198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index 3572f75c55f..88be11e9118 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -35,31 +35,31 @@ autoSql (.as) schema file defining the fields of the bigBarChart.

Below is an example of the barChart format in 'full' visibility mode

BarChart example in full mode

The 'squish' display mode draws one colored rectangle indicating the category (e.g. tissue) with highest value of the measured metric (e.g. gene expression) if it contributes more than 10% to the total expression, otherwise the chart is colored black. The following image shows the GTEx Genes track in 'squish' mode; the beige colored item (tissue) has the highest expression in the ACE2 gene and represents more than 10% of total expression. -Click into the colored rectange for more information.

+Click into the colored rectangle for more information.

barChart format definition

The following autoSql definition illustrates the basic schema supporting barChart (and bigBarChart) tracks.

table bigBarChart
 "bigBarChart bar graph display"  
@@ -105,31 +105,31 @@
 "XYZ gene expression barChart"
 (
 string chrom;               "Reference sequence chromosome or scaffold"
 uint chromStart;            "Start position in chromosome"
 uint chromEnd;              "End position in chromosome"
 string name;                "Transcript name"
 uint score;                 "Score (0-1000), derived from total expScores (below)"
 char[1] strand;             "+, -, or ., indicating orientation of the item"
 string name2;               "Gene name" 
 uint expCount;              "Number of tissues"
 float[expCount] expScores;  "Comma separated list of median expression in RPKM for each tissue."
 bigint _dataOffset;         "Offset of sample data in data matrix file"
 int _dataLen;               "Length of sample data row in data matrix file"
 )

-Customing this file will make your data more easily interpreted by users, who will +Customizing this file will make your data more easily interpreted by users, who will see the field descriptions when accessing the track data from the Table Browser, when viewing items on the Genome Browser details pages (via the "view table schema" link), and (for users who download files), from the -as option of the bigBedInfo tool.

Creating barChart and bigBarChart custom tracks

The steps for creating barChart tracks differ from the process for creating bigBarChart tracks. The steps also differ based on whether you have an input matrix file (generated perhaps from an RNA-Seq differential expression analysis pipeline) or not. If you have an expression matrix-like file, skip to Example #3, otherwise follow example 1 below.

@@ -427,31 +427,31 @@ Once loaded, click into an item to see the details page, in this case for the gene ACE2 at the default position in hg38. On the details page, rather than a static bar chart image, there is a dynamic interactive selection screen with checkbox facets to narrow down the display. Adding barChartMerge on enables the display of the "merge" button, and barChartFacets tissue,cell_class,cell_type sources information in barChartStatsUrl ...tissue_cell_type.facets to enable the facet options. To interact with this example, click the first two "merge" buttons next to "tissue" and "cell_class."

With those two merged selections, then click on the "Macrophage" option to see just this one cell type selection.

By then clicking the "unmerge" button next to "tissue" the single bar chart will expand with tissue clusters.

In these ways the new barChartFacets, barChartStatsUrl, and barChartMerge 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)