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JBrowse - client-side genome browser
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</script></nav></div><div class="container mainContainer"><div class="wrapper"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle">Pre-rendered Image Tracks</h1></header><article><div><span><h1><a class="anchor" aria-hidden="true" id="pre-rendered-image-tracks"></a><a href="#pre-rendered-image-tracks" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Pre-rendered Image Tracks</h1>
<p>JBrowse supports tracks based on pre-generated PNG or JPEG images that are tiled along the reference sequence. Currently, JBrowse ships with two different image track generators: <a href="#wig-to-jsonpl" title="wikilink">wig-to-json.pl</a>, which generates images showing simple quantitative (wiggle) data, and <a href="#draw-basepair-trackpl" title="wikilink">draw-basepair-track.pl</a>, which draws arcs to show the base pairing structure of RNAs.</p>
<h2><a class="anchor" aria-hidden="true" id="wig-to-jsonpl"></a><a href="#wig-to-jsonpl" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>wig-to-json.pl</h2>
<hr>
<p>Using a <a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html">wiggle</a> file, this script creates a single Image track that displays data from the wiggle file. <strong>Beginning with JBrowse 1.5, this is no longer the recommended method of displaying wiggle data: it has largely been replaced by the direct-access BigWig data store coupled with the next-generation Wiggle track type. See <a href="/#Wiggle/BigWig_Tracks_(XYPlot,_Density)" title="wikilink">Wiggle Tracks</a>.</strong></p>
<p>In wiggle data, a numeric value is associated with each nucleotide position in the reference sequence. This is represented in JBrowse as a track that looks like a histogram, where the horizontal axis is for each nucleotide position, and the vertical axis is for the number associated with that position. The vertical axis currently does not have a scale; rather, the heights for each position are relative to each other.</p>
<p>Special dependencies: <a href="http://www.libpng.org/pub/png/libpng.html">libpng</a></p>
<p>In order to use wig-to-json.pl, the code for wig2png must be compiled. Normally, this is done automatically by <code>setup.sh</code> but it can be done manually if necessary. See the Quick Start Tutorial packaged with JBrowse for details.</p>
<h3><a class="anchor" aria-hidden="true" id="basic-usage"></a><a href="#basic-usage" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Basic usage</h3>
<p><code>bin/wig-to-json.pl --wig <wig file> --tracklabel <track name> [options]</code></p>
<p>Hint: If you are using this type of track to plot a measure of a prediction's quality, where the range of possible quality scores is from some lowerbound to some upperbound (for instance, between 0 and 1), you can specify these bounds with the max and min options.</p>
<p><img src="/docs/assets/config/Wiggle-options.png" alt="600px|center|thumb|Summary of wig-to-json.pl options."></p>
<table>
<thead>
<tr><th>Option</th><th>Value</th></tr>
</thead>
<tbody>
<tr><td>wig</td><td>The name of the wig file that will be used. This option must be specified.</td></tr>
<tr><td>tracklabel</td><td>The internal name that JBrowse will give to this feature track. This option requires a value.</td></tr>
<tr><td>key</td><td>The external, human-readable label seen on the feature track when it is viewed in JBrowse. The value of key defaults to the value of tracklabel.</td></tr>
<tr><td>out</td><td>A path to the output directory (default is 'data' in the current directory).</td></tr>
<tr><td>tile</td><td>The directory where the tiles, or images corresponding to each zoom level of the track, are stored. Defaults to data/tiles.</td></tr>
<tr><td>bgcolor</td><td>The color of the track background. Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "255,255,255".</td></tr>
<tr><td>fgcolor</td><td>The color of the track foreground (i.e. the vertical bars of the wiggle track). Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "105,155,111".</td></tr>
<tr><td>width</td><td>The width in pixels of each tile. The default value is 2000.</td></tr>
<tr><td>height</td><td>The height in pixels of each tile. Changing this parameter will cause a corresponding change in the top-to-bottom height of the track in JBrowse. The default value is 100.</td></tr>
<tr><td>min</td><td>The lowerbound to use for the track. By default, this is the lowest value in the wiggle file.</td></tr>
<tr><td>max</td><td>The upperbound to use for the track. By default, this will be the highest value in the wiggle file.</td></tr>
</tbody>
</table>
<h3><a class="anchor" aria-hidden="true" id="system-specific-tips-for-building-wig2png"></a><a href="#system-specific-tips-for-building-wig2png" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>System-specific tips for building wig2png</h3>
<h4><a class="anchor" aria-hidden="true" id="apple-os-x"></a><a href="#apple-os-x" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Apple OS X</h4>
<p>You need libpng and a C++ compiler; you can get these with <a href="http://mxcl.github.com/homebrew/">Homebrew</a>, <a href="http://www.macports.org/">MacPorts</a>, or <a href="http://www.finkproject.org/">Fink</a>.</p>
<p>Once you have those installed, you need to compile the JBrowse wiggle-processing program. JBrowse includes a makefile to do this, but you may need to add the paths for <code>libpng</code> and <code>png.h</code> to your compiler's library and include paths. For example, if libpng is in <code>/usr/X11</code>, you can run <code>configure</code> like this:</p>
<p><code>./configure CXXFLAGS=-I/usr/X11/include LDFLAGS=-L/usr/X11/lib</code></p>
<p>Depending on which OS X you have (and whether you're using MacPorts/fink/etc.), libpng might be somewhere other than <code>/usr/X11</code>, like <code>/opt/local</code> for example. To find where libpng is, try <code>locate libpng</code>.</p>
<h4><a class="anchor" aria-hidden="true" id="ubuntu-debian-linux"></a><a href="#ubuntu-debian-linux" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Ubuntu / Debian Linux</h4>
<p>Be sure to install the <code>libpng\#\#</code> and <code>libpng\#\#-dev</code> packages, where <code>\#\#</code> is a number such as 12 or 15, depending on the version of Ubuntu.</p>
<h4><a class="anchor" aria-hidden="true" id="red-hat-centos-fedora-linux"></a><a href="#red-hat-centos-fedora-linux" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Red Hat/CentOS/Fedora Linux</h4>
<p>Be sure to install the <code>libpng</code> and <code>libpng-devel</code> packages.</p>
<h1><a class="anchor" aria-hidden="true" id="draw-basepair-trackpl"></a><a href="#draw-basepair-trackpl" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a># draw-basepair-track.pl</h1>
<p>This script inputs a single base pairing track into JBrowse. A base pairing track is a distinctive track type that represents base pairing between nucleotides as arcs. In addition, it is intended to demonstrate the Perl API for writing your own image track generators.</p>
<h3><a class="anchor" aria-hidden="true" id="basic-usage-1"></a><a href="#basic-usage-1" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Basic usage</h3>
<p><code>bin/draw-basepair-track.pl --gff <gff file> --tracklabel <track name> [options]</code>
<img src="/docs/assets/config/Basepair-options.png" alt="600px|center|thumb|Summary of draw-basepair-track.pl options."></p>
<table>
<thead>
<tr><th>Option</th><th>Value</th></tr>
</thead>
<tbody>
<tr><td>gff</td><td>The name of the gff file that will be used. This option must be specified.</td></tr>
<tr><td>tracklabel</td><td>The internal name that JBrowse will give to this feature track. This option requires a value.</td></tr>
<tr><td>key</td><td>The external, human-readable label seen on the feature track when it is viewed in JBrowse. The value of key defaults to the value of tracklabel.</td></tr>
<tr><td>out</td><td>A path to the output directory (default is 'data' in the current directory).</td></tr>
<tr><td>tile</td><td>The directory where the tiles, or images corresponding to each zoom level of the track, are stored. Defaults to data/tiles.</td></tr>
<tr><td>bgcolor</td><td>The color of the track background. Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "255,255,255".</td></tr>
<tr><td>fgcolor</td><td>The color of the track foreground (i.e. the base pairing arcs). Specified as "RED,GREEN,BLUE" in base ten numbers between 0 and 255. Defaults to "0,255,0".</td></tr>
<tr><td>width</td><td>The width in pixels of each tile. The default value is 2000.</td></tr>
<tr><td>height</td><td>The height in pixels of each tile. Changing this parameter will cause a corresponding change in the top-to-bottom height of the track in JBrowse. The default value is 100.</td></tr>
<tr><td>thickness</td><td>The thickness of the base pairing arcs in the track. The default value is 2.</td></tr>
<tr><td>nolinks</td><td>Disables use of file system links to compress duplicate image files.</td></tr>
</tbody>
</table>
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