margin-right: 20px; width: 90%;"> + <div id="controls"> + <button id="scrollLeft" type="button" > + <i class="fas fa-arrow-left"></i> + </button> + <button id="scrollRight" type="button" > + <i class="fas fa-arrow-right"></i> + </button> + <button id="zoomOut" type="button" > + <i class="fas fa-search-minus"></i> + </button> + <button id="zoomIn" type="button" > + <i class="fas fa-search-plus"></i> + </button> + <button id="reset" type="button" >Reset</button> + </div> + <div id="infoBox"></div> + </div> + </div> + {% endif %} + </div> + </div> + <div style="float: left;"> + {% if nperm > 0 and permChecked == "ON" %} + <br><br> + <div id="perm_histogram" class="barchart"></div> + <br><br> + Total of {{ nperm }} permutations <a href="javascript:;" id="download_perm" target="_blank" >Download Permutation Results</a> + <br> + {% endif %} + </div> + + </form> + {% if selectedChr == -1 %} + <div class="container" style="padding-left: 30px; margin-top: 50px; position: relative; float: left;"> + <h2>Mapping Statistics</h2> + <br /> + <button class="btn btn-default" id="select_all"><span class="glyphicon glyphicon-ok"></span> Select All</button> + <button class="btn btn-default" id="deselect_all"><span class="glyphicon glyphicon-remove"></span> Deselect All</button> + <button class="btn btn-default" id="invert"><span class="glyphicon glyphicon-resize-vertical"></span> Invert</button> + {% if geno_db_exists == "True" %}<button class="btn btn-success" id="add" disabled><span class="glyphicon glyphicon-plus-sign"></span> Add</button>{% endif %} + <button class="btn btn-default export_mapping_results" ><span class="glyphicon glyphicon-download"></span> Download</span></button> + <br /> + <br /> + <div id="trait_table_container" style="width:{% if 'additive' in trimmed_markers[0] %}600{% else %}550{% endif %}px;"> + <table class="table-hover table-striped cell-border no-footer" id='trait_table' style="float: left;"> + <tbody> + <td colspan="100%" align="center"><br><b><font size="15">Loading...</font></b><br></td> + </tbody> + </table> + </div> + </div> + {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} + <div style="width: 100%;"> + <h2>Interval Analyst</h2> + <div id="table_container"> + <table id="trait_table" class="table-hover table-striped cell-border dataTable" style="float: left; width:100%;"> + <thead> + <tr> + {% for header in gene_table_header %} + <th>{{ header|safe }}</th> + {% endfor %} + </tr> + </thead> + <tbody> + {% for row in gene_table_body %} + <tr> + {% for n in range(row|length) %} + {% if n == 0 %} + <td align="center" style="padding: 1px 0px 1px 0px;">{{ row[n]|safe }}</td> + {% else %} + <td>{{ row[n]|safe }}</td> + {% endif %} + {% endfor %} + </tr> + {% endfor %} + </tbody> + </table> + </div> + </div> + {% endif %} + </div> + + <!-- End of body --> + +{% endblock %} + +{% block js %} + + <script type="text/javascript" src="{{ url_for('js', filename='d3js/d3.min.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='js_alt/md5.min.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='js_alt/underscore.min.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='underscore-string/underscore.string.min.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='d3-tip/d3-tip.js') }}"></script> + <script type="text/javascript" src="{{ url_for('js', filename='plotly/plotly.min.js') }}"></script> + {% if manhattan_plot == True and selectedChr == -1 %} + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='jscolor/jscolor.js') }}"></script> + + {% endif %} + + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/buttons/js/dataTables.buttons.min.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/scroller/js/dataTables.scroller.min.js') }}"></script> + + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/scientific.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTablesExtensions/plugins/sorting/natural.js') }}"></script> + <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='purescript-genome-browser/js/purescript-genetics-browser.js') }}"></script> + + <script> + var js_data = {{ js_data | safe }}; + var markersJson = {{ trimmed_markers|safe }}; + </script> + + <script language="javascript" type="text/javascript" src="/static/new/javascript/search_results.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/table_functions.js"></script> + <script language="javascript" type="text/javascript" src="/static/new/javascript/create_datatable.js"></script> + {% if mapping_method == "gemma" or mapping_method == "reaper" %} + <script language="javascript" type="text/javascript" src="/static/new/javascript/init_genome_browser.js"></script> + {% endif %} + + <script type="text/javascript" charset="utf-8"> + $(document).ready( function () { + {% if selectedChr == -1 %} + tableId = "trait_table" + + columnDefs = [ + { + 'data': null, + 'width': "5px", + 'orderDataType': "dom-checkbox", + 'targets': 0, + 'render': function(data, type, row, meta) { + return '<input type="checkbox" name="selectCheck" class="checkbox trait_checkbox" value="'+ data.hmac + '">' + } + }, + { + 'title': "Row", + 'type': "natural", + 'width': "35px", + 'searchable': false, + 'orderable': false, + 'targets': 1, + 'render': function(data, type, row, meta) { + return meta.row + } + }, + { + 'title': "Marker", + 'type': "natural", + 'width': "20%", + 'targets': 2, + {% if geno_db_exists == "True" %} + 'data': null, + 'render': function(data, type, row, meta) { + return '<a target="_blank" href="/show_trait?trait_id=' + data.name + '&dataset={{ dataset.group.name }}Geno">' + data.name + '</a>' + } + {% else %} + 'data': "name" + {% endif %} + }, + { + 'title': "<div style='text-align: right;'>{{ LRS_LOD }}</div>", + 'type': "natural", + 'width': "60px", + 'targets': 3, + 'orderSequence': [ "desc", "asc"], + 'data': null, + 'render': function(data, type, row, meta) { + {% if (LRS_LOD == "LOD") or (LRS_LOD == "-logP") %} + if ('lod_score' in data){ + return String(parseFloat(data.lod_score).toFixed(2)) + } else { + return String((parseFloat(data.lrs_value) / 4.61).toFixed(2)) + } + {% else %} + if ('lod_score' in data){ + return String((parseFloat(data.lod_score) * 4.61).toFixed(2)) + } else { + return String(parseFloat(data.lrs_value).toFixed(2)) + } + {% endif %} + } + }, + { + 'title': "<div style='text-align: right;'>Position ({% if plotScale == 'physic' %}Mb{% else %}cM{% endif %})</div>", + 'type': 'natural', + 'targets': 4, + 'data': "display_pos" + }, + {% if 'additive' in trimmed_markers[0] %} + { + 'title': "<div style='text-align: right;'>Add Eff</div>", + 'type': "natural", + 'targets': 5, + 'data': null, + 'render': function(data, type, row, meta) { + {% if geno_db_exists == "True" %} + return '<a target"_blank" href="corr_scatter_plot?method=pearson&dataset_1={{ dataset.group.name }}Geno&dataset_2={{ dataset.name }}&trait_1=' + data.name + '&trait_2={{ this_trait.name }}&cached_trait=trait_2&dataid={{ dataid }}">' + String(parseFloat(data.additive).toFixed(3)) + '</a>' + {% else %} + return String(parseFloat(data.additive).toFixed(3)) + {% endif %} + } + }, + {% endif %} + {% if ('dominance' in trimmed_markers[0]) and (dataset.group.genetic_type != "riset") %} + { + 'title': "<div style='text-align: right;'>Add Eff</div>", + 'type': "natural", + 'targets': {% if ('additive' in trimmed_markers[0]) %}6{% else %}5{% endif %}, + 'data': null, + 'render': function(data, type, row, meta) { + return String(parseFloat(data.dominance).toFixed(2)) + } + } + {% endif %} + ] + + tableSettings = { + "createdRow": function ( row, data, index ) { + $('td', row).eq(0).attr("style", "text-align: center; padding: 0px 10px 2px 10px;"); + $('td', row).eq(1).attr("align", "right"); + $('td', row).eq(1).attr('data-export', index+1); + $('td', row).eq(2).attr('data-export', $('td', row).eq(2).text()); + $('td', row).eq(3).attr("align", "right"); + $('td', row).eq(3).attr('data-export', $('td', row).eq(3).text()); + $('td', row).eq(4).attr("align", "right"); + $('td', row).eq(4).attr('data-export', $('td', row).eq(4).text()); + {% if 'additive' in trimmed_markers[0] %} + $('td', row).eq(5).attr("align", "right"); + $('td', row).eq(5).attr('data-export', $('td', row).eq(5).text()); + {% endif %} + {% if 'dominance' in trimmed_markers[0] %} + $('td', row).eq(6).attr("align", "right"); + $('td', row).eq(6).attr('data-export', $('td', row).eq(6).text()); + {% endif %} + }, + "language": { + "info": "Showing from _START_ to _END_ of " + js_data.total_markers + " records", + }, + "order": [[1, "asc" ]], + "scrollY": "1000px", + "scroller": true + } + + create_table(tableId, markersJson, columnDefs, tableSettings) + + {% elif selectedChr != -1 and plotScale =="physic" and (dataset.group.species == 'mouse' or dataset.group.species == 'rat') %} + $('#trait_table').dataTable( { + "drawCallback": function( settings ) { + $('#trait_table tr').off().on("click", function(event) { + if (event.target.type !== 'checkbox' && event.target.tagName.toLowerCase() !== 'a') { + var obj =$(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 ) { + $('td', row).eq(1).attr("align", "right"); + $('td', row).eq(3).attr("align", "right"); + $('td', row).eq(4).attr("align", "right"); + $('td', row).eq(5).attr("align", "right"); + $('td', row).eq(6).attr("align", "right"); + $('td', row).eq(7).attr("align", "right"); + $('td', row).eq(8).attr("align", "center"); + $('td', row).eq(9).attr("align", "right"); + }, + "columns": [ + { "orderDataType": "dom-checkbox" }, + { "type": "natural"}, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" , "orderDataType": "dom-inner-text" }, + { "type": "natural" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" }, + { "type": "natural-minus-na" , "orderDataType": "dom-inner-text" }, + { "type": "natural" } + ], + "columnDefs": [ { + "targets": 0, + "sortable": false + }], + "order": [[3, "asc" ]], + "sDom": "RZtir", + "iDisplayLength": -1, + "autoWidth": false, + "deferRender": true, + "bSortClasses": false, + "scrollCollapse": false, + "paging": false + } ); + {% endif %} + + $('#vector_map_tab').click(function(){ + $('div#gn1_map_options').hide(); + }); + + $('#gn1_map_tab').click(function(){ + $('div#gn1_map_options').show(); + }); + + }); + + var mapping_input_list = ['temp_uuid', 'trait_id', 'dataset', 'tool_used', 'form_url', 'method', 'transform', 'trimmed_markers', 'selected_chr', 'chromosomes', 'mapping_scale', 'sample_vals', + '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', 'color_scheme', 'manhattan_single_color', 'control_marker', 'do_control', 'genofile', + 'pair_scan', 'startMb', 'endMb', 'graphWidth', 'lrsMax', 'additiveCheck', 'showSNP', 'showHomology', 'showGenes', 'viewLegend', 'haplotypeAnalystCheck', + 'mapmethod_rqtl_geno', 'mapmodel_rqtl_geno', 'temp_trait', 'group', 'species', 'reaper_version', 'primary_samples', 'n_samples'] + + $('input[name=wanted_inputs]').val(mapping_input_list.join(",")); + + chrView = function(this_chr, chr_mb_list) { + $('input[name=selected_chr]').val(this_chr) + $('input[name=chr_mb_list]').val(chr_mb_list) + + $('#marker_regression_form').attr('action', '/loading'); + $('#marker_regression_form').submit(); + }; + + rangeView = function(this_chr, start_mb, end_mb) { + $('input[name=selected_chr]').val(this_chr) + $('input[name=startMb]').val(start_mb) + $('input[name=endMb]').val(end_mb) + //$('input[name=mb_range]').val(start_mb + "," + end_mb) + + $('#marker_regression_form').attr('action', '/loading'); + $('#marker_regression_form').submit(); + }; + + remap = function() { + $('input[name=selected_chr]').val($('select[name=chromosomes]').val()); + $('input[name=color_scheme]').val($('select#color_scheme').val()); + $('#marker_regression_form').attr('action', '/loading'); + return $('#marker_regression_form').submit(); + }; + + {% if manhattan_plot == True and selectedChr == -1 %} + $('#color_scheme').change(function(){ + if ($(this).val() == "single"){ + $('#point_color_picker').show(); + } else { + $('#point_color_picker').hide(); + } + }); + {% endif %} + + {% if mapping_method != "gemma" and mapping_method != "plink" and nperm > 0 and permChecked == "ON" %} + $('#download_perm').click(function(){ + perm_info_dict = { + perm_data: js_data.perm_results, + num_perm: "{{ nperm }}", + trait_name: "{{ this_trait.display_name }}", + trait_description: `{{ this_trait.description_display }}`, + cofactors: "{{ covariates }}", + n_samples: {{ n_samples }}, + n_genotypes: {{ qtl_results|length }}, + {% if genofile_string is defined %} + genofile: "{{ genofile_string }}", + {% else %} + genofile: "", + {% endif %} + units_linkage: "{{ LRS_LOD }}", + strat_cofactors: js_data.categorical_vars + } + json_perm_data = JSON.stringify(perm_info_dict); + + $('input[name=perm_info]').val(json_perm_data); + $('#marker_regression_form').attr('action', '/export_perm_data'); + return $('#marker_regression_form').submit(); + }); + + modebar_options = { + modeBarButtonsToAdd:[{ + name: 'Export as SVG', + icon: Plotly.Icons.disk, + click: function(gd) { + Plotly.downloadImage(gd, {format: 'svg'}) + } + }], + modeBarButtonsToRemove:['toImage', 'sendDataToCloud', 'hoverClosest', 'hoverCompare', 'hoverClosestCartesian', 'hoverCompareCartesian', 'lasso2d', 'toggleSpikelines'], + displaylogo: false + //modeBarButtons:['toImage2', 'zoom2d', 'pan2d', 'select2d', 'zoomIn2d', 'zoomOut2d', 'autoScale2d', 'resetScale2d'], + } + + perm_data = js_data.perm_results + var hist_trace = { + x: perm_data, + type: 'histogram' + }; + histogram_data = [hist_trace]; + histogram_layout = { + bargap: 0.05, + title: "<b>Histogram of Permutation Test</b>", + xaxis: { + autorange: true, + title: "<b>{{ LRS_LOD }}</b>", + titlefont: { + family: "arial", + size: 20 + }, + ticklen: 4, + tickfont: { + size: 16 + } + }, + yaxis: { + autorange: true, + title: "<b>Count</b>", + titlefont: { + family: "arial", + size: 20 + }, + showline: true, + ticklen: 4, + tickfont: { + size: 16 + }, + automargin: true + }, + width: 500, + height: 300, + margin: { + l: 70, + r: 30, + t: 100, + b: 50 + } + }; + + Plotly.newPlot('perm_histogram', histogram_data, histogram_layout, modebar_options); + {% endif %} + + export_mapping_results = function() { + $('#marker_regression_form').attr('action', '/export_mapping_results'); + return $('#marker_regression_form').submit(); + } + + $('.export_mapping_results').click(export_mapping_results); + + $('#browser_tab').click(function() { + $('#gn1_map_options').css("display", "none") + }) + $('#gn1_map_tab').click(function() { + $('#gn1_map_options').css("display", "block") + }) + + hash = $('input[name=inputs_hash]').val(); + mappingLink = window.location.origin + "/run_mapping/"+ hash; + $('input[name=mappingLink]').width(mappingLink.length*0.95 + "ch") + $('input[name=mappingLink]').val(mappingLink); + $('.share-results').click(function() { + $.ajax({ + method: "POST", + url: "/cache_mapping_inputs", + data: { + inputs_hash: hash + }, + success: function() { + document.querySelector("input[name='mappingLink']").select(); + document.execCommand('copy'); + } + }); + }) + + </script> + +{% endblock %} + |