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interface.html
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<html>
<head>
<!-- check the browser -->
<!-- <script type="text/javascript">
var ua= navigator.userAgent, tem,
M= ua.match(/(opera|chrome|safari|firefox|msie|trident(?=\/))\/?\s*(\d+)/i) || [];
if(M[1]!="Chrome"){
alert("Chrome is tested browser!")
}else{
if(M[2]<85){
alert("Chrome v85 or higher is required!")
}
}
</script> -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
<link rel="stylesheet" type="text/css" href="https://interactivereport.github.io/cellxgene_VIP/static/gridstack/gridstack.min.css">
<link rel="stylesheet" type="text/css" href="https://interactivereport.github.io/cellxgene_VIP/static/gridstack/gridstack-extra.min.css">
<script src="https://interactivereport.github.io/cellxgene_VIP/static/gridstack/gridstack-h5.js"></script>
<!-- for datatables -->
<link rel="stylesheet" type="text/css" href="https://interactivereport.github.io/cellxgene_VIP/static/DataTables/datatables.min.css">
<script src="https://interactivereport.github.io/cellxgene_VIP/static/jquery-ui.min.js"></script>
<!-- for d3 volcano -->
<script src="https://interactivereport.github.io/cellxgene_VIP/static/d3plot/volcanoPlot.js"></script>
<link rel="stylesheet" href="https://interactivereport.github.io/cellxgene_VIP/static/d3plot/volcanoPlot.css">
<!-- for gene sets -->
<script src="https://bxaf.net/genesets/bootstrap-3/js/bootstrap.min.js"></script>
<script>
var GENESET_ACTION_URL = "https://bxaf.net/genesets/genesets3.php";
</script>
<link href="https://bxaf.net/genesets/genesets3.css" rel="stylesheet">
<script src="https://bxaf.net/genesets/genesets3.js"></script>
<!-- for save & load session -->
<script src="https://interactivereport.github.io/cellxgene_VIP/static/saveVIP.js"></script>
<!-- <script src="static/saveVIP.js"></script> -->
<!-- for testing the VIP -->
<script src="https://interactivereport.github.io/cellxgene_VIP/static/testVIP.js"></script>
<!-- <script src="static/testVIP.js"></script>-->
<!-- For Fuzzy Search -->
<script src="https://cdn.jsdelivr.net/npm/[email protected]"></script>
<!-- For Plotly.js -->
<script src="https://cdn.plot.ly/plotly-2.20.0.min.js" charset="utf-8"></script>
<!-- end -->
<style>
.dropup,
.dropdown {
position: relative;
}
.dropdown-toggle:focus {
outline: 0;
}
.dropdown-menu {
position: absolute;
top: 100%;
left: 0;
z-index: 1000;
display: none;
float: left;
min-width: 160px;
padding: 5px 0;
margin: 2px 0 0;
font-size: 14px;
text-align: left;
list-style: none;
background-color: #ffffff;
-webkit-background-clip: padding-box;
background-clip: padding-box;
border: 1px solid #cccccc;
border: 1px solid rgba(0, 0, 0, 0.15);
border-radius: 4px;
-webkit-box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
box-shadow: 0 6px 12px rgba(0, 0, 0, 0.175);
}
.dropdown-menu.pull-right {
right: 0;
left: auto;
}
.dropdown-menu .divider {
height: 1px;
margin: 9px 0;
overflow: hidden;
background-color: #e5e5e5;
}
.dropdown-menu > li > a {
display: block;
padding: 3px 20px;
clear: both;
font-weight: 400;
line-height: 1.42857143;
color: #333333;
white-space: nowrap;
}
.dropdown-menu > li > a:hover,
.dropdown-menu > li > a:focus {
color: #262626;
text-decoration: none;
background-color: #f5f5f5;
}
.dropdown-menu > .active > a,
.dropdown-menu > .active > a:hover,
.dropdown-menu > .active > a:focus {
color: #ffffff;
text-decoration: none;
background-color: #337ab7;
outline: 0;
}
.dropdown-menu > .disabled > a,
.dropdown-menu > .disabled > a:hover,
.dropdown-menu > .disabled > a:focus {
color: #777777;
}
.dropdown-menu > .disabled > a:hover,
.dropdown-menu > .disabled > a:focus {
text-decoration: none;
cursor: not-allowed;
background-color: transparent;
background-image: none;
filter: progid:DXImageTransform.Microsoft.gradient(enabled = false);
}
.open > .dropdown-menu {
display: block;
}
.open > a {
outline: 0;
}
.dropdown-menu-right {
right: 0;
left: auto;
}
.dropdown-menu-left {
right: auto;
left: 0;
}
.dropdown-header {
display: block;
padding: 3px 20px;
font-size: 12px;
line-height: 1.42857143;
color: #777777;
white-space: nowrap;
}
.dropdown-backdrop {
position: fixed;
top: 0;
right: 0;
bottom: 0;
left: 0;
z-index: 990;
}
.pull-right > .dropdown-menu {
right: 0;
left: auto;
}
.dropup .caret,
.navbar-fixed-bottom .dropdown .caret {
content: "";
border-top: 0;
border-bottom: 4px dashed;
border-bottom: 4px solid \9;
}
.dropup .dropdown-menu,
.navbar-fixed-bottom .dropdown .dropdown-menu {
top: auto;
bottom: 100%;
margin-bottom: 2px;
}
.modal-open {
overflow: hidden;
}
.modal {
position: fixed;
top: 0;
right: 0;
bottom: 0;
left: 0;
z-index: 1050;
display: none;
overflow: hidden;
-webkit-overflow-scrolling: touch;
outline: 0;
}
.modal.fade .modal-dialog {
-webkit-transform: translate(0, -25%);
-ms-transform: translate(0, -25%);
-o-transform: translate(0, -25%);
transform: translate(0, -25%);
-webkit-transition: -webkit-transform 0.3s ease-out;
-o-transition: -o-transform 0.3s ease-out;
transition: transform 0.3s ease-out;
}
.modal.in .modal-dialog {
-webkit-transform: translate(0, 0);
-ms-transform: translate(0, 0);
-o-transform: translate(0, 0);
transform: translate(0, 0);
}
.modal-open .modal {
overflow-x: hidden;
overflow-y: auto;
}
.modal-dialog {
position: relative;
width: auto;
margin: 10px;
}
.modal-content {
position: relative;
background-color: #ffffff;
-webkit-background-clip: padding-box;
background-clip: padding-box;
border: 1px solid #999999;
border: 1px solid rgba(0, 0, 0, 0.2);
border-radius: 6px;
-webkit-box-shadow: 0 3px 9px rgba(0, 0, 0, 0.5);
box-shadow: 0 3px 9px rgba(0, 0, 0, 0.5);
outline: 0;
}
.modal-backdrop {
position: fixed;
top: 0;
right: 0;
bottom: 0;
left: 0;
z-index: 1040;
background-color: #000000;
}
.modal-backdrop.fade {
filter: alpha(opacity=0);
opacity: 0;
}
.modal-backdrop.in {
filter: alpha(opacity=50);
opacity: 0.5;
}
.modal-header {
padding: 15px;
border-bottom: 1px solid #e5e5e5;
}
.modal-header .close {
margin-top: -2px;
}
.modal-title {
margin: 0;
line-height: 1.42857143;
}
.modal-body {
position: relative;
padding: 15px;
}
.modal-footer {
padding: 15px;
text-align: right;
border-top: 1px solid #e5e5e5;
}
.modal-footer .btn + .btn {
margin-bottom: 0;
margin-left: 5px;
}
.modal-footer .btn-group .btn + .btn {
margin-left: -1px;
}
.modal-footer .btn-block + .btn-block {
margin-left: 0;
}
.modal-scrollbar-measure {
position: absolute;
top: -9999px;
width: 50px;
height: 50px;
overflow: scroll;
}
button.link{background:none;border:none;}
#sortable { list-style-type: none; margin: 0; padding: 0; width: 60%; }
#sortable li { margin: 0 3px 3px 3px; padding: 0.4em; padding-left: 1.5em; font-size: 1.4em; height: 18px; cursor:move; }
#sortable li span { position: absolute; margin-left: -1.3em; }
#sortable li.fixed{cursor:default; color:#959595; opacity:0.5;}
.splitter {
display: flex;
width: 100%;
}
#separator {
cursor: col-resize;
min-width: 6px;
background-color: #aaa;
background: url('data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAgAAAAhCAQAAABOpSL+AAAAIklEQVR4AWMwbb/PdR+JZDD9f1/oPhI5sgVGBSruc9xHIgGdSQqqQJGkRgAAAABJRU5ErkJggg==') center center no-repeat #F1F1F1;
/* prevent browser's built-in drag from interfering */
-moz-user-select: none;
-ms-user-select: none;
user-select: none;
}
#panel-left {
background-color: #dde;
width: 20%;
white-space: nowrap;
}
#panel-right {
background-color: #fff;
width: 80%;
}
#separator, #panel-left, #panel-right {
vertical-align: top;
}
#STACBARplot {
margin: 40px;
position: relative;
}
.axis path,
.axis line {
fill: none;
stroke: #000;
shape-rendering: crispEdges;
}
.fly-in {
font-size: 8px;
}
.axis .tick line {
stroke: #ccc;
/*opacity: 0.5;*/
pointer-events: none;
}
/*.axis .minor line{*/
/*stroke: red;*/
/*}*/
.highlight {
font-weight: bold ;
}
svg {
overflow: visible;
}
.block {
display: block;
width: 100%;
border: none;
background-color: #B6B6B6;
color: white;
padding: 4px 28px;
font-size: 18px;
cursor: pointer;
text-align: center;
}
.block:hover {
background-color: #ffff33;
color: black;
}
.colorButton{
color: #008cba;
}
.tab {
float: left;
width: 100%;
height: 100%;
border: 1px solid #ccc;
background-color: #f1f1f1;
}
.tab button {
display: block;
width: 100%;
text-align: left;
background-color: inherit;
border: none;
outline: none;
cursor: pointer;
padding: 5px 10px;
transition: 0.3s;
}
.tab button:hover {
background-color: #ddd;
}
.tab button.active {
background-color: #ccc;
}
.tabcontent {
float: left;
border-left: none;
width:100%;
display: none;
padding: 0px 10px;
}
.topTab {
overflow: hidden;
border: 1px solid #ccc;
background-color: #f1f1f1;
}
.topTab button{
text-align: top;
text-align: left;
background-color: inherit;
float: left;
border: none;
outline: none;
cursor: pointer;
padding: 5px 5px;
transition: 0.3s;
}
.topTab button:hover {
background-color: #ddd;
}
.topTab button.active {
background-color: #ccc;
}
.DEGcontent {
float: left;
border-left: none;
width:100%;
display: none;
padding: 0px 10px;
}
h3 {
display: block;
font-size: 1.17em;
margin-top: 1em;
margin-bottom: 1em;
margin-left: 0;
margin-right: 0;
font-weight: bold;
}
.loading {
width: 50%;
height: auto;
position: relative;
}
.loading-wheel {
width: 70px;
height: 70px;
margin-top: -60px;
margin-left: -60px;
position: absolute;
top: 50%;
left: 50%;
border-width: 30px;
border-radius: 50%;
-webkit-animation: spin 2s linear infinite;
}
.style-2 .loading-wheel {
border-style: double;
border-color: #99f transparent;
}
@-webkit-keyframes spin {
0% {
-webkit-transform: rotate(0);
}
100% {
-webkit-transform: rotate(-360deg);
}
}
tr:nth-child(even) {background-color: #F1F1F1;}
input[type=number]{
width: 60px;
}
input,textarea,select{ font-size: 14px; }
.ace_editor p,.ace_editor div,.ace_editor input,.ace_editor label,.ace_editor span,.ace_editor text {font-family: 'Monaco', 'Menlo', 'Droid Sans Mono', 'Courier New', monospace !important;}
pre span {font-size: 12px; font-family: 'Arial', monospace !important;}
pre { display: block; padding: 0; margin: 0; font-size: 12px; white-space: pre-wrap; background-color: #f5f5f5; border: 1px solid #ccc; }
table {
border-collapse: collapse;
}
th {
background-color: #D4D8DE;
color: black;
}
.switch {
position: relative;
display: inline-block;
width: 40px;
height: 22px;
}
.switch input {
opacity: 0;
width: 0;
height: 0;
}
.slider {
position: absolute;
cursor: pointer;
top: 0;
left: 0;
right: 0;
bottom: 0;
background-color: #ccc;
-webkit-transition: .4s;
transition: .4s;
}
.slider:before {
position: absolute;
content: "";
height: 18px;
width: 18px;
left: 2px;
bottom: 2px;
background-color: white;
-webkit-transition: .4s;
transition: .4s;
}
input:checked + .slider {
background-color: #2196F3;
}
input:focus + .slider {
box-shadow: 0 0 1px #2196F3;
}
input:checked + .slider:before {
-webkit-transform: translateX(18px);
-ms-transform: translateX(18px);
transform: translateX(18px);
}
.grid-stack {
background: #F1F1F1;
}
.grid-stack-item-content {
color: #2c3e50;
text-align: center;
background-color: #CCCCCC;
}
.column1 {
float: left;
width:50%;
padding:10px;
}
.column2 {
float: right;
width:50%;
padding:10px;
}
</style>
</head>
<body>
<div class="splitter">
<div id="panel-left">
<div class="tab">
<button class="tablinks" onclick="selFun(event, 'paraCell_Help')"><b>Help</b></button>
<button class="tablinks" onclick="selFun(event, 'ADDG');populate_geneset_dropdown()"><b>Add Genes</b></button>
<button class="tablinks" onclick="selFun(event, 'geneSearch');getAllCells()">Advanced Gene Search</button>
<button class="tablinks" onclick="selFun(event, 'CellPopView');getAllCells()">Cell Population View</button>
<button class="tablinks" onclick="selFun(event, 'TIA');defaultTopSel('TIA','pseudo_tab');getAllCells()">Trajectory Inference</button>
<button class="tablinks" onclick="selFun(event, 'TradeSeq');getAllCells();tradeSeq_setup()">TradeSeq</button>
<button class="tablinks" onclick="selFun(event, 'HPA');defaultTopSel('HPA','HPA_graphs');getAllCells();">Host-Parasite Interactions</button>
<hr size="1" noshade>
<button class="tablinks" onclick="selFun(event, 'SGV');defaultTopSel('SGV','SGVsingle')">Violin</button>
<button class="tablinks" onclick="selFun(event, 'HEAT')">Heatmap</button>
<button class="tablinks" onclick="selFun(event, 'EMBED')">Embedding Plot</button>
<button class="tablinks" onclick="selFun(event, 'DOT')">Dot Plot</button>
<button class="tablinks" onclick="selFun(event, 'TRAK')">Track Plot</button>
<button class="tablinks" onclick="selFun(event, 'DENS')">Density Plot</button>
<button class="tablinks" onclick="selFun(event, 'DENS2D')">Density Scatter</button>
<button class="tablinks" onclick="selFun(event, 'DUAL')">Dual Genes</button>
<button class="tablinks" onclick="selFun(event, 'SANK')">Sankey Diagram</button>
<button class="tablinks" onclick="selFun(event, 'STACBAR')">Stacked Barplot</button>
<button class="tablinks" onclick="selFun(event, 'GSP')">Gene Specificity</button>
<button class="tablinks" onclick="selFun(event, 'GD')">Gene Detected</button>
<button class="tablinks" onclick="selFun(event, 'DEG');defaultTopSel('DEGtop','DEGtopBT1')">DEG</button>
<button id="preDEGpanelBT" class="tablinks" onclick="selFun(event, 'preDEGpanel');defaultTopSel('DEG','DEGlinksPlot')" style="display: none;">Pre-Computed DEG</button>
<button class="tablinks" onclick="selFun(event, 'MARK')">Marker Genes</button>
<button id="browserBT" class="tablinks" onclick="selFun(event, 'BROW')" style="display: none;">Multiome</button>
<button class="tablinks" onclick="selFun(event, 'SPATIAL');defaultTopSel('SPATIAL','SPATIALimage')">Spatial Transcriptomics</button>
<button class="tablinks" onclick="selFun(event, 'CLI')">Command Line Interface</button>
<button id="metaCellBT" class="tablinks colorButton" onclick="metaSel()" style="display: none;">Show MetaCell</button>
<div id="metaCellBTspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<hr size="1" noshade>
<button class="tablinks" onclick="selFun(event, 'IMG')">Global Setting</button>
<button class="tablinks" onclick="selFun(event, 'ABBR')">Comb. & Abbr.</button>
<button class="tablinks" onclick="saveLocal()">Save Session</button>
<button class="tablinks" onclick="selFun(event, 'LOAD')">Load Session</button>
<button class="tablinks" onclick="ABBRall()">Check All Annotations</button>
<button class="tablinks" onclick="selFun(event, 'BRUSH');">Brush</button>
<button class="tablinks" onclick="sync();">Sync</button>
<button id="VIPtestBT" class="tablinks" onclick="selFun(event, 'tVIP')" style="display: none;">Test</button>
</div>
</div>
<div id="separator" ></div>
<div id="panel-right" >
<div id="ABBR" class="tabcontent"> <!-- Abbreviation -->
<h3>Create a combinatorial annotation <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-comb.-abbr." target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<p>First, check below categorical annotations to be combined. Second, select items in each annotation. Then, click <button onclick="ABBRcombineNew()">Combine</button>. The max combinatorial number <input type="number" id="ABBRcomBmax" min=2 value="200"></p>
<p id="ABBRcomBgrp"></p>
<p id="ABBRcomBnote"></p>
<p id="ABBRcomBtable"></p>
<!--
<ol type="1">
<li><button onclick="ABBRclear()">Uncheck All Annotations</button></li>
<li><p>Select the annotations of interest on the left panel of main window, then
<button onclick="ABBRcombine();ABBRall()">Create</button> a new annotation named "Custom_combine" includes the
following categories: <p id="ABBRcombine"></p>
</li>
</ol>
-->
<div id="ABBRcombineList" style="display:none;">
<p>It will become categorical annotation named "Custom_combine". Change the order by dragging items up or down:</p>
<ul id="ABBRdynList" class="sortable-list"></ul><!-- -->
</div>
<hr>
<h3>Create abbreviations of annotations</h3><!-- <button onclick="ABBRsave()">Save to local</button><input id="ABBRfile" type="file" value="Load from local" onchange="ABBRload()"/>-->
<p>Choose annotation(s):</p>
<p id="ABBRgrp"></p>
<p id="ABBRtable"></p>
</div><!--ABBR-->
<div id="ADDG" class="tabcontent">
<h3>Add genes of interest for plotting <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-add-genes-gene-sets" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<p>Please input a list of genes separated by comma, semicolon, space or tab:</p>
<p><textarea id="ADDGinput" rows="5" cols="70"></textarea></p>
<p><button onclick="ADDGadd()"><b>Add</b></button></p>
<p>The following genes were added (click on a gene name to remove): <span id="ADDGsel"></span></p>
<p>The following genes are not in the data: <span id="ADDGdel" style="color:red"></span></p>
<h3>User-defined gene sets:</h3>
<p id="ADDGsets"></p>
<h4>Export GeneSets from cellxgene to paraCell.</h4>
<p><select id="cxg_genesets_dropdown"></select></p>
<p><button onclick="add_CXG_GeneSet()"><b>Add Gene Set</b></button></p>
<h3>Add gene sets of interest manually</h3>
<p>Gene set name: <input id="Geneset_Name0" type="text" size=10/>
Gene names: <input id="Geneset_Genes0" type="text" size=35/>
<p></p>
<button onclick="ADDGsetAdd(0)"><b>Add</b></button>
</p>
<h3>Add gene sets from databases</h3>
<div id="div_geneset1" class="div_geneset">
<div class="my-3 dropdown input-group">
<input id="Geneset_Name1" name="Geneset_Name1" placeholder="enter geneset name" type="text" class="form-control geneset_name dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"/>
<button class="input-group-addon btn_browse_geneset"><b>Search</b></button>
<div id="Dropdown1" class="geneset_dropdown dropdown-menu" aria-labelledby="Geneset_Name1"></div>
</div>
<input class="geneset_id" type="hidden" id="Geneset_ID1" name="Geneset_ID1" />
<textarea class="form-control my-3 geneset_genes" style="width: 30rem; margin-top: 1rem;" rows="5" id="Geneset_Genes1" name="Geneset_Genes1" placeholder="Here will list all genes in a geneset"></textarea>
<p><button onclick="ADDGsetAdd(1)"><b>Add</b></button></p>
</div>
<span id="ADDGsetError" style="color:red"></span><br>
<h3>Search Database with a User Defined Gene Set</h3>
<p>Select a Gene Set:
<select id="gene_set"></select></p>
<button class="gs_db_bt" onclick="geneset_to_database()"><b>Search database</b></button>
<p></p>
</div><!--ADDG-->
<div id="paraCell_Help" class="tabcontent">
<h3>Welcome to paraCell!</h3>
<p>paraCell is an interactive tool for the analysis and visualization of scRNA-seq data, based on <a href="https://github.com/interactivereport/cellxgene_VIP" target="_blank">cellxgene_VIP</a>.</p>
<div id="help_text_1">
<h4>The basics of paraCell</h4>
<p>paraCell adds connections between base cellxgene, VIP and external databases.</p>
<p>Gene Sets created in cellxgene can be imported into paraCell via the "Add Genes" tab.</p>
<p>"Add Genes" also enables users to search external resources (such as the NCBI gene database) using existing gene-sets.</p>
</div>
<div id="help_text_2">
<h4>paraCell Tabs</h4>
<p>paraCell adds five new options to VIP.</p>
<ul>
<li>Advanced Gene Search</li>
<li>Cell Population View</li>
<li>Trajectory Inference</li>
<li>TradeSeq</li>
<li>Host-Parasite Interactions</li>
</ul>
</div>
<p>Further information on the functionality of each tab can be found at the <a href="https://github.com/iii-cell-atlas/cellxgene_VIP/wiki" target="_blank">paraCell wiki</a>.</p>
</div><!--paraCell_HELP-->
<div id="CellPopView" class="tabcontent">
<div id="CellPopInput">
<h3>For a given cell population, compare gene expression between two conditions <a href="https://github.com/iii-cell-atlas/cellxgene_VIP/wiki/2.-Cell-Population-View" target="_blank"><i class="fa fa-question-circle" style="color:purple;font-size:20px"></i></a></h3>
<p>Select Cell Population Annotation:
<select id="CPV_ClusterKey" onclick="CellPopList('CPV_ClusterKey',['CPV_Cluster'])"></select></p>
<p>Select a Cell Population:
<select id="CPV_Cluster"></select></p>
<p>Select Condition Annotation:
<select id="CPV_ConditionKey" onclick="CellPopList('CPV_ConditionKey',['CPV_C1','CPV_C2'])"></select></p>
<p>Select Condition 1:
<select id="CPV_C1"></select></p>
<p>Select Condition 2:
<select id="CPV_C2"></select></p>
<p>Select gene metadata category:
<select id="gene_MetaCat"></select></p>
</div>
<button class="CPVbt" onclick="CellPopPlot()"><b>Plot</b></button>
<button class="CPVTablebt" onclick="CellPopTable(); helpText('#Table_Help')"><b>Table</b></button>
<p id="CPVnote" style="color:red;"></p>
<div id="CPVspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="CPVresize" style="height: 'auto'; width: 'auto'; padding: 0.5em;">
<p id="CPVfig"></p>
</div>
<ul id="Table_Help" style="color:green"></ul>
<p></p>
<p id="LFC_Note" style="visibility: hidden;">Select a Log Fold Change Threshold:
<input type="number" id="DEG_LFC" value="0.5" step="0.1" style="visibility: hidden;"></p>
<p></p>
<table id="CPVdatatable" class="display"></table>
</div><!--CellPopView-->
<div id="TradeSeq" class="tabcontent">
<h3>Display TradeSeq Analysis results within paraCell <a href="https://github.com/iii-cell-atlas/cellxgene_VIP/wiki/4.-tradeSeq" target="_blank"><i class="fa fa-question-circle" style="color:purple;font-size:20px"></i></a></h3>
<p id="tradeSeq_SetUpNote" style="color:green;"></p>
<h4>Table Options:</h4>
<p id = "pts_to">Lineage:
<select id="ts_to" onclick = "tsDropDownUpdate()"></select></p>
<p id = "pts_C" style="visibility: hidden;">Condition:
<select id="ts_C"></select></p>
<button class="tradeSeqTable" onclick="tsTable()"><b>TradeSeq Table</b></button>
<h4>Plot Options:</h4>
<p>Choose lineage-condition combinations to plot:</p>
<p id = "tsCombos">Combos</p>
<p></p>
<div id="tradeSeqSpin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<p id="tradeSeqNote" style="color:red;"></p>
<p></p>
<table id="tradeSeqdatatable" class="display"></table>
<p id="tradeSeqfig"></p>
</div><!--TradeSeq-->
<div id="geneSearch" class="tabcontent">
<h3>Advanced Search Options <a href="https://github.com/iii-cell-atlas/cellxgene_VIP/wiki/1.-Advanced-Gene-Search" target="_blank"><i class="fa fa-question-circle" style="color:purple;font-size:20px"></i></a></h3>
<p style="color: green;">Tabs compatible with user defined gene-sets include: Violin (multi-genes), Dot Plot, and Track Plot.</p>
<div id="gsInput">
<h4>Search by Gene Name or Function:</h4>
<p>
<select id="gs_level" onchange="addAutoComplete('geneSearchAutoComplete,searchResultsHTML,names')">
<option value="names">Name</option>
<option value="functions">Function</option>
</select>
<input type="text" id="gs_geneInput"></p>
<button class="geneSearch" onclick="addToGeneList()"><b>Add to Gene-List</b></button>
<button class="geneSearch" onclick="select_or_clear_ags('select')"><b>Select All</b></button>
<button class="geneSearch" onclick="select_or_clear_ags('clear')"><b>Clear Selection</b></button>
<p id="geneSearchResults"></p>
<p id="gsResultNote"></p>
</div>
<div id="geneSearchSpin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<h4>Gene-List</h4>
<input type="text" id="gs_geneList_title" value="Custom Gene Set"><p>Gene-List Title</p>
<p id="gs_geneList"></p>
<p id="gs_geneList_Note" style="color:blue"></p>
<button class="geneSearch" onclick="clear_GS_GeneSet()"><b>Clear Gene-List</b></button>
<button class="geneSearch" onclick="add_GS_GeneSet()"><b>Add as Gene-Set</b></button>
<h4>Search by GO term:</h4>
<p>
<select id="go_level">
<option value="go_processes">Biological Process</option>
<option value="go_functions">Molecular Function</option>
<option value="go_components">Cellular Component</option></select>
<input type="text" id="gs_goTerm"></p>
<p id="gs_goNote" style="color:red;"></p>
<ul id="gs_go_Results"></ul>
<ul id="gs_go_gene_Results"></ul>
<button class="goe_search" onclick="get_go_genes()"><b>Get GO Term Genes</b></button>
<button class="goe_search" onclick="add_GO_GeneSet()"><b>Add as Gene-Set</b></button>
</div><!--geneSearch-->
<div id="HPA" class="tabcontent">
<div class="topTab">
<button id="HPA_graphs" class="HPAlinks" onclick="selTop(event, 'HostParasiteG','HPA')">Host-Parasite Visualizations</button>
<button id="HPA_table" class="HPAlinks" onclick="selTop(event, 'HostParasiteT','HPA')">Host-Parasite Cluster Marker Analysis</button>
</div>
<div id="HostParasiteG" class="HPAcontent">
<div id="hpInput">
<h3>Run Host-Parasite Interaction analyses within paraCell <a href="https://github.com/iii-cell-atlas/cellxgene_VIP/wiki/5.-Host-Parasite-Interactions" target="_blank"><i class="fa fa-question-circle" style="color:purple;font-size:20px"></i></a></h3>
<!-- <p style="color: green;">*Under Development!</p> -->
<p id="hp_exported_cells"></p>
<p>Host-Parasite Percent Concent Violin Plots:
<button class="hpViol" onclick="hpViolins()"><b>Host-Parasite Violins</b></button>
<button class="hpViolpngBT" onclick="saveImg('hpViolinsimg')" disabled>Save</button>
<div id="hpSpin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<p id="hpViolinsfig"></p>
</p>
<p>Host-Parasite UMAPs:
<button class="hpCC" onclick="hp_umap('hostFig')"><b>Cluster by Host</b></button>
<button class="hpCC" onclick="hp_umap('parasiteFig')"><b>Cluster by Parasite</b></button>
<button class="hpCC" onclick="export_HPCells()"><b>Save Selected Cells</b></button>
<p>Host-Parasite UMAP Update Option:
<select id="hp_update_opt">
<option value="highlight_cells">Highlight Selected Cells</option>
<option value="recluster">Recluster</option></select></p>
</div>
<p id="hpGraphsNote" style="color:blue;"></p>
<div class="column1">
<p id="hostFig"></p>
</div>
<div class="column2">
<p id="parasiteFig"></p>
</div>
</div><!--HostParasite Graphs-->
<div id = "HostParasiteT" class="HPAcontent">
<div>
<h3>Host-Parasite Cluster Marker Analysis:</h3>
<div id="hpSpin2" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<p>Select an Annotation:
<select id="hp_cm_annot"></select>
</p>
<p>Select Host or Parasite:
<select id="hp_host_or_parasite"><option value="host_genes">Host</option><option value="parasite_genes">Parasite</option></select>
</p>
<p>Method:
<select id="hp_cm_method">
<option value="t-test">t-test</option>
<option value="wilcoxon">wilcoxon</option>
<option value="t-test_overestim_var">t-test_overestim_var</option>
</select>
</p>
<p>Genes per Group:
<input id="hp_cm_num" type="number" step="1" value="5" min="3"/>
</p>
<button class="hpCM" onclick="hpClusterMarker_Analysis()"><b>HP Cluster Markers</b></button>
<p id="hpTableNote" style="color:blue;"></p>
</p>
</div>
<table id="hp_clusterMarker_table" class="display"></table>
</div><!--HostParasite Cluster Marker Analysis-->
</div><!--HostParasite-->
<div id="GD" class=tabcontent>
<div id="GDinput">
<h3>Genes detected in cell selections <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-gene-detected" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<p>In selection 1 (<span class="cellN1" style="color:red;">0</span>) cells and selection 2 (<span class="cellN2" style="color:red;">0</span>) cells</p>
<p>Expression cutoff:
<input id="GDcutoff" type="number" step="0.1" value="1"/></p>
</div>
<button class="GDbt" onclick="GDplot()"><b>Plot</b></button>
<button onclick="ZoomIn('GDresize')">Zoom In</button>
<button onclick="ZoomOut('GDresize')">Zoom Out</button>
<button class="GDpngBT" onclick="saveImg('GDimg')" disabled>Save</button>
<button onclick="hideShow($('#GDinput'),$(this));">Hide Input</button>
<pre id="GDnote" style="color:red;"></pre>
<div id="GDspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="GDresize" style="height: 'auto'; padding: 0.5em; border: 1px solid #B6B6B6">
<p id="GDfig"></p></div>
</div><!--GD-->
<div id="MARK" class="tabcontent">
<div id="MARKinput">
<h3>Marker genes of annotation categories from selected cells <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-marker-genes" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<p>Choose cell selection(s):
<label><input class="MARKcell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="MARKcell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label>
</p>
<p>Select an annotation:
<select id="MARKgrp"></select></p>
<p>By method:
<select id="MARKmethod">
<option value="logreg">logreg</option>
<option value="t-test">t-test</option>
<option value="wilcoxon">wilcoxon</option>
<option value="t-test_overestim_var">t-test_overestim_var</option>
</select> with the number of genes per group: <input id="MARKn" type="number" step="1" value="10" min="3"/></p>
</div>
<button class="MARKbt" onclick="MARKplot()"><b>Find/Plot</b></button>
<button onclick="ZoomIn('MARKresize')">Zoom In</button>
<button onclick="ZoomOut('MARKresize')">Zoom Out</button>
<button class="MARKpngBT" onclick="saveImg('MARKimg')" disabled>Save</button>
<button onclick="hideShow($('#MARKinput'),$(this));">Hide Input</button>
<pre id="MARKnote" style="color:red;"></pre>
<div id="MARKspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<table id="MARKtable" class="display"></table>
<div id="MARKresize" style="height: 'auto'">
<p id="MARKfig"></p>
</div>
</div><!--MARK-->
<div id="SGV" class="tabcontent">
<div class="topTab">
<button id="SGVsingle" class="SGVlinks" onclick="selTop(event, 'SGVsingleV','SGV')">Single Gene</button>
<button id="SGVcompare" class="SGVlinks" onclick="selTop(event, 'SGVcompareV','SGV')">Single Gene/Multi-factors</button>
<button id="SGVcompare" class="SGVlinks" onclick="selTop(event, 'PGV','SGV')">Multi-genes</button>
<button id="SGVcompare" class="SGVlinks" onclick="selTop(event, 'PGVcompareV','SGV')">Multi-genes/Multi-factors</button>
</div>
<div id="SGVsingleV" class="SGVcontent">
<h3>Violin plot of a gene from selected cells <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-violin-plot" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<div id="SGVinput">
<p>Choose cell selection(s):
<label><input class="SGVcell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="SGVcell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label>
</p>
<p>Choose a gene ('Add Genes' first): <select id="SGVgene"></select></p>
<p>Expression cutoff for cell filtering: <input id="SGVcutoff" type="number" step="0.1" value="1" min="0"/></p>
<p>Group by:
<select id="SGVgrp"></select></p>
</div>
<button class="SGVbt" onclick="SGVplot('plot')"><b>Plot</b></button>
<button class="SGVsaveBT" onclick="SGVplot('data')">Get Data</button>
<button onclick="ZoomIn('SGVresize')">Zoom In</button>
<button onclick="ZoomOut('SGVresize')">Zoom Out</button>
<button class="SGVpngBT" onclick="saveImg('SGVimg')" disabled>Save</button>
<button onclick="hideShow($('#SGVinput'),$(this));">Hide Input</button>
<pre id="SGVnote" style="color:red;"></pre>
<div id="SGVspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="SGVresize" style="height: 'auto'; padding: 0.5em; border: 1px solid #B6B6B6"><p id="SGVfig"></p></div>
</div> <!-- SGVsingleV -->
<div id="SGVcompareV" class="SGVcontent">
<h3>Plot sub-grouped violin <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<div id="SGVcompareinput">
<p>Choose cell selection(s):
<label><input class="SGVcomparecell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="SGVcomparecell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label>
</p>
<p>Choose a gene ('Add Genes' first): <select id="SGVcomparegene"></select></p>
<p>Expression cutoff (for cell filtering): <input id="SGVcompareCellcutoff" type="number" step="0.01" value="0.01" min="0"/></p>
<p>Expression cutoff (for percentage calculation): <input id="SGVcomparecutoff" type="number" step="0.1" value="1" min="0"/></p>
<p>Group by:
<select id="SGVcompareorder"></select></p>
<p>Sub-group by:
<select id="SGVcomparegrp"></select></p>
</div>
<button class="SGVcomparebt" onclick="SGVcompareplot()"><b>Plot</b></button> <!-- 'plot' -->
<!-- <button class="SGVsaveBT" onclick="SGVplot('data')">Get Data</button> -->
<button onclick="ZoomIn('SGVcompareresize')">Zoom In</button>
<button onclick="ZoomOut('SGVcompareresize')">Zoom Out</button>
<button class="SGVcomparepngBT" onclick="saveImg('SGVcompareimg')" disabled>Save</button>
<button onclick="hideShow($('#SGVcompareinput'),$(this));">Hide Input</button>
<pre id="SGVcomparenote" style="color:red;"></pre>
<div id="SGVcomparespin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="SGVcompareresize" style="height: 'auto'; padding: 0.5em; border: 1px solid #B6B6B6"><p id="SGVcomparefig"></p></div>
</div> <!-- SGVcompareV -->
<div id="PGV" class="SGVcontent">
<h3>Stacked violin plot of genes from selected cells <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-stacked-violin" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<div id="PGVinput">
<p>Choose cell selection(s):
<label><input class="PGVcell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="PGVcell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label>
</p>
<p>Choose genes ('Add Genes' first): <input type="checkbox" checked onclick="$('.PGVgenes').prop('checked', this.checked);">Uncheck / Check All</p>
<p id="PGVgene"></p>
<p>Expression cutoff for cell filtering: <input id="PGVcutoff" type="number" step="0.1" value="1"/></p>
<p>Select user-defined gene sets:</p><p id="PGVgeneGrp"></p>
<div id="PVGgeneGrpCollapsing">
<p>Collapsing the above gene sets:
<input type="radio" name="PGVgeneGrpColl" value="Yes" onclick="$('#PGVgeneGrpCollShow').show()">Yes
<input type="radio" name="PGVgeneGrpColl" value="No" onclick="$('#PGVgeneGrpCollShow').hide()" checked>No
</p>
<div id='PGVgeneGrpCollShow'><p>By:
<input type="radio" name="PGVgeneGrpCollCal" value="mean" checked>Average
<input type="radio" name="PGVgeneGrpCollCal" value="median">Median</p>
</div>
</div>
<p>Group by:<select id="PGVgrp"></select> as<select id="PGVgrpXY">
<option value="Rows">Rows</option>
<option value="Columns">Columns</option>
</select></p>
<p>Color:<select id="PGVcolor">
<option value='Purples'>Purples</option>
<option value='Blues'>Blues</option>
<option value='Greens'>Greens</option>
<option value='Oranges'>Oranges</option>
<option value='Reds' selected>Reds</option>
<option value='YlOrBr'>YlOrBr</option>
<option value='YlOrRd'>YlOrRd</option>
<option value='OrRd'>OrRd</option>
<option value='PuRd'>PuRd</option>
<option value='RdPu'>RdPu</option>
<option value='BuPu'>BuPu</option>
<option value='PuBu'>PuBu</option>
<option value='PuBuGn'>PuBuGn</option>
<option value='BuGn'>BuGn</option>
<option value='GnBu'>GnBu</option>
<option value='YlGnBu'>YlGnBu</option>
<option value='YlGn'>YlGn</option>
<option value='Spectral'>Spectral</option>
<option value='PiYG'>PiYG</option>
<option value='PRGn'>PRGn</option>
<option value='BrBG'>BrBG</option>
<option value='PuOr'>PuOr</option>
<option value='RdGy'>RdGy</option>
<option value='RdBu'>RdBu</option>
<option value='RdYlBu'>RdYlBu</option>
<option value='RdYlGn'>RdYlGn</option>