25c7fb6207262a9cef4903850c0e300e3457d4ec brianlee Fri Apr 29 14:29:53 2022 -0700 Adding a news announcement about new bigBarChart settings, discussion email with Max diff --git src/hg/htdocs/goldenPath/newsarch.html src/hg/htdocs/goldenPath/newsarch.html index 8fb88cc..88e7952 100755 --- src/hg/htdocs/goldenPath/newsarch.html +++ src/hg/htdocs/goldenPath/newsarch.html @@ -106,30 +106,84 @@ <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=placentaVentoTormo&position=default">Placenta Vento-Tormo</a> </li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=rectumWang&position=default">Rectum Wang</a> </li> <li> <a target="_blank" href="/cgi-bin/hgTrackUi?db=hg38&g=skinSoleBoldo&position=default">Skin Sole-Boldo</a> </li> </ul> We hope that this combined format will facilitate research and comparison with the recently released <a href="#033122">Tabula Sapiens</a> expression tracks. </p> END PREPPED FOR RELEASE --> +<a name="050222"></a> +<h2>May 2, 2022 New Track Hub bigBarChart display and selection features</h2> +<p> +We are pleased to announce new settings to support the display of bigBarChart data in Track Hubs. +<a href="help/hgTrackHubHelp.html#Intro">Track Hubs</a> are web-accessible directories of +genomic data that can be viewed on the UCSC Genome Browser. Track Hubs allow a lab to share and +host all their genomic data (<a href="help/bam.html">BAMs</a>, <a href="help/vcf.html">VCFs</a>, +etc.) via a single Genome Browser link. The <a href="help/barChart.html">bigBarChart</a> +track format displays a bar graph of category-specific values over genomic regions and is +useful for displaying gene expression across a spectrum of tissues or other datasets where +it is desirable to compare a set of related variables over specific genomic regions.</p> +<p> +Two new settings <a href="help/trackDb/trackDbHub.html#barChartBarMinWidth">barChartBarMinWidth</a> +and <a href="help/trackDb/trackDbHub.html#barChartBarMinPadding">barChartBarMinPadding</a> +allow customizing the width and padding between bars as can be seen in these two example +tracks using these settings on the same source data.</p> +<div class="text-center"> + <img src="../images/barChartPadWidth_1.png" alt="barChartBarMinPadding/MinWidth ex" width="700"> +</div> +<p> +See this example with more details on the <a target="_blank" +href="help/barChart.html#example5">bigBarChart help page</a>.</p> +<p> +Another set of new <a href="help/barChart.html#example6">bigBarChart</a> track +settings aid in the selection of bar charts on the details page: +<a href="help/trackDb/trackDbHub.html#barChartFacets" target="_blank">barChartFacets</a>, +<a href="help/trackDb/trackDbHub.html#barChartStatsUrl" target="_blank">barChartStatsUrl</a>, +and <a href="help/trackDb/trackDbHub.html#barChartMerge" target="_blank">barChartMerge</a>.</p> +<div class="text-center"> + <img src="../images/barChartFacets1.png" alt="barChartBarMinPadding/MinWidth ex" width="700"> +</div> +<p> +These new settings allow users to explore the bigBarChart data on the individual details page more +closely. By presenting a button to "merge" or "unmerge" categories of data +organized by groups such as "tissue," "cell_class," and "cell_type" +the data can be compacted. Also, the column headers can be clicked (cluster/count/val) to +reorder the displayed data by numerical value or alphabetical name. By using the facet checkboxes +a more narrow set of specific cell types can be selected, such as just "macrophage" +where the "unmerge" button can then expand the details on tissues, as seen in the below image.</p> +<div class="text-center"> + <img src="../images/barChartFacets3.png" alt="barChartBarMinPadding/MinWidth ex" width="700"> +</div> +<p> +After making selections, a "Return to Genome Browser" link on the details page allows +a user to return to the main view. Only the bars that were just selected by the facet selections +will then be displayed.</p> +<div class="text-center"> + <img src="../images/barChartFacets4.png" alt="barChartBarMinPadding/MinWidth ex" width="700"> +</div> +<p> +Track Hub developers wishing to use these new bigBarChart facet selection options can see +this example illustrating these new settings on the <a target="_blank" +href="help/barChart.html#example6">bigBarChart help page</a>.</p> + <a name="042622"></a> <h2>Apr. 26, 2022 ReMap Atlas of Regulatory Regions for human, mouse, and drosophila</h2> <p> We are happy to announce the release of the ReMap Atlas of Regulatory Regions track for <a href="/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=ReMap">hg38</a>, <a href="/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=ReMap">hg19</a>, <a href="/cgi-bin/hgTrackUi?db=mm39&c=chrX&g=ReMap">mm39</a>, <a href="/cgi-bin/hgTrackUi?db=mm10&c=chrX&g=ReMap">mm10</a>, and <a href="/cgi-bin/hgTrackUi?db=dm6&c=chr4&g=ReMap">dm6</a>. These tracks represent the <a href="https://remap.univ-amu.fr/" target="_blank">ReMap Atlas</a> of regulatory regions, which consists of a large-scale integrative analysis of all Public ChIP-seq data for transcriptional regulators from GEO, ArrayExpress, and ENCODE. Each transcription factor follows a specific RGB color. Individual BED files for specific TFs, cells/biotypes, or data sets can be found and downloaded on the <a href="https://remap.univ-amu.fr/download_page" target="_blank">ReMap website</a>.