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<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>Heatmapper</title>
<link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/3.3.5/css/bootstrap.min.css"/>
<style>
.border-img {
border:0.2em solid black;
width:100%;
height:15em;
border-radius:0.4em;
max-width:20em;
/*max-width: 70%;*/
display: block;
margin-left: auto;
margin-right: auto;
}
.logo {
/* These options are to prevent anti-aliasing */
image-rendering: optimizeSpeed; /* STOP SMOOTHING, GIVE ME SPEED */
image-rendering: -moz-crisp-edges; /* Firefox */
image-rendering: -o-crisp-edges; /* Opera */
image-rendering: -webkit-optimize-contrast; /* Chrome (and eventually Safari) */
image-rendering: pixelated; /* Chrome */
image-rendering: optimize-contrast; /* CSS3 Proposed */
-ms-interpolation-mode: nearest-neighbor; /* IE8+ */
}
.myTable {
table-layout: fixed;
border-spacing:1em;
width: 1024px; /* virtual pixel width of many iPads */
}
.myRow {
display:table-row;
}
.myCol {
display:table-cell;
}
.well.myCol {
display:table-cell;
}
.sectionStats {
text-align: left;
}
.heatmapTitle {
font-size: large;
font-weight: 500;
position: relative;
top: 3px;
}
figcaption {
text-align:center;
margin-bottom:0.5em;
}
td {
padding: 5px;
vertical-align: top;
}
.notice-holder {
display:table-cell;
width: 67%;
text-align: center;
}
.notice {
display:inline-block;
vertical-align: middle;
width: 80%;
padding: 1.0em 1.0em 0.5em 1.0em;
background-color: #eae0ff;
border-style: solid;
border-width: 2px;
border-color: #c9b1ff;
}
</style>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1.8.2/jquery.min.js"></script>
<script src="http://netdna.bootstrapcdn.com/bootstrap/3.0.3/js/bootstrap.min.js"></script>
<script> $(function(){ $("#navbar").load("www/navbar.html"); }); </script>
<script type="text/javascript" src="www/js/google-analytics.js"></script>
<script>
function ChangeButton(button_id){
var text = document.getElementById(button_id).firstChild;
text.data = text.data == "Show Details" ? "Hide Details" : "Show Details";
}
</script>
<noscript>
<div class="alert alert-danger" style="margin: 1em;">
<strong>JavaScript not enabled!</strong> Heatmapper requires JavaScript to be
enabled in your browser in order to function. To enable JavaScript, do one of the
following:<br /><br />
<div style="font-size: small;">
<table>
<tr>
<td>
<i>In Google Chrome:</i>
<ol>
<li>Click the Chrome menu icon <img src="www/images/GoogleChromeMenuIcon.png"> on the browser toolbar.</li>
<li>Select <b>Settings</b>.</li>
<li>On the "Settings" page, click the <b>Show advanced settings...</b> link at the bottom.</li>
<li>In the "Privacy" section, click <b>Content settings...</b></li>
<li>Select <b>Allow all sites to run JavaScript (recommended)</b> in the "JavaScript" section.</li>
<li>Click <b>Done.</b></li>
<li>Refresh your Heatmapper page.</li>
</ol>
</td>
<td>
<i>In Windows Internet Explorer:</i>
<ol>
<li>On the <b>Tools</b> menu, click <b>Internet Options</b>, and then click the <b>Security</b> tab.</li>
<li>Click the <b>Internet</b> zone.</li>
<li>If you do not have to customize your Internet security settings, click <b>Default Level</b>. Then do step 4.<br /><br />
If you have to customize your Internet security settings, follow these steps:</li>
<ol type="a">
<li>Click <b>Custom Level</b>.</li>
<li>In the <b>Security Settings – Internet Zone</b> dialog box, click <b>Enable</b> for <b>Active Scripting</b> in the <b>Scripting</b> section.</li>
</ol>
<br />
<li>Click the <b>Back</b> button to return to the previous page, and then click the <b>Refresh</b> button to refresh Heatmapper.</li>
</ol>
</td>
</tr>
<tr>
<td>
<i>In Mozilla Firefox:</i><br />
<ul><li>In Firefox, JavaScript is enabled by default, but may be blocked if a privacy extension
such as NoScript or Ghostery was installed. Please edit the settings for the
particular extension you have installed to un-block Heatmapper.</li></ul><br /><br />
</td>
<td>
<i>In Apple Safari:</i>
<ol>
<li>From the <b>Safari</b> (on Mac) or <b>Edit</b> (on Windows) drop-down menu, select <b>Preferences...</b></li>
<li>Select the <b>Security</b> icon/tab at the top on the window.</li>
<li>Then, check the <b>Enable JavaScript</b> checkbox.</li>
<li>Refresh your Heatmapper page.</li>
</ol>
</td>
</tr>
</table>
</div>
</div>
</noscript>
</head>
<body>
<div id="navbar"></div>
<div class="myTable">
<h2 style="margin-left:0px; padding-left:1.9em;">Welcome to Heatmapper!</h2>
<div class="notice-holder">
<div class="notice"">
<p style="text-align:justify; width:100%;">
In response to COVID-19, Heatmapper has been adapted to
map cold- and flu-like symptoms in Colombia, South America, to enable officials
to better respond to the crisis. People in Colombia can self-report symptoms at
<a href="https://cov19col.herokuapp.com" target="_blank">cov19col.herokuapp.com</a>.
Please help get the word out!
</p>
<p style="text-align:justify; width:100%;">
The project is open source, for both the
<a href="https://github.com/WishartLab/heatmapper/tree/symptom_mapping" target="_blank">heatmapping</a>
and
<a href="https://github.com/Marco8301/QT-Cov19-OS" target="_blank">self-reporting</a>
apps.
</p>
<p style="text-align:justify; width:100%;">
We will also soon be launching a separate site for mapping COVID-19 data.
</p>
</div>
</div>
<div class="myRow" style="width:67%;">
<!--
<div style="display:table-cell; width:100%;">
-->
<div class="myCol" style="display:table-cell; width:67%; padding-left:3em; padding-right:3em;">
<img src="www/images/logo.png" class="logo" style="width:240px; padding-left:1em; padding-bottom:1em; float:right;">
<div style="width:57%; border: 2px solid #002aff; background-color: #deffce; padding-top:0.6em; padding-left:0.6em; margin:0.25em; margin-bottom:1em;">
<img src="www/images/arrow.png" style="width:48px; padding-left:0.2em; padding-right:0.8em; padding-top:0.1em; float:left;">
<p style="text-align:left;">
<i>Click in the menu above or on the buttons below to start making your heat map!</i>
</p>
</div>
<p style="text-align:justify; width:100%;">
Heatmapper is a freely available web server that allows users to interactively
visualize their data in the form of heat maps through an easy-to-use graphical
interface. Heatmapper is a versatile tool that allows users to easily create a
wide variety of heat maps for many different data types and applications.
Heatmapper allows users to generate, cluster and visualize: 1) <b>expression-based
heat maps</b> from transcriptomic, proteomic and metabolomic experiments;
2) <b>pairwise distance maps</b>; 3) <b>correlation maps</b>; 4) <b>image overlay heat maps</b>;
5) <b>latitude and longitude heat maps</b> and 6) <b>geopolitical (choropleth) heat maps</b>.
Heatmapper offers a number of simple and intuitive customization options for
easy adjustments to each heat map’s appearance and plotting parameters.
Heatmapper also allows users to interactively explore their numeric data values
by hovering their cursor over each heat map, or by using a searchable/sortable
data table view.
</p>
</div>
<!--
</div>
<div class="well" style="display:table-cell; width:100%; float:right; ">
-->
<div class="myCol well" style="display:table-cell; width:33%;">
<h5>Please cite:</h5>
<p>
Sasha Babicki, David Arndt, Ana Marcu, Yongjie Liang, Jason R. Grant,
Adam Maciejewski, and David S. Wishart. Heatmapper: web-enabled heat mapping for all.
<a href="http://www.ncbi.nlm.nih.gov/pubmed/27190236" target="_blank">
<i>Nucleic Acids Res.</i> 2016 May 17 (epub ahead of print). doi:10.1093/nar/gkw419</a>
</p>
<br />
<h5>Funding</b>
<p>
<a href="http://www.cihr-irsc.gc.ca" target="_blank">
<img src="www/images/cihr.png" style="width:118px; margin-left:0px; margin-right:20px; margin-top:10px;">
</a>
<a href="http://genomealberta.ca" target="_blank">
<img src="www/images/galberta.png" style="width:118px; margin-left:0px; margin-right:20px; margin-top:10px;">
</a>
</p>
</div>
</div>
</div>
<div class="myTable" style="display:table;">
<div class="myRow">
<div class="well myCol">
<figure>
<a href="/expression">
<img src="www/images/expression.png" alt="Expression" class="border-img">
</a>
<figcaption>
<div style="margin-top:5px; margin-bottom:10px;">
<span class="heatmapTitle">Expression</span>
<button type="button" class="btn btn-primary" style="margin-left:20px;" onclick="heatmapperLink('expression');return false;">Try it!</button>
</div>
<a id="exp_btn" data-toggle="collapse" data-target="#exp" onClick="ChangeButton('exp_btn');">Show Details</a>
<div id="exp" class="collapse">
<br />
<em>
Displays unclustered expression data, such as from a <a href="https://en.wikipedia.org/wiki/Microarray" target="_blank">microarray</a> experiment, as a heatmap.
Hierarchical clustering can also be performed on the data and the resulting dendrogram can be viewed.
</em>
<div class = "sectionStats">
<br />
<strong>Input Formats:</strong> Comma-Separated Values (.csv), Tab Delimited (.txt, .dat, .tsv, .tab), or Microsoft Excel (.xls, .xlsx).
<br />
<strong>Example Usage:</strong> Cluster and visualize the results of a DNA microarray experiment to analyze gene expression levels
<br />
<strong>Number of Features:</strong> 18
</div>
<div>
</figcaption>
</figure>
</div>
<div class="well myCol">
<figure>
<a href="/pairwise">
<img src="www/images/pairwise.jpg" alt="pairwise comparison" class="border-img">
</a>
<figcaption>
<div style="margin-top:5px; margin-bottom:10px;">
<span class="heatmapTitle">Pairwise Comparison</span>
<button type="button" class="btn btn-primary" style="margin-left:20px;" onclick="heatmapperLink('pairwise');return false;">Try it!</button>
</div>
<a id="pair_btn" data-toggle="collapse" data-target="#pair" onClick="ChangeButton('pair_btn');">Show Details</a>
<div id="pair" class="collapse">
<br />
<em>
Displays heatmap of user data either as a <a href=" https://en.wikipedia.org/wiki/Distance_matrix" target="_blank">distance matrix</a>,
as a <a href="https://en.wikipedia.org/wiki/Correlation_and_dependence#Correlation_matrices" target="_blank">correlation matrix</a>, or as-is.
</em>
<div class = "sectionStats">
<br />
<strong>Input Formats:</strong> Comma-Separated Values (.csv), Tab Delimited (.txt, .dat, .tsv, .tab), Microsoft Excel (.xls, .xlsx), or Protein Data Bank format (.pdb).
<br />
<strong>Example Usage:</strong> Visualize pairwise distances for predicting protein structure
<br />
<strong>Number of Features:</strong> 14
</div>
</div>
</figcaption>
</figure>
</div>
<div class="well myCol">
<figure>
<a href="/image">
<img src="www/images/image.jpg" alt="image overlay" class="border-img">
</a>
<figcaption>
<div style="margin-top:5px; margin-bottom:10px;">
<span class="heatmapTitle">Image Overlay</span>
<button type="button" class="btn btn-primary" style="margin-left:20px;" onclick="heatmapperLink('image');return false;">Try it!</button>
</div>
<a id="img_btn" data-toggle="collapse" data-target="#img" onClick="ChangeButton('img_btn');">Show Details</a>
<div id="img" class="collapse">
<br />
<em>
Displays a heatmap of densities based on values at plot coordinates corresponding to an image.
</em>
<div class = "sectionStats">
<br />
<strong>Input Formats:</strong>
Comma-Separated Values (.csv), Tab Delimited (.txt, .dat, .tsv, .tab), or Microsoft Excel (.xls, .xlsx) for the data values.
For the image upload, PNG (.png), JPEG (.jpeg or .jpg) or TIFF (.tiff or .tif) formats are supported.
<br />
<strong>Example Usage:</strong> Create a custom heatmap of measured bacterial presence and abundance on different parts of the body
<br />
<strong>Number of Features:</strong> 18
</div>
</div>
</figcaption>
</figure>
</div>
</div>
<div class="myRow">
<div class="well myCol">
<figure>
<a href="/geomap">
<img src="www/images/geomap.png" alt="geomap" class="border-img">
</a>
<figcaption>
<div style="margin-top:5px; margin-bottom:10px;">
<span class="heatmapTitle">Geomap</span>
<button type="button" class="btn btn-primary" style="margin-left:20px;" onclick="heatmapperLink('geomap');return false;">Try it!</button>
</div>
<a id="map_btn" data-toggle="collapse" data-target="#map" onClick="ChangeButton('map_btn');">Show Details</a>
<div id="map" class="collapse">
<br />
<em>
Displays a <a href="https://en.wikipedia.org/wiki/Choropleth_map" target="_blank">choropleth</a>
heatmap specified by values assigned to locations based on political boundaries.
</em>
<div class = "sectionStats">
<br />
<strong>Input Formats:</strong> Comma-Separated Values (.csv), Tab Delimited (.txt, .dat, .tsv, .tab), or Microsoft Excel (.xls, .xlsx).
<br />
<strong>Example Usage:</strong> Visualize disease prevalence by country
<br />
<strong>Number of Features:</strong> 12
</div>
</div>
</figcaption>
</figure>
</div>
<div class="well myCol">
<figure>
<a href="/geocoordinate">
<img src="www/images/geocoordinate.jpg" alt="Geocoordinate" class="border-img">
</a>
<figcaption>
<div style="margin-top:5px; margin-bottom:10px;">
<span class="heatmapTitle">Geocoordinate</span>
<button type="button" class="btn btn-primary" style="margin-left:20px;" onclick="heatmapperLink('geocoordinate');return false;">Try it!</button>
</div>
<a id="geo_btn" data-toggle="collapse" data-target="#geo" onClick="ChangeButton('geo_btn');">Show Details</a>
<div id="geo" class="collapse">
<br />
<em>
Displays a heatmap of densities based on values assigned to locations specified by latitude and longitude coordinates.
Density estimation calculation can be performed based on density of points or weighted by values specified for each coordinate.
</em>
<div class = "sectionStats">
<br />
<strong>Input Formats:</strong> Comma-Separated Values (.csv), Tab Delimited (.txt, .dat, .tsv, .tab), or Microsoft Excel (.xls, .xlsx).
<br />
<strong>Example Usage:</strong> Visualize observed animal population densities in a region
<br />
<strong>Number of Features:</strong> 13
</div>
</div>
</figcaption>
</figure>
</div>
<div class="well myCol">
<figure>
<a href="/about/instructions">
<img src="www/images/about.png" alt="about" class="border-img">
</a>
<figcaption>
<h4>About</h4>
<a id="about_btn" data-toggle="collapse" data-target="#about" onClick="ChangeButton('about_btn');">Show Details</a>
<div id="about" class="collapse">
<br />
<em>
Provides information about heatmapper.ca.
The about section contains four subsections: Instructions, Gallery, Contact, and GitHub.
</em>
<div class = "sectionStats">
<br />
<strong>Instructions:</strong>
View instructions on how to use each section
<br />
<strong>Gallery:</strong>
View a gallery of examples
<br />
<strong>Contact:</strong>
Get the contact information for the author of heatmapper.ca and additional information about the project
<br />
<strong>GitHub:</strong>
View the project source code
</div>
</div>
</figcaption>
</figure>
</div>
</div>
</div>
<div style="font-size: small; text-align:center;">
Questions or comments? Please use our <a href="http://feedback.wishartlab.com/?site=heatmapper" target="_blank">feedback page</a>.
License: <a href="http://creativecommons.org/licenses/by-sa/2.0/" target="_blank">CC-BY-SA</a>
</div>
</body>
</html>