c2d89521bf18225fe182b52e75307aac96e1a9e9 ccpowell Thu Apr 25 14:03:58 2019 -0700 Adding images and updating hgWiggleTrackHelp.html, refs #23300 diff --git src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html index 8936760..b61bb7e 100755 --- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html +++ src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html @@ -77,16 +77,74 @@ <strong>Draw indicator lines</strong>:</p> <ul> <li> <strong>at y=0.0</strong>: Select the "ON" setting to display a line marking the 0.0 position on the graph (default is "OFF").</li> <li> <strong>at y= </strong>: Select the "ON" setting to display a line on the graph at the specified numerical value (defaults are "0" and "OFF"). This line can be used to mark a significant threshold on the graph.</li> </ul> <p> When you have finished making your configuration changes, click the <em>Apply</em> button to preview your changes, or click the <em>Submit</em> button to return to the annotation track display page.</p> +<a name="TRACK_CONT"></a> +<h3>Annotation track display modes</h3> +<p> +Each annotation track within the window may have up to five display modes: +<p> +<ul class="gbsNoBullet"> + <li> + <strong>Hide:</strong> the track is not displayed at all. To hide all the annotation tracks, click + the <em>hide all</em> button. This mode is useful for restricting the display to only those tracks + in which you are interested. For example, someone who is not interested in SNPs or mouse synteny + may want to hide these tracks to reduce track clutter and improve speed. There are a few + annotation tracks that pertain only to one specific chromosome, e.g. Sanger22, Rosetta. In these + cases, the track and its associated controller will be hidden automatically when the track window + is not open to the relevant chromosome.</li> + <li> + <strong>Dense:</strong> the track is displayed with all features collapsed into a single line. + This mode is useful for reducing the amount of space used by a track when you don't need + individual line item details or when you just want to get an overall view of an annotation. For + example, by opening an entire chromosome and setting the RefSeq Genes track to dense, you can get + a feel for the known gene density of the chromosome without displaying excessive detail. <br> + <img src="../../images/wiggle_dense-1.png" width="800px"> + </li> + <li> + <strong>Full:</strong> the track is displayed with each annotation feature on a separate line. It + is recommended that you use this option sparingly, due to the large number of individual track + items that may potentially align at the selected position. For example, hundreds of ESTs might + align with a specified gene. When the number of lines within a requested track location exceeds + 250, the track automatically defaults to a more tightly-packed display mode. In this situation, + you can restore the track display to full mode by narrowing the chromosomal range displayed or by + using a track filter to reduce the number of items displayed. On tracks that contain only hide, + dense, and full modes, you can toggle between full and dense display modes by clicking on the + track's center label.<br> + <img src="../../images/wiggle_full-1.png" width="800px"> + </li> + <li> + <strong>Squish:</strong> the track is displayed with each annotation feature shown separately, but + at 50% the height of full mode. Features are unlabeled, and more than one may be drawn on the same + line. This mode is useful for reducing the amount of space used by a track when you want to view a + large number of individual features and get an overall view of an annotation. It is particularly + good for displaying tracks in which a large number of features align to a particular section of a + chromosome, e.g. EST tracks.<br> + <img src="../../images/wiggle_squish-1.png" width="800px"> + </li> + <li> + <strong>Pack:</strong> the track is displayed with each annotation feature shown separately and + labeled, but not necessarily displayed on a separate line. This mode is useful for reducing the + amount of space used by a track when you want to view the large number of individual features + allowed by squish mode, but need the labeling and display size provided by full mode. When the + number of lines within the requested track location exceeds 250, the track automatically defaults + to squish display mode. In this situation, you can restore the track display to pack mode by + narrowing the chromosomal range displayed or by using a track filter to reduce the number of items + displayed. To toggle between pack and full display modes, click on the track's center label.<br> + + <img src="../../images/wiggle_pack-1.png" width="800px" > + </li> + + + <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->