f85252e8231a8fef12bfcc37a3a6c20a7e1f9e19 jcasper Mon Jan 12 10:03:34 2026 -0800 Adjustments to the default hicArcLimit value, refs #36774 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index fd12de9a664..c56669c6cf8 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -2230,30 +2230,41 @@ <P><B>Example:</B></P> <pre> searchIndex name</pre> </DIV> <DIV class="searchTrix"><span class="types bed bigBed"></span> <div class="format"><code>searchTrix <url/relativePath></code></div> <P> Specifies the URL to a TRIX file that maps free text to a set of indices that are assumed to have indicies in the associated bigBed file. See <a href="../trix.html">here</a> for instructions on how to build a TRIX file and a <a href="../hubQuickStartSearch.html">Searchable Track Hub Quick Start Guide</a> here.</li> <P><B>Example:</B></P> <pre> searchTrix url or relative path </pre> </DIV> +<DIV class="style"><span class="types bigBed"></span> +<div class="format"><code>style <heatmap></code></div> + <P>BigBed tracks can be created with a variety of extra fields. When created + according to the <a href="../heatmap.html">heatmap schema</a>, the extra + fields include data to support a positional heatmap display. This setting + causes the browser to use those data for a heatmap display mode instead of the + standard bigBed display.</P> + <P><B>Example:</B></P> + <pre> style heatmap</pre> +</DIV> + <DIV class="thickDrawItem"><span class="types bed bigBed"></span> <div class="format"><code>thickDrawItem <off/on></code></div> <P>In bed tracks that have 8 or more standard bed fields, portions of items in tracks such as gene models can be drawn thicker to differentiate exon regions from introns. When data is displayed at different scales, the items and the thick portions of the items should scale proportionally. However, it may be more important to see the existence of the thick regions than it is to attempt to maintain the proportion. By setting thickDrawItem on, the thick display regions of items are always drawn at a minimum of 3 pixels, even when zoomed out greatly.</P> <P><B>Example:</B></P> <pre> thickDrawItem on</pre> </DIV> @@ -5508,31 +5519,31 @@ in nucleotides for the heatmap. If a portion of the heatmap represents an interaction farther than the value of the maximum distance setting, that portion of the heatmap simply isn't drawn. This setting, hicDistanceMax, controls the default value for that maximum (without this setting, the default is 0). A value of 0 means that no filter is applied. </p> </div> <div class="hicArcLimit"><span class="types hic"></span> <div class="format"><code>hicArcLimit <integer></code></div> <p>The "arc" display mode for Hi-C tracks can become difficult to read if too many arcs are being drawn, particularly if many of them have scores close to the saturation score. This setting can be used to restrict the display to only the N highest scoring arcs (it has no effect in other display modes). The companion setting, hicArcLimitEnabled, controls whether this filter is applied to the track by default or not. The default -value for this setting is 10000. +value for this setting is 5000. </p> </div> <div class="hicArcLimitEnabled"><span class="types hic"></span> <div class="format"><code>hicDistanceMax <true|false></code></div> <p>The "arc" display mode for Hi-C tracks can become difficult to read if too many arcs are being drawn, so there is an option to limit the display to the N highest scoring interactions. The value of N is controlled by the companion setting, hicArcLimit, while this setting controls whether the filter is automatically turned on when the track is loaded. The default value is false. </p> </div> <DIV class="hic_example"><span class="types hic"></span> <div class="format"><B>Example of a hic track</B></div>