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 @@ Draw indicator lines:

at y=0.0: Select the "ON" setting to display a line marking the 0.0 position on the graph (default is "OFF").
at y= : 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.

When you have finished making your configuration changes, click the Apply button to preview your changes, or click the Submit button to return to the annotation track display page.

+ +

Annotation track display modes

+Each annotation track within the window may have up to five display modes: +

+ Hide: the track is not displayed at all. To hide all the annotation tracks, click + the hide all 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.
+ Dense: 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.
+ +
+ Full: 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.
+ +
+ Squish: 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.
+ +
+ Pack: 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.
+ + +