{% 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" type="text/css" href="{{ url_for('css', filename='fontawesome/css/font-awesome.min.css') }}" />
<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" value="{{ mapmethod_rqtl }}">
<input type="hidden" name="mapmodel_rqtl" value="{{ mapmodel_rqtl }}">
<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', 'mapmodel_rqtl', '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 %}