fcd19999608dd4b9e0ca67016a838ca7dce1fd3f gperez2 Thu Mar 5 09:46:22 2026 -0800 Documenting the singleCellColumnNames trackDb setting, refs #37176 diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index 6821bd55d0d..3572f75c55f 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -442,32 +442,37 @@ <img src="../../images/barChartFacets2.png" alt="Example2git l of Facets on barCharts" width="700"> </div> <p> By then clicking the "unmerge" button next to "tissue" the single bar chart will expand with tissue clusters.</p> <div class="text-center"> <img src="../../images/barChartFacets3.png" alt="Example3 of Facets on barCharts" width="700"> </div> <p> In these ways the new <a href="trackDb/trackDbHub.html#barChartFacets" target="_blank">barChartFacets</a>, <a href="trackDb/trackDbHub.html#barChartStatsUrl" target="_blank">barChartStatsUrl</a>, and <a href="trackDb/trackDbHub.html#barChartMerge" target="_blank">barChartMerge</a> settings allow users to explore the barChart data on the individual details page more closely. One can use the facets -to further select certain types and also click the columns (val/count/cluster) to arrange -by numerical value or alphabetical name.</p> +to further select certain types and also click the columns (<b>val</b>/<b>count</b>/<b>cluster</b>) +to arrange by numerical value or alphabetical name. The setting +<a href="trackDb/trackDbHub.html#singleCellColumnNames" +target="_blank">singleCellColumnNames off</a> can be added to the trackDb to change the display +column to <b>count</b> instead of the default display <b>cell count</b>. This setting is useful for +non-single-cell datasets such as bulk RNA-seq, where <b>count</b> represents the number of samples +or replicates rather than cells.</p> <p> Also, if you click the "Return to Genome Browser" link, you will see only these selection bars are displayed.</p> <div class="text-center"> <img src="../../images/barChartFacets4.png" alt="Example4 of Facets on barCharts" width="700"> </div> <p> In this image after making the selections browsing ACE2 the "zoom out" button has been clicked to also view nearby genes where the expression of these tissue selections for the gene PIR is quite noticeably different.</p> <h6 id="example7">Example #7</h6> <p> In this example, we will be using command-line tools that were used to create the single-cell tracks available on hg38. For more in-depth examples of these tools, take a look at the following