c54a66ee94ad1fe7272022742fbe022d82c15021 brianlee Thu Apr 28 16:51:26 2022 -0700 Fixing and adding links to new barChart examples on barChart.html diff --git src/hg/htdocs/goldenPath/help/barChart.html src/hg/htdocs/goldenPath/help/barChart.html index f334c64..e34b184 100755 --- src/hg/htdocs/goldenPath/help/barChart.html +++ src/hg/htdocs/goldenPath/help/barChart.html @@ -404,60 +404,67 @@ To help with the selection and exploration of large data sets the new settings <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> were introduced where on the details page checkboxes enable slicing data down to smaller collections based on metadata.</p> <p>The setting <code>barChartFacets <column1,column2,...columnN></code> turns on the faceted selection on the track details and configure page which is useful for selecting which bars out of a large number to display by clicking designated checkboxes. The setting <code>barChartStatsUrl <url></code> associates a table in tab-separated values with the barChart, with one line per bar. And the setting <code>barChartMerge on</code> enables a merge button inside of the faceted selections. It is particularly useful when there are many bars and many facets to condense a related group, such as tissue source.</p> <p> Below is an example track using these settings on source data for a -<a href="../cgi-bin/hgTracks?db=hg38&hideTracks=1&tabulaSapiensTissueCellType=pack&tabulaSapiens=show" +<a href="/cgi-bin/hgTracks?db=hg38&hideTracks=1&tabulaSapiensTissueCellType=pack&tabulaSapiens=show" target="_blank">Tabula Sapiens single cell RNA data from many tissues</a> track. This excerpt of settings from that track allows experimenting to see these settings in action, and to be loaded by going to the My Data, Custom Tracks page.</p> <pre> track type=bigBarChart name="ex Tabula Sapiens" description="A bigBarChart using Tabula Sapiens data to illustrate new Details pages" visibility=pack barChartCategoryUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.categories barChartFacets=tissue,cell_class,cell_type barChartStatsUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/bw_edit_tissue_cell_type.facets barChartMerge=on bigDataUrl=http://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/tabulaSapiens/tissue_cell_type.bb </pre> <p> 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. Click the first two "merge" buttons next to +the display. Adding <code>barChartMerge on</code> enables the display of the "merge" +button, and <code>barChartFacets tissue,cell_class,cell_type</code> sources information in +<code>barChartStatsUrl ...tissue_cell_type.facets</code> to enable the facet options. +To interact with this example, click the first two "merge" buttons next to "tissue" and "cell_class."</p> <div class="text-center"> <img src="../../images/barChartFacets1.png" alt="Example1 of Facets on barCharts" width="700"> </div> <p> With those two merged selections, then click on the "Macrophage" option to see just this one cell type selection.</p> <div class="text-center"> <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 barChartFacets, barChartStatsUrl, and barChartMerge settings allow users +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> <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> <h2>Sharing your data with others</h2>