d19b85083618569a8b3400a8d17a3d2028ef223d lrnassar Tue Sep 29 15:38:31 2026 -0700 The itemRgb doc said a color setting "in the same stanza" loses to an explicit itemRgb on, which is narrower than bedItemRgb() behaves: both settings go through trackDbSetting(), which walks the parent chain, and the two lookups are independent, so a parent's itemRgb on beats a color set on the child itself. Reworded that and the matching colorFields sentence, and added the changes.html row this should have had. Caught by CR of 64adf565f28. refs #36212 diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml index 77fa9a20c91..ddf0a6cc56b 100644 --- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml +++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml @@ -2283,38 +2283,40 @@ at least 9 standard bed fields, this setting can be used to activate item coloring using the value in the ninth field, <code>itemRgb</code>. The value of the item field must be an R,G,B triplet. When loaded into a table, this field appears as an integer with the RGB values in specific bits of the integer. To observe this field, specify the type as, <code>type bigBed 9</code>, or, <code>type bigBed 9+</code>, for additional <A HREF="../../../FAQ/FAQformat.html#format1" target="_blank">non-standard columns</A>, in the trackDb stanza for the bigBed file.</P> <P>Note that the display of color is affected by the <code>maxItems</code> option. When the track is zoomed to the point that the number of items to display exceeds <code>maxItems</code>, the track is forced into dense mode and the items are drawn from the bigBed summary in the default track color rather than using the <code>itemRgb column</code>. </P> <P>Whether the items are drawn from the <code>itemRgb</code> column also depends on - the <A onclick="jumpTo(this)" href="#color"><code>color</code></A> setting:</P> + the <A onclick="jumpTo(this)" href="#color"><code>color</code></A> setting. Both + settings are inherited from a track's <code>parent</code>, and an explicit + <code>itemRgb</code> wins wherever it is set:</P> <ul> <li><code>itemRgb on</code>: items take the colors in the file. A <code>color</code> - setting in the same stanza still colors the track label, but it does not override - the items.</li> + setting still colors the track label, but it does not override the items.</li> <li><code>itemRgb off</code>: items take the <code>color</code> setting, or black if there is none.</li> - <li><code>color</code> alone: items take the <code>color</code> setting.</li> + <li><code>color</code> with no <code>itemRgb</code>: items take the <code>color</code> + setting.</li> <li>Neither setting: items take the colors in the file. This is the default on genome.ucsc.edu.</li> </ul> <P><B>Example:</B></P> <pre> itemRgb on</pre> </DIV> <DIV class="colorFields"><span class="types bigBed bigGenePred"></span> <div class="format"> <code>colorFields default="<label>" <fieldName1>="<label1>" <fieldName2>="<label2>" ...</code> </div> <P> Enables a <b>Color by:</b> dropdown in the track controls that lets the user switch among multiple pre-computed color schemes without leaving the track display. </P> @@ -2323,32 +2325,32 @@ extra bigBed field (defined in the track's <code>.as</code> file) that contains a pre-computed <code>R,G,B</code> color string, the same format as the standard <A onclick="jumpTo(this)" href="#itemRgb">itemRgb</A> field. The label in double quotes is shown in the dropdown; if omitted, a label is derived automatically by stripping a leading <code>colorBy</code> prefix and replacing underscores with spaces. </P> <P> The special name <code>default</code> (with an optional label) represents the track's existing <code>itemRgb</code> field (column 9) and is placed first in the dropdown. When no <code>default=</code> entry is given, an unlabeled "Default" option is added automatically. </P> <P> Item coloring must be active for <code>colorFields</code> to work. It is active by default on bigBed tracks with more than 9 fields. It is suppressed by - <code>itemRgb off</code>, or by a <code>color</code> setting in a stanza that does not - also say <code>itemRgb on</code>. The currently + <code>itemRgb off</code>, or by a <code>color</code> setting when neither the track nor + its parent says <code>itemRgb on</code>. The currently selected scheme is stored in the cart variable <code><trackName>.colorField</code>. When a non-default scheme is active, the track long label gains a <em>(Coloring by: <label>)</em> suffix. </P> <P><B>Example:</B></P> <pre> colorFields default="Kozak strength" colorByEvidence="Evidence type" colorByHlaClass="HLA class" </pre> <P>This creates a three-option dropdown. <code>colorByEvidence</code> and <code>colorByHlaClass</code> must be extra fields in the bigBed whose values are <code>R,G,B</code> strings.</P> </DIV> <DIV class="maxItems"><span class="types bed bigBed broadPeak psl"></span> <div class="format"><code>maxItems <integer></code></div>