5b7f712d3aa7c7843ba13018b4337cdb8288e19c
ccpowell
Fri Apr 12 15:20:19 2019 -0700
Adding images to hgTracksHelp.html, refs #23285
diff --git src/hg/htdocs/goldenPath/help/hgTracksHelp.html src/hg/htdocs/goldenPath/help/hgTracksHelp.html
index 3d4edbf..6ba09a3 100755
--- src/hg/htdocs/goldenPath/help/hgTracksHelp.html
+++ src/hg/htdocs/goldenPath/help/hgTracksHelp.html
@@ -399,57 +399,65 @@
-
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.
+ 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.
+ 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.
+ 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.
+ displayed. To toggle between pack and full display modes, click on the track's center label.
+
+
The track display controls are grouped into categories that reflect the type of data in the track,
e.g., Gene Prediction Tracks, mRNA and EST tracks, etc. To change the display mode for a track, find
the track's controller in the Track Controls section at the bottom of the Genome Browser page,
select the desired mode from the control's display menu, and then click the refresh button.
Alternatively, you can change the display mode by using the Genome Browser's
right-click navigation feature, or can toggle between dense and full
modes for a displayed track (or pack mode when available) by clicking on the optional center label
for the track.
Changing the display mode for a group of tracks
Track display modes may be set individually or as a group on the Genome Browser Track Configuration
page. To access the configuration page, click the configure button on the annotation tracks