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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>-->
<!-- 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;
}
</style>
</head>
<body>
<div class="splitter">
<div id="panel-left">
<div class="tab">
<button class="tablinks" onclick="selFun(event, 'ADDG')"><b>Add Genes</b></button>
<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, '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>
<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/>
<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>
</div><!--ADDG-->
<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="$('#PGVgeneGrpCollShow').hide()" checked>No
</p>
<div id='PGVgeneGrpCollShow'><p>By:
<input type="radio" name="PGVgeneGrpCollCal" value="mean" checked>Average
<input type="radio" name="PGVgeneGrpCollCal" value="median">Median</p>
</div>
</div>
<p>Group by:<select id="PGVgrp"></select> as<select id="PGVgrpXY">
<option value="Rows">Rows</option>
<option value="Columns">Columns</option>
</select></p>
<p>Color:<select id="PGVcolor">
<option value='Purples'>Purples</option>
<option value='Blues'>Blues</option>
<option value='Greens'>Greens</option>
<option value='Oranges'>Oranges</option>
<option value='Reds' selected>Reds</option>
<option value='YlOrBr'>YlOrBr</option>
<option value='YlOrRd'>YlOrRd</option>
<option value='OrRd'>OrRd</option>
<option value='PuRd'>PuRd</option>
<option value='RdPu'>RdPu</option>
<option value='BuPu'>BuPu</option>
<option value='PuBu'>PuBu</option>
<option value='PuBuGn'>PuBuGn</option>
<option value='BuGn'>BuGn</option>
<option value='GnBu'>GnBu</option>
<option value='YlGnBu'>YlGnBu</option>
<option value='YlGn'>YlGn</option>
<option value='Spectral'>Spectral</option>
<option value='PiYG'>PiYG</option>
<option value='PRGn'>PRGn</option>
<option value='BrBG'>BrBG</option>
<option value='PuOr'>PuOr</option>
<option value='RdGy'>RdGy</option>
<option value='RdBu'>RdBu</option>
<option value='RdYlBu'>RdYlBu</option>
<option value='RdYlGn'>RdYlGn</option>
</select> <input id="PGVcolor_r" type="checkbox">Reverse <button onclick="hideShow($('#PGVcolorhelp'),$(this),'Color Help');">Show Color Help</button></p>
<div id="PGVcolorhelp" style="display:none;">
<table border=0>
<tr valign="top"><td><img src="https://interactivereport.github.io/cellxgene_VIP/static/color_brewer_sequential.png" width="300"></td><td><img src="https://interactivereport.github.io/cellxgene_VIP/static/color_brewer_diverging.png" width="300"></td></tr>
</table>
</div>
</div>
<button class="PGVbt" onclick="PGVplot('plot')"><b>Plot</b></button>
<button class="PGVsaveBT" onclick="PGVplot('data')">Get Data</button>
<button onclick="ZoomIn('PGVresize')">Zoom In</button>
<button onclick="ZoomOut('PGVresize')">Zoom Out</button>
<button class="PGVpngBT" onclick="saveImg('PGVimg')" disabled>Save</button>
<button onclick="hideShow($('#PGVinput'),$(this));">Hide Input</button>
<pre id="PGVnote" style="color:red;"></pre>
<div id="PGVspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="PGVresize" style="height: 'auto'; padding: 0.5em; border: 1px solid #B6B6B6"><p id="PGVfig"></p></div>
</div><!--PGV-->
<div id="PGVcompareV" class="SGVcontent">
<h3>Violins of selected genes splitted on two group annotations <small><a href="https://github.com/TheHumphreysLab/plot1cell">plot1cell</a></small></h3>
<div id="PGVcompareinput">
<p>Choose cell selection(s):
<label><input class="PGVcomparecell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="PGVcomparecell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label></p>
<p>Choose genes ('Add Genes' first): <input type="checkbox" checked onclick="$('.PGVcomparegenes').prop('checked', this.checked);">Uncheck / Check All</p>
<p id="PGVcomparegene"></p>
<p>Expression cutoff for cell filtering: <input id="PGVcomparecutoff" type="number" step="0.1" value="0.5"/></p>
<p>Group by (row panels):<select id="PGVcompareRow"></select></p>
<p>Sub-group by (within a subpanel):<select id="PGVcompareGrp"></select></p>
<p>Width: <input id="PGVcomparewidth" type="number" step="0.5" value="6" min="1" max="24"/>
Height: <input id="PGVcompareheight" type="number" step="0.5" value="8" min="1" max="24"/>
</p>
</div>
<button class="PGVcomparebt" onclick="PGVcomparebt()"><b>Plot</b></button>
<button onclick="ZoomIn('PGVcompareresize')">Zoom In</button>
<button onclick="ZoomOut('PGVcompareresize')">Zoom Out</button>
<button class="PGVcomparepngBT" onclick="saveImg('PGVcompareimg')" disabled>Save</button>
<button onclick="hideShow($('#PGVcompareinput'),$(this));">Hide Input</button>
<pre id="PGVcomparenote" style="color:red;"></pre>
<div id="PGVcomparespin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="PGVcompareresize" style="height: 'auto'; padding: 0.5em; border: 1px solid #B6B6B6"><p id="PGVcomparefig"></p></div>
</div>
</div><!--SGV panel-->
<div id="HEAT" class="tabcontent">
<div id="HEATinput">
<h3>Heatmap of selected cells and genes <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-heatmap" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<p>Choose cell selection(s):
<label><input class="HEATcell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="HEATcell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label>
</p>
<p>Choose genes ('Add Genes' first): <input id='HEATgenesAll' type="checkbox" checked onclick="$('.HEATgenes').prop('checked', this.checked);">Uncheck / Check All <span id="HEATgeneAnno"><input id="HEATgeneAnnoCK" type="checkbox" checked>Using protein atlas annotation</span></p>
<p id="HEATgene"></p>
<p>Or upload a gene annotation csv file (first column header is 'gene'): <input type='file' id='HEATgeneFile' onchange="HEATgeneFileUpdate()" /></p>
<p>Choose categorical annotation(s):</p>
<p id="HEATgrp"></p>
<p>Choose continuous annotation(s):</p>
<p id="HEATmeta"></p>
<p>Select plotting value:
<select id="HEATnorm">
<option value="X">Expression</option>
<option value="zscore">Expression Z-score</option>
</select></p>
<p>Color:
<select id="HEATcolor">
<option value='Purples'>Purples</option>
<option value='Blues'>Blues</option>
<option value='Greens'>Greens</option>
<option value='Oranges'>Oranges</option>
<option value='Reds' selected>Reds</option>
<option value='YlOrBr'>YlOrBr</option>
<option value='YlOrRd'>YlOrRd</option>
<option value='OrRd'>OrRd</option>
<option value='PuRd'>PuRd</option>
<option value='RdPu'>RdPu</option>
<option value='BuPu'>BuPu</option>
<option value='PuBu'>PuBu</option>
<option value='PuBuGn'>PuBuGn</option>
<option value='BuGn'>BuGn</option>
<option value='GnBu'>GnBu</option>
<option value='YlGnBu'>YlGnBu</option>
<option value='YlGn'>YlGn</option>
<option value='Spectral'>Spectral</option>
<option value='PiYG'>PiYG</option>
<option value='PRGn'>PRGn</option>
<option value='BrBG'>BrBG</option>
<option value='PuOr'>PuOr</option>
<option value='RdGy'>RdGy</option>
<option value='RdBu'>RdBu</option>
<option value='RdYlBu'>RdYlBu</option>
<option value='RdYlGn'>RdYlGn</option>
</select> <input id="HEATcolor_r" type="checkbox">Reverse <button onclick="hideShow($('#HEATcolorhelp'),$(this),'Color Help');">Show Color Help</button></p>
<div id="HEATcolorhelp" style="display:none;">
<table border=0>
<tr valign="top"><td><img src="https://interactivereport.github.io/cellxgene_VIP/static/color_brewer_sequential.png" width="300"></td><td><img src="https://interactivereport.github.io/cellxgene_VIP/static/color_brewer_diverging.png" width="300"></td></tr>
</table>
</div>
<p>Select plotting methods:
<select id="HEATplotMethod" onchange="if($(this).val()=='cHeatmap'){$('#HEATcomplexSetting').show();$('#HEATseabornSetting').hide()}else{$('#HEATcomplexSetting').hide();$('#HEATseabornSetting').show()}">
<option value="cHeatmap">ComplexHeatmap (R)</option>
<option value="sns">Seaborn (python)</option>
</select></p>
<div id="HEATcomplexSetting">
<p>Gene as
<input type="radio" name="HEATswapAxes" value="F" checked onchange="$('#HEATcomplexSettingSwap').hide()">Column
<input type="radio" name="HEATswapAxes" value="T" onchange="$('#HEATcomplexSettingSwap').show()">Row
<span id="HEATcomplexSettingSwap" style="display:none"> || Max legend row: <input id="HEATcomplexSettingLegendRow" type="number" step="1" value="5" min="1" max="20"/></span>
</p>
<p>Width: <input id="HEATwidth" type="number" step="0.5" value="6" min="1" max="24"/>
Height: <input id="HEATheight" type="number" step="0.5" value="8" min="1" max="24"/>
</p>
Annotation fontsize adjust: <input id="HEATcomplexSettingFontadj" type="number" step="1" value="-4" min="-10" max="10"/>
<p>
</p>
<p>Cluster by:
<select id="HEATcomplexSortby" onchange="if($(this).val()=='Annotation'){$('#HEATorderGrp').show()}else{$('#HEATorderGrp').hide()}">
<option value="Annotation">Annotation</option>
<option value="Expression">Expression</option>
</select>
</p>
<div id='HEATorderGrp'>
<p>Change the annotation order by dragging items up or down, cluster annotations can also be removed by clicking <i class='fa fa-trash-o'></i>:</p>
<ul id="HEATdynList" class="sortable-list"></ul><!-- -->
</div>
</div>
<div id="HEATseabornSetting" style="display:none">
<p>Cluster by:
<select id="HEATorder"></select></p>
</div>
</div>
<button class="HEATbt" onclick="HEATplot()"><b>Plot</b></button>
<button class="HEATsaveBT" onclick="HEATdata()" disabled>Get Data</button>
<button onclick="ZoomIn('HEATresize')">Zoom In</button>
<button onclick="ZoomOut('HEATresize')">Zoom Out</button>
<button class="HEATpngBT" onclick="saveImg('HEATimg')" disabled>Save</button>
<button onclick="hideShow($('#HEATinput'),$(this));">Hide Input</button>
<pre id="HEATnote" style="color:red;"></pre>
<div id="HEATspin" class="loading style-2" style="visibility: hidden;"><div class="loading-wheel"></div></div>
<div id="HEATresize" style="height: 'auto'; padding: 0.5em; border: 1px solid #B6B6B6"><p id="HEATfig"></p></div>
<div id="HEATdata" style="visibility: hidden;"></div>
</div><!--HEAT-->
<div id="DOT" class="tabcontent">
<div id="DOTinput">
<h3>Dot plot shows per group, the fraction of cells expressing a gene (dot size) and the mean expression of the gene in those cell (color scale) <a href="https://interactivereport.github.io/cellxgene_VIP/tutorial/docs/how-to-use-cellxgene-vip.html#vip-dot-plot" target="_blank"><i class="fa fa-question-circle" style="font-size:20px"></a></i></h3>
<p>Choose cell selection(s):
<label><input class="DOTcell" type="checkbox" value="celllist1" checked/>Selection 1 (<span class="cellN1" style="color:red">0</span>)</label>
<label><input class="DOTcell" type="checkbox" value="celllist2" checked/>Selection 2 (<span class="cellN2" style="color:red">0</span>)</label>
</p>
<p>Choose genes ('Add Genes' first): <input type="checkbox" checked onclick="$('.DOTgenes').prop('checked', this.checked);">Uncheck / Check All</p>
<p id="DOTgene"></p>
<p>Expression cutoff for cell fraction (dot size): <input id="DOTcutoff" type="number" step="0.1" value="1"/></p>
<p>Expression is averaged only over cells expressing a given gene above the cutoff: <input type="radio" name="mean_only_expressed" value="Yes">Yes<input type="radio" name="mean_only_expressed" value="No" checked>No</p>
<p>Select user-defined gene sets:</p><p id="DOTgeneGrp"></p>
<div id="DOTgeneGrpCollapsing">
<p>Collapsing the above gene sets:
<input type="radio" name="DOTgeneGrpColl" value="Yes" onclick="$('#DOTgeneGrpCollShow').show()">Yes
<input type="radio" name="DOTgeneGrpColl" value="No" onclick="$('#DOTgeneGrpCollShow').hide()" checked>No
</p>
<div id='DOTgeneGrpCollShow'><p>By:
<input type="radio" name="DOTgeneGrpCollCal" value="mean" checked>Average
<input type="radio" name="DOTgeneGrpCollCal" value="median">Median</p>
</div>
</div>
<p>Group by: <select id="DOTgrp"></select></p>
<p>Adjust the legend width: <input id="DOTlegendW" type="number" step="0.1" value="1.5"/></p>
<p>Color:
<select id="DOTcolor">
<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>
</select> <input id="DOTcolor_r" type="checkbox">Reverse <button onclick="hideShow($('#DOTcolorhelp'),$(this),'Color Help');">Show Color Help</button></p>
<div id="DOTcolorhelp" style="display:none;">
<table border=0>
<tr valign="top"><td><img src="https://interactivereport.github.io/cellxgene_VIP/static/color_brewer_sequential.png" width="300"></td><td><img src="https://interactivereport.github.io/cellxgene_VIP/static/color_brewer_diverging.png" width="300"></td></tr>
</table>
</div>
<pre id="DOTnote" style="color:red;">Note: Unscaled data is used as the visualiztion is hard to interpret for scaled or corrected matrices in which zero counts had been replaced by other values. Scaling option in Global Setting does not apply to Dot plot</pre>
</div>