17cda45b082befcc4b38faa51661b519e5669752 lrnassar Tue Mar 17 10:53:48 2026 -0700 Feedback from CR, refs #37247 diff --git src/hg/htdocs/goldenPath/help/heatmap.html src/hg/htdocs/goldenPath/help/heatmap.html index 59eeafc8d62..9f828e02135 100755 --- src/hg/htdocs/goldenPath/help/heatmap.html +++ src/hg/htdocs/goldenPath/help/heatmap.html @@ -3,31 +3,31 @@ <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <h1>Positional Heatmap Display</h1> <h2>Overview</h2> <p>The standard display mode for a bigBed track is a simple block or exon/intron marker in the window. Extra fields in the bigBed, however, can contain a variety of additional data. When data in the extra fields meet the schema described below, then the simple block display can be replaced with a positional heatmap. The heatmap provides a sparse 2-dimensional grid for information like expression of allele-specific point mutations across a transcript.</p> <div class="text-center"> - <a href="https://genome.ucsc.edu/s/jcasper/heatmap_example" target="_blank"> + <a href="https://genome.ucsc.edu/s/view/heatmap_example" target="_blank"> <img alt="Heatmap track showing a color-coded grid of expression values across genomic positions" src="/images/heatmap_example.png" style="width:80%;max-width:1083px"></a> </div> <h2>Contents</h2> <h6><a href="#extrafields">The Extra Fields</a></h6> <h6><a href="#gettingStarted">Getting Started</a></h6> <h6><a href="#displaying">Displaying Your Heatmap</a></h6> <h6><a href="#troubleshooting">Troubleshooting</a></h6> <a id="extrafields"></a> <h2>The Extra Fields</h2> <p>A heatmap bigBed file starts with the standard 12 BED fields, but adds 7 more. In a heatmap, the standard BED <code>blockCount</code>, <code>blockSizes</code>, and <code>chromStarts</code> fields define the columns of the grid (one column per block), while the extra field @@ -221,31 +221,31 @@ chr1 1000 2000 T1 1000 + 1000 2000 0 4 1,100,100,1 0,100,700,999 2 "Case 1","Case 2" -5,0,5 #0000ff,#ffffff,#ff0000 ,2.8,,,,-4,8.9,, ,"2.8, medium","no data",,,"-4, low","8.9, extreme",,, "Example on transcript 1" chr1 1200 2400 T2 1000 - 1200 2400 0 4 1,100,100,1 0,200,900,1199 2 "Case 1","Case 2" -5,0,5 #0000ff,#ffffff,#ff0000 ,0.1,-2,,,1.1,-3.5,, ,"0.1, negligible","-2, low",,,"1.1 marginal","-3.5 low",, "Example on transcript 2" </pre> <p>Here is this example in a <a href="examples/heatmap.bed" target="_blank">BED file</a> (using tabs as field separators), and the corresponding <a href="examples/heatmap.bb" target="_blank">bigBed file</a>. The bigBed was created from the BED file using the following command:</p> <pre> bedToBigBed -tab -type=bed12+ -as=heatmap.as heatmap.bed chrom.sizes heatmap.bb </pre> <p>A copy of heatmap.as is available <a href="examples/heatmap.as" target="_blank">here</a>. chrom.sizes files for most assemblies can be found on our <a href="https://hgdownload.soe.ucsc.edu" target="_blank">download server</a>. </p> <div class="text-center"> - <a href="https://genome.ucsc.edu/s/jcasper/heatmap_example" target="_blank"> + <a href="https://genome.ucsc.edu/s/view/heatmap_example" target="_blank"> <img alt="Heatmap track with customized color scale displaying allele-specific data" src="/images/heatmap_example2.png" style="width:80%;max-width:1083px"></a> </div> <a id="displaying"></a> <h2>Displaying your heatmap</h2> <p>Once you have created a bigBed file, you need to tell the Genome Browser to display it as a heatmap rather than a standard bigBed track. This is done by adding the <a href="trackDb/trackDbHub.v3.html#style"><code>style heatmap</code></a> setting to your track's trackDb configuration. Without this setting, the browser will render the file as an ordinary bigBed track and the heatmap extra fields will be ignored.</p> <p>The most common way to load a heatmap track is through a <a href="hubBasics.html">track hub</a>. A minimal trackDb entry for a heatmap track looks like this:</p> <pre> track myHeatmap