b5ec4fbbfb04f97ebe23fbf6fbdf091dc120944e lrnassar Tue Aug 4 14:47:26 2026 -0700 Remove barChartMerge from the mouseDevTimecourse tracks, it washes out the bar colors. refs #37001 barChartMerge fades a merged group's color toward white when the group has fewer than 100 members. scaleColorPart() in facetedTable.c blends with maxVal 240 by (threshold - count)/threshold, with threshold 100. That is built for the Cell Browser single-cell tracks, where the facet count is a cell count in the hundreds or thousands. This track is bulk RNA-seq and its .facets count is 1 per sample, so merging by tissue and time point gives a group count of 2. The blend is then 0.02*color + 0.98*240, which lands every channel at roughly 235-240: thymus #C8B400 rendered as #EFEFEB. Measured on a rendered image at chr12:56694976-56714605, the track went from 40 saturated colors to 0. Reverting the setting restores the colors on both assemblies, verified against the .facets palette. Also reverts the description page wording back to one bar per replicate, and drops "grouped and" from the shared Display include since grouping was only available through this setting. The rest of the QA changes are unaffected: maxWindowToDraw, barChartMetric, labelFields and defaultLabelFields are still in place, whole-chromosome renders are still 245 ms, and the details page reports 156 of 156 bars again. diff --git src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html index ffdfeec964b..1cab6d7cac7 100644 --- src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html +++ src/hg/makeDb/trackDb/mouseDevTimecourseDisplay.shared.html @@ -1,20 +1,20 @@ <h2>Display Conventions and Configuration</h2> <p> Tracks are displayed as <a href="/goldenPath/help/barChart.html" target="_blank">bigBarCharts</a>. -Bars can be grouped and filtered by tissue and time point using the track +Bars can be filtered by tissue and time point using the track configuration controls.</p> <p>Bars are colored by tissue, with a gradient that darkens as the time point advances through the eight developmental time points (e10.5, e11.5, e12.5, e13.5, e14.5, e15.5, e16.5, and P0). Not all tissues are available at all time points.</p> <table border="1" cellpadding="4" cellspacing="0"> <tr><th>Tissue</th><th>Colors by time point (earliest to latest)</th></tr> <tr><td>thymus</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#C8B400;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr> <tr><td>spleen</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#A0856C;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr> <tr><td>liver</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e0e0e0;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#cfcfcf;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b5b5b5;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#9a9a9a;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#7f7f7f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#666666;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#4d4d4d;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr> <tr><td>heart</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f7c6c6;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e10.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#f19999;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e11.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#ec6b6b;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e12.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#e64545;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e13.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#d93030;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e14.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#b71f1f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e15.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#8f1515;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">e16.5</div></div><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#6f0f0f;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr> <tr><td>skeletal muscle tissue</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#FF6B6B;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr> <tr><td>urinary bladder</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#FF8C00;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr> <tr><td>adrenal gland</td><td><div style="display:inline-block;text-align:center;margin-right:4px;"><div style="background-color:#000000;width:36px;height:20px;border:1px solid #888;"></div><div style="font-size:0.8em;">P0</div></div></td></tr>