66fafe88184bb3a8a45a50026f4d6c7fbbc24109 markd Tue Sep 29 10:12:53 2026 -0700 Rebuild the TSS tracks as traditional composites, for wiggle control. refs #35528 A faceted composite is routed to facetedCompositeUi(), which returns before cfgByCfgType(), so it never draws the wiggle controls: no data view scaling, no viewing range, no windowing function, no track height. Signal tracks need those, so proCapNet and encode4ProCap are now traditional composites. They stay separate composites under the TSS container. The multiWig strand overlays survive the change. The old comment here claimed a multiWig under a plain composite "is flattened away and never drawn"; that is wrong for drawing, which #36320 fixed. Only the hgTrackUi subtrack list flattens, because compositeUiSubtracks() walks to leaves, so the overlays get no inline config block and are configured from their own pages. Raised as #38441. The matrix has to be declared over the leaves, since that is the level hgTrackDb checks: declaring it on the containers fails -strict with "has groups not defined in parent". So a strand is a matrix cell, and the containers carry no subGroups. Sample class survives as a filterComposite dimension, replacing the facet. configurable on gives each subtrack its own config namespace. Drop the faceted machinery: the metadata table, the color file, the constants feeding them and the gbdbDir argument, 39 lines. The metadata.tsv and colors.json already written under /gbdb are now unreferenced and can be deleted. Put the ENCODE accession in each subtrack longLabel, and add a linked table of them to both description pages. A longLabel cannot carry a link, since printSubtrackTableBody() htmlEncodes it, hence the table. The label wording is shortened to keep the longest at 74 characters. diff --git src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra index d9ddd11813f..aeb8aa11a02 100644 --- src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra +++ src/hg/makeDb/trackDb/human/hs1/transcriptionStart.ra @@ -1,230 +1,246 @@ # Generated by hg/makeDb/outside/proCapNet/proCapNetTrackDb for hs1. # Do not edit by hand, edit the script and regenerate. track transcriptionStart superTrack on show shortLabel Transcription Initiation (TSS) longLabel Transcription initiation (TSS) group rna track proCapNet parent transcriptionStart - compositeTrack faceted + compositeTrack on type bigWig shortLabel ProCapNet longLabel ProCapNet predicted PRO-cap - metaDataUrl /gbdb/hs1/proCapNet/metadata.tsv - colorSettingsUrl /gbdb/hs1/proCapNet/colors.json - primaryKey Cell_line - dataTypes pred|"Predicted PRO-cap" - subtrackUrls Experiment=https://www.encodeproject.org/annotations/$$/ - defaultSortField Cell_line - maxCheckboxes 50 + subGroup1 cellLine Cell_line A673=A673 Caco2=Caco-2 Calu3=Calu3 HUVEC=HUVEC K562=K562 MCF10A=MCF10A + subGroup2 dataType Data_type predPos=Predicted_+ predNeg=Predicted_- + subGroup3 sampleClass Sample_class Cancer=Cancer Noncancer=Non-cancer + dimensions dimensionX=dataType dimensionY=cellLine dimA=sampleClass + filterComposite dimA + sortOrder cellLine=+ dataType=+ + configurable on + autoScale group + alwaysZero on + maxHeightPixels 100:40:8 + windowingFunction maximum noInherit on visibility hide priority 2 track proCapNet_A673_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 0,114,178 shortLabel A673 Predicted - longLabel A673 ProCapNet predicted PRO-cap, plus strand up and minus strand down + longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 1 track proCapNet_A673_pred_pos parent proCapNet_A673_pred + subGroups cellLine=A673 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/A673.proCapNet.pos.bw color 0,114,178 shortLabel A673 Predicted + - longLabel A673 ProCapNet predicted PRO-cap, plus strand + longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, plus strand track proCapNet_A673_pred_neg parent proCapNet_A673_pred + subGroups cellLine=A673 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/A673.proCapNet.neg.bw color 0,114,178 altColor 0,114,178 negateValues on shortLabel A673 Predicted - - longLabel A673 ProCapNet predicted PRO-cap, minus strand + longLabel A673 (ENCSR072YCM) ProCapNet predicted PRO-cap, minus strand track proCapNet_Caco-2_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 213,94,0 shortLabel Caco-2 Predicted - longLabel Caco-2 ProCapNet predicted PRO-cap, plus strand up and minus strand down + longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 2 track proCapNet_Caco-2_pred_pos parent proCapNet_Caco-2_pred + subGroups cellLine=Caco2 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Caco-2.proCapNet.pos.bw color 213,94,0 shortLabel Caco-2 Predicted + - longLabel Caco-2 ProCapNet predicted PRO-cap, plus strand + longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, plus strand track proCapNet_Caco-2_pred_neg parent proCapNet_Caco-2_pred + subGroups cellLine=Caco2 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Caco-2.proCapNet.neg.bw color 213,94,0 altColor 213,94,0 negateValues on shortLabel Caco-2 Predicted - - longLabel Caco-2 ProCapNet predicted PRO-cap, minus strand + longLabel Caco-2 (ENCSR182QNJ) ProCapNet predicted PRO-cap, minus strand track proCapNet_Calu3_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 0,158,115 shortLabel Calu3 Predicted - longLabel Calu3 ProCapNet predicted PRO-cap, plus strand up and minus strand down + longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 3 track proCapNet_Calu3_pred_pos parent proCapNet_Calu3_pred + subGroups cellLine=Calu3 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Calu3.proCapNet.pos.bw color 0,158,115 shortLabel Calu3 Predicted + - longLabel Calu3 ProCapNet predicted PRO-cap, plus strand + longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, plus strand track proCapNet_Calu3_pred_neg parent proCapNet_Calu3_pred + subGroups cellLine=Calu3 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/Calu3.proCapNet.neg.bw color 0,158,115 altColor 0,158,115 negateValues on shortLabel Calu3 Predicted - - longLabel Calu3 ProCapNet predicted PRO-cap, minus strand + longLabel Calu3 (ENCSR797DEF) ProCapNet predicted PRO-cap, minus strand track proCapNet_HUVEC_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 204,121,167 shortLabel HUVEC Predicted - longLabel HUVEC ProCapNet predicted PRO-cap, plus strand up and minus strand down + longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 4 track proCapNet_HUVEC_pred_pos parent proCapNet_HUVEC_pred + subGroups cellLine=HUVEC dataType=predPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/HUVEC.proCapNet.pos.bw color 204,121,167 shortLabel HUVEC Predicted + - longLabel HUVEC ProCapNet predicted PRO-cap, plus strand + longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, plus strand track proCapNet_HUVEC_pred_neg parent proCapNet_HUVEC_pred + subGroups cellLine=HUVEC dataType=predNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/HUVEC.proCapNet.neg.bw color 204,121,167 altColor 204,121,167 negateValues on shortLabel HUVEC Predicted - - longLabel HUVEC ProCapNet predicted PRO-cap, minus strand + longLabel HUVEC (ENCSR801ECP) ProCapNet predicted PRO-cap, minus strand track proCapNet_K562_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 230,159,0 shortLabel K562 Predicted - longLabel K562 ProCapNet predicted PRO-cap, plus strand up and minus strand down + longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 5 track proCapNet_K562_pred_pos parent proCapNet_K562_pred + subGroups cellLine=K562 dataType=predPos sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/K562.proCapNet.pos.bw color 230,159,0 shortLabel K562 Predicted + - longLabel K562 ProCapNet predicted PRO-cap, plus strand + longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, plus strand track proCapNet_K562_pred_neg parent proCapNet_K562_pred + subGroups cellLine=K562 dataType=predNeg sampleClass=Cancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/K562.proCapNet.neg.bw color 230,159,0 altColor 230,159,0 negateValues on shortLabel K562 Predicted - - longLabel K562 ProCapNet predicted PRO-cap, minus strand + longLabel K562 (ENCSR740IPL) ProCapNet predicted PRO-cap, minus strand track proCapNet_MCF10A_pred parent proCapNet on container multiWig aggregate solidOverlay showSubtrackColorOnUi on type bigWig autoScale on alwaysZero on maxHeightPixels 100:40:8 windowingFunction maximum color 86,180,233 shortLabel MCF10A Predicted - longLabel MCF10A ProCapNet predicted PRO-cap, plus strand up and minus strand down + longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, plus up minus down onlyVisibility full priority 6 track proCapNet_MCF10A_pred_pos parent proCapNet_MCF10A_pred + subGroups cellLine=MCF10A dataType=predPos sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/MCF10A.proCapNet.pos.bw color 86,180,233 shortLabel MCF10A Predicted + - longLabel MCF10A ProCapNet predicted PRO-cap, plus strand + longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, plus strand track proCapNet_MCF10A_pred_neg parent proCapNet_MCF10A_pred + subGroups cellLine=MCF10A dataType=predNeg sampleClass=Noncancer type bigWig bigDataUrl /gbdb/hs1/proCapNet/pred/MCF10A.proCapNet.neg.bw color 86,180,233 altColor 86,180,233 negateValues on shortLabel MCF10A Predicted - - longLabel MCF10A ProCapNet predicted PRO-cap, minus strand + longLabel MCF10A (ENCSR860TYZ) ProCapNet predicted PRO-cap, minus strand