3ee43997901d9226d78f052f521fdaa69c2c2975 dschmelt Mon Apr 19 17:06:56 2021 -0700 Updating doc images for MR change, deleting old files too refs #26385 diff --git src/hg/htdocs/goldenPath/help/multiRegionHelp.html src/hg/htdocs/goldenPath/help/multiRegionHelp.html index 95105a7..8b1a6a3 100755 --- src/hg/htdocs/goldenPath/help/multiRegionHelp.html +++ src/hg/htdocs/goldenPath/help/multiRegionHelp.html @@ -68,65 +68,65 @@ </ul> <a name="GetStarted"></a> <h2>Getting started With Multi-Region view</h2> <p> Follow these steps to activate and configure multi-region view in the Genome Browser.</p> <p> <strong>Step 1. Pick a genome assembly and region</strong><br> Open the Genome Browser tracks display to a region of interest within a standard genome assembly, or open a custom region within an assembly hub.</p> <p> <strong>Step 2. Open the multi-region view configuration window</strong><br> Click <button type="button">multi-region</button> under the tracks display to open the multi-region configuration window.</p> <p> -<img src="../../images/MultiRegionButton.png" alt="Multi-Region button" width="799" +<img src="../../images/multiRegionButton.png" alt="Multi-Region button" width="799" height="201"></p> <p> <strong>Step 3. Configure the multi-region view</strong><br> By default, the <strong>Exit multi-region mode</strong> button is selected. This button returns the display to the traditional view.</p> <p> -<img src="../../images/MultiRegionConfigurationWindow2.png" alt="Configure Multi-Region view" +<img src="../../images/multiRegionConfig.png" alt="Configure Multi-Region view" width="701" height="387"> </p> <p> To activate a multi-region view, click one of these options:</p> <ul> <li> <strong>Show exons using</strong> -- display only the exonic regions (keyboard shortcut: "e v")</li> <li> <strong>Show genes using</strong> -- display only those regions with gene annotations in the specified genes track</li> <li> <strong>Enter custom regions as BED, or a URL to them</strong> -- display only those regions entered into the text box in BED format, or listed in a specified BED file</li> <li> <strong>Show one alternate haplotype</strong> -- display the specified alternate haplotype in place on the reference chromosome (human assemblies hg17 and later only)</li> <li> (Optional) Select <strong>Highlight alternating regions in multi-region view</strong> to color alternating slices in blue.</li> </ul> <p> Click <button type="button">submit</button> to save your changes and return to the Genome Browser tracks display.</p> <p> Here is a view of the Genome Browser with the "Show exons" and "Highlight alternating regions" options selected:</p> <p> -<img src="../../images/MultiRegionMouseHighlighted.png" alt="Exon-only screenshot" width="950" +<img src="../../images/multiRegionExample.png" alt="Exon-only screenshot" width="950" height="380"></p> <p> <strong>Navigation and display</strong><br> With a few exceptions, most browser navigation and display features function the same in both multi-region and single-chromosome modes, including zooming in and out, reversing and resizing the view, highlighting and zooming to a selected region, and track search. Searching and zooming conventions differ when displaying custom BED regions. See <a href="#CustomRegions">About Custom Regions</a> for more information.</p> <a name="About"></a> <h2>About the Multi-Region modes</h2> <a name="ExonOnly"></a> <h3>Exon-only mode</h3> <p> @@ -379,24 +379,24 @@ <p> Click <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/ goldenPath/help/examples/sessions/bed12Session.txt">here</a> to view this example in the Genome Browser. To quickly exit multi-region mode and return to the default single chromosome view, use the keyboard shortcut "d v".</p> <a name="Example5"></a> <h3>Example 5. Haplotype</h3> <p> This example shows how the human hg38 haplotype chr1_KI270762v1_alt fits onto chromosome 1. Note that annotations from the standard browser display do not extend into or out of the haplotype region, since haplotypes are annotated separately from regular chromosomes.</p> <p> <img src="../../images/MultiRegionHaplotypeView.png" alt="Multi-Region haplotype view" -width="881" height="344"></p> +width="881" height="359"></p> <p> Click <a href="../../cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/ goldenPath/help/examples/sessions/haplotypeSession.txt">here</a> to view this example in the Genome Browser. To quickly exit multi-region mode and return to the default single chromosome view, use the keyboard shortcut "d v".</p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->