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/trackDbSettings.yaml src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml
index e801fc6c5bf..5c463de48d2 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbSettings.yaml
@@ -1674,70 +1674,71 @@
   level: base
   required: false
   summary: In bed formats supporting at least 9 standard bed fields, this setting can be used to activate
     item coloring using the value in the ninth field, itemRgb .
   description: 'In bed formats supporting at least 9 standard bed fields, this setting can be used to
     activate item coloring using the value in the ninth field, itemRgb . 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, type bigBed 9 , or, type
     bigBed 9+ , for additional non-standard columns , in the trackDb stanza for the bigBed file.
 
     Note that the display of color is affected by the maxItems option. When the track is zoomed to the
     point that the number of items to display exceeds maxItems , 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 itemRgb
     column .
 
-    Whether the items are drawn from the itemRgb column also depends on the color setting:
+    Whether the items are drawn from the itemRgb column also depends on the color setting. Both settings
+    are inherited from a track''s parent , and an explicit itemRgb wins wherever it is set:
 
-    - itemRgb on : items take the colors in the file. A color setting in the same stanza still colors
-    the track label, but it does not override the items.
+    - itemRgb on : items take the colors in the file. A color setting still colors the track label, but
+    it does not override the items.
 
     - itemRgb off : items take the color setting, or black if there is none.
 
-    - color alone: items take the color setting.
+    - color with no itemRgb : items take the color setting.
 
     - Neither setting: items take the colors in the file. This is the default on genome.ucsc.edu.'
   format: itemRgb on
   examples:
   - itemRgb on
 - name: colorFields
   types:
   - bigBed
   - bigGenePred
   roles:
   - leaf
   category: bigBed - Item or Region Track Settings
   context: trackDb
   level: new
   required: false
   summary: 'Enables a Color by: dropdown in the track controls that lets the user switch among multiple
     pre-computed color schemes without leaving the track display.'
   description: 'Enables a Color by: dropdown in the track controls that lets the user switch among multiple
     pre-computed color schemes without leaving the track display.
 
     Each entry is a fieldName="Human Label" pair. The field name must be an extra bigBed field (defined
     in the track''s .as file) that contains a pre-computed R,G,B color string, the same format as the
     standard itemRgb field. The label in double quotes is shown in the dropdown; if omitted, a label is
     derived automatically by stripping a leading colorBy prefix and replacing underscores with spaces.
 
     The special name default (with an optional label) represents the track''s existing itemRgb field (column
     9) and is placed first in the dropdown. When no default= entry is given, an unlabeled "Default" option
     is added automatically.
 
     Item coloring must be active for colorFields to work. It is active by default on bigBed tracks with
-    more than 9 fields. It is suppressed by itemRgb off , or by a color setting in a stanza that does
-    not also say itemRgb on . The currently selected scheme is stored in the cart variable <trackName>.colorField
+    more than 9 fields. It is suppressed by itemRgb off , or by a color setting when neither the track
+    nor its parent says itemRgb on . The currently selected scheme is stored in the cart variable <trackName>.colorField
     . When a non-default scheme is active, the track long label gains a (Coloring by: <label>) suffix.
 
     This creates a three-option dropdown. colorByEvidence and colorByHlaClass must be extra fields in
     the bigBed whose values are R,G,B strings.'
   format: colorFields default="<label>" <fieldName1>="<label1>" <fieldName2>="<label2>" ...
   examples:
   - colorFields default="Kozak strength" colorByEvidence="Evidence type" colorByHlaClass="HLA class"
 - name: colorByStrand
   types:
   - bed
   - bigBed
   roles:
   - leaf
   category: bigBed - Item or Region Track Settings
   context: trackDb