819fe0dd688e9a31a6e57e46f2bdc31d6c023150 dschmelt Tue Aug 25 16:02:57 2020 -0700 Minor edits for barChart squish refs #23679 diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index ba058a6..9dbf8b9 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -29,33 +29,38 @@ features (i.e. schema customization, and label configuration support), and is recommended for users who can use command-line tools and have web-accessible data storage. If you do not have web-accessible data storage, please see the <a href="hgTrackHubHelp.html#Hosting"> Hosting</a> section of the Track Hub Help documentation. barChart format files are converted to bigBarChart files using the program <code>bedToBigBed</code>, run with the <code>-as</code> option to pull in a special <a href="http://www.linuxjournal.com/article/5949" target="_blank">autoSql</a> (<em>.as</em>) schema file defining the fields of the bigBarChart. </p> <p> Below is an example of the barChart format in 'full' visibility mode</p> <p class='text-center'> <img class='text-center' src="../../images/barChartFull.png" alt="BarChart example in full mode" width="883" height="143"> </p> <p> -The Squish display mode draws a rectangle for each gene, colored to indicate the tissue -with highest expression level if it contributes more than 10% to the overall expression -(and colored black if no tissue predominates).</p> +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 chart for more information.</p> + <p class='text-center'> <img class='text-center' src="../../images/barChartSquish.png" alt="BarChart example in squish mode" width="883" height="143"> </p> <a name=barChart></a> <h2>barChart format definition</h2> <p> The following autoSql definition illustrates the basic schema supporting barChart (and bigBarChart) tracks.</p> <pre><code>table bigBarChart "bigBarChart bar graph display" ( string chrom; "Reference sequence chromosome or scaffold" uint chromStart; "Start position in chromosome"