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cohort_analysis.html
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<!doctype html>
<html lang="en">
<head>
<!-- Required meta tags -->
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
<!-- CSS and JS libraries-->
<link rel="stylesheet" href="lib/css/bootstrap.min.css">
<link rel="stylesheet" href="lib/css/bootstrap-table.min.css">
<link rel="stylesheet" href="lib/css/tabulator.min.css">
<link rel="stylesheet" type="text/css" href="lib/css/jquery.dataTables.min.css">
<link rel="stylesheet" type="text/css" href="lib/css/select.dataTables.min.css">
<link rel="stylesheet" type="text/css" href="lib/css/searchPanes.dataTables.min.css">
<script src="lib/js/popper.min.js"></script>
<script src="lib/js/jquery-3.3.1.slim.min.js"></script>
<script src="lib/js/bootstrap.min.js"></script>
<script src="lib/js/jquery.min.js"></script>
<script src="lib/js/d3.min.js"></script>
<script src="lib/js/plotly-latest.min.js"></script>
<script src="lib/js/mannwhitneyu.js"></script>
<script src="lib/js/wilcoxon_signed_rank_test.js"></script>
<script src="lib/js/tabulator.min.js"></script>
<script src="lib/js/papaparse.min.js"></script>
<script src="lib/js/jquery.dataTables.min.js"></script>
<script src="lib/js/dataTables.select.min.js"></script>
<script src="lib/js/dataTables.buttons.min.js"></script>
<script src="lib/js/buttons.html5.min.js"></script>
<script src="lib/js/dataTables.searchPanes.min.js"></script>
<!-- CSS and JS specifically for HTML report -->
<link rel="stylesheet" href="css/styling.css">
<link rel="stylesheet" href="css/sample_select.css">
<script src="js/load_sections.js"></script>
<script src="js/functions.js"></script>
<script src="js/populate.js"></script>
<script src="js/top_navbar.js"></script>
<script src="js/plot.js"></script>
<script src="js/overlap.js"></script>
<title>Immune Repertoire | VisualizIRR</title>
</head>
<body>
<div id="top_navbar"></div>
<div class="container-fluid">
<div class="row flex-column-reverse flex-md-row">
<nav class="col-md-2 bg-light sidebar bd-links">
<div class="sidebar-sticky sticky-top" style="padding-top: 1rem">
<ul class="nav flex-column">
<li class="nav-item" style='padding-top: 40px;'>
<a class="nav-link" href="#" onclick="show_all()" style="font-size: 1rem">Show All</a>
<!-- <a class="nav-link" href="#STAT" onclick="show_class('.static')" style="font-size: 1rem">Static Plots</a>
<ul>
<li class="nav-item" id="content_pca_nav">
<a class="nav-link nav-pad" href="#PCA" onclick="hide_others('#PCA')">PCA</a>
</li>
</ul> -->
<a class="nav-link" href="#" onclick="show_class('.dynamic')" style="font-size: 1rem">Dynamic Plots</a>
<ul>
<li class="nav-item" id="content_ica_nav">
<a class="nav-link nav-pad" href="#" onclick="hide_others('#ICA')">Intracohort Analysis</a>
</li>
<li class="nav-item" id="content_psca_nav" style="display:none;">
<a class="nav-link nav-pad" href="#" onclick="hide_others('#PSCA')">Paired Sample Cohort Analysis</a>
</li>
<li class="nav-item" id="content_ol_nav" style="display:none;">
<a class="nav-link nav-pad" href="#" onclick="hide_others('#OL')">Overlap Analysis</a>
</li>
</ul>
<a class="nav-link" href="#" onclick="show_class('.cohort_overview')" style="font-size: 1rem">Cohort
Overview</a>
<ul>
<li class="nav-item">
<a class="nav-link nav-pad" href="#" onclick="hide_others('#CT')">Cohort Tables</a>
</li>
<li class="nav-item">
<a class="nav-link nav-pad" href="#" onclick="hide_others('#CS')">Cohort Scatterplot</a>
</li>
</ul>
<a class="nav-link">
<div class="p-control custom-switch">
<input type="checkbox" class="custom-control-input" id="p-switch">
<label class="custom-control-label" for="p-switch">Numerical P-value</label>
</div>
</a>
<a class="nav-link">
n.s.: p > .05<br>
*: p ≤ .05<br>
**: p ≤ .005<br>
***: p ≤ .0005
</a>
<a class="nav-link" id='sample-selection-button'>
<button class="btn btn-primary" type="button" data-toggle="collapse" data-target="#filterTableContainer" aria-expanded="false" aria-controls="filterTableContainer">
Show Sample Selection Table</button>
</a>
</li>
<div id="compressed-view-fix" style="height: 80px;"> </div>
</ul>
</div>
</nav>
<main role="main" class="col-md-9 ml-sm-auto col-lg-10 px-4" style="margin-bottom: 6rem;margin-top: 1rem;">
<div
class="d-flex justify-content-between flex-wrap flex-md-nowrap align-items-center pt-3 pb-2 mb-3 border-bottom">
<h1 class="h2">Cohort Analysis</h1>
</div>
<div class="collapse" id="filterTableContainer">
<div class="card card-body">
<table id="filterTable" class="display" cellspacing="0" width="100%">
<thead>
</thead>
</table>
</div>
</div>
<div class="content_row dynamic" id="content_ICA">
<h2 class="h3">Intracohort Analysis</h2>
<div class="row">
<div class="col text-center">
<div id="intracohortDiv" style="max-width: 800px;max-height: 600px;margin-left: auto;margin-right: auto;"
class="d-flex justify-content-center"></div>
<div id="accordion">
<div class="card">
<div class="card-header" id="headingTwo">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseTwo"
aria-expanded="false" aria-controls="collapseTwo">
P-value Tables ▼
</button>
</h5>
</div>
<div id="collapseTwo" class="collapse" aria-labelledby="headingTwo" data-parent="#accordion">
<div class="card-body align-items-center d-flex justify-content-center">
<p class="justify-content-center" id="pval_table_space"></p>
</div>
<p>Blue: Row < Col, Red: Col < Row, Bold: p ≤ .05</p>
</div>
</div>
</div>
<br>
<div class="dropdown btn-group">
<button class="btn btn-secondary dropdown-toggle" type="button" id="dropdownChain"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Chain
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="chain_selection">
</div>
</div>
<div class="btn-group-vertical" id="cond_buttons" style="display:none;">
<div class="dropdown btn-group">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdownCondition"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Condition
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="condition_selection">
</div>
</div>
<div class="dropdown btn-group" id="button2nd_condition" style="display:none;">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdown2ndCondition"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Secondary Condition
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="condition2nd_selection">
</div>
</div>
</div>
<div class="dropdown btn-group">
<button class="btn btn-dark dropdown-toggle" type="button" id="dropdownFunction" data-toggle="dropdown"
aria-haspopup="true" aria-expanded="false">
Select Function
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="function_selection">
</div>
</div>
<div class="dropdown btn-group">
<button class="btn btn-info dropdown-toggle" type="button" id="dropdownPlotType" data-toggle="dropdown"
aria-haspopup="true" aria-expanded="false">
Box Plot
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="plot_type_selection">
<a class="dropdown-item" onclick="plot_type_change('box')">Box Plot</a>
<a class="dropdown-item" onclick="plot_type_change('violin')">Violin Plot</a>
</div>
</div>
<div style="line-height:100%;"><br></div>
x: <input type="text" class="xval-in" value="700" size="5">
y: <input type="text" class="yval-in" value="450" size="5">
<button type="button" class="btn btn-success btn-export save-png">Save PNG</button>
<button type="button" class="btn btn-success btn-export save-svg">Save SVG</button>
</div>
<div class="col text-center">
<div id="heatmapDiv" style="max-width: 800px;max-height: 600px;margin-left: auto;margin-right: auto;"
class="d-flex justify-content-center"></div>
<div style="line-height:100%;"><br></div>
x: <input type="text" class="xval-in" value="1000" size="5">
y: <input type="text" class="yval-in" value="800" size="5">
<button type="button" class="btn btn-success btn-export save-png">Save PNG</button>
<button type="button" class="btn btn-success btn-export save-svg">Save SVG</button>
</div>
</div>
</div>
<div class="content_row dynamic" id="content_PSCA" style="visibility: hidden">
<h2 class="h3">Paired Sample Cohort Analysis</h2>
<div class="row">
<div class="col text-center">
<div id="pscaDiv" style="max-width: 960px;max-height: 640px;margin-left: auto;margin-right: auto;"
class="d-flex justify-content-center"></div>
<div class="dropdown btn-group">
<button class="btn btn-secondary dropdown-toggle" type="button" id="dropdownChainPSCA"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Chain
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="chain_selection_psca">
</div>
</div>
<div class="btn-group-vertical">
<div class="dropdown btn-group">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdownSplitPSCA"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
No Split
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="split_selection_psca">
<a class="dropdown-item" onclick="dataMorphPSCA(undefined,'none',undefined)">No Split</a>
</div>
</div>
</div>
<div class="dropdown btn-group">
<button class="btn btn-dark dropdown-toggle" type="button" id="dropdownFunctionPSCA"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Function
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="function_selection_psca">
</div>
</div>
<div style="line-height:100%;"><br></div>
x: <input type="text" class="xval-in" value="1200" size="5">
y: <input type="text" class="yval-in" value="800" size="5">
<button type="button" class="btn btn-success btn-export save-png">Save PNG</button>
<button type="button" class="btn btn-success btn-export save-svg">Save SVG</button>
</div>
<div class="col text-center">
<div id="heatmapPairedDiv" style="max-width: 800px;max-height: 600px;margin-left: auto;margin-right: auto;"
class="d-flex justify-content-center"></div>
<div style="line-height:100%;"><br></div>
x: <input type="text" class="xval-in" value="1000" size="5">
y: <input type="text" class="yval-in" value="800" size="5">
<button type="button" class="btn btn-success btn-export save-png">Save PNG</button>
<button type="button" class="btn btn-success btn-export save-svg">Save SVG</button>
</div>
</div>
</div>
<div class="content_row dynamic" id="content_ol" style="visibility: hidden">
<h2 class="h3">Overlap Analysis</h2>
<div class="row">
<div class="col text-center">
<div id="overlapDiv" style="max-width: 800px;max-height: 600px;margin-left: auto;margin-right: auto;"
class="d-flex justify-content-center"></div>
<div class="dropdown btn-group">
<button class="btn btn-secondary dropdown-toggle" type="button" id="dropdownChainOverlap"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Chain
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="chain_selection_overlap">
</div>
</div>
<div class="btn-group-vertical" id="cond_buttons_overlap" style="display:none;">
<div class="dropdown btn-group">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdownConditionOverlap"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Condition
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;"
id="condition_selection_overlap">
</div>
</div>
<div class="dropdown btn-group" id="button2nd_condition_overlap" style="display:none;">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdown2ndConditionOverlap"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Secondary Condition
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;"
id="condition2nd_selection_overlap">
</div>
</div>
</div>
<div class="dropdown btn-group">
<button class="btn btn-dark dropdown-toggle" type="button" id="dropdownFunctionOverlap"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Function
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="function_selection_overlap">
</div>
</div>
<div style="line-height:100%;"><br></div>
x: <input type="text" class="xval-in" value="700" size="5">
y: <input type="text" class="yval-in" value="450" size="5">
<button type="button" class="btn btn-success btn-export save-png">Save PNG</button>
<button type="button" class="btn btn-success btn-export save-svg">Save SVG</button>
</div>
</div>
</div>
<div class="content_row cohort_overview" id="content_ct">
<h2 class="h3">Cohort Tables</h2>
<div id="accordionCst">
<div class="card">
<div class="card-header" id="headingCst">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseCst"
aria-expanded="false" aria-controls="collapseCst">
Cohort Statistics Table ▼
</button>
</h5>
</div>
<div id="collapseCst" class="collapse" aria-labelledby="headingCst" data-parent="#accordionCst">
<div id="data-table"></div>
<a id="statsCSV" href="" download>Download CSV</a>
</div>
</div>
</div>
<p></p>
<div id="cohortMetaTable" style="visibility: hidden">
<div id="accordionCmt">
<div class="card">
<div class="card-header" id="headingCmt">
<h5 class="mb-0">
<button class="btn btn-link collapsed" data-toggle="collapse" data-target="#collapseCmt"
aria-expanded="false" aria-controls="collapseCmt">
Cohort Meta-information Table ▼
</button>
</h5>
</div>
<div id="collapseCmt" class="collapse" aria-labelledby="headingCmt" data-parent="#accordionCmt">
<div id="meta-table"></div>
<a id="metaCSV" href="" download>Download CSV</a>
</div>
</div>
</div>
</div>
</div>
<div class="content_row cohort_overview" id="content_cs">
<h2 class="h3">Cohort Scatterplot</h2>
<div class="row">
<div class="col text-center">
<div id="scatterDiv" style="max-width: 600px;max-height: 600px;margin-left: auto;margin-right: auto;"
class="d-flex justify-content-center"></div>
<div class="dropdown btn-group">
<button class="btn btn-secondary dropdown-toggle" type="button" id="dropdownChainScatter"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Chain
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="chain_selection_scatter">
</div>
</div>
<div class="dropdown btn-group">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdownXScatter"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select X Data
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="x_selection_scatter">
</div>
</div>
<div class="dropdown btn-group">
<button class="btn btn-primary dropdown-toggle" type="button" id="dropdownYScatter"
data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
Select Y Data
</button>
<div class="dropdown-menu" style="position: relative; z-index: 10000;" id="y_selection_scatter">
</div>
</div>
<div style="line-height:100%;"><br></div>
x: <input type="text" class="xval-in" value="600" size="5">
y: <input type="text" class="yval-in" value="600" size="5">
<button type="button" class="btn btn-success btn-export save-png">Save PNG</button>
<button type="button" class="btn btn-success btn-export save-svg">Save SVG</button>
</div>
</div>
</div>
</main>
</div>
</div>
</main>
</div>
</div>
</body>
</html>