cc108658460e00acfb5380658d844e82a1c72a1f ccpowell Fri May 3 10:26:28 2019 -0700 Adding negate values image & text to hgWiggle docs, refs #23300 diff --git src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html index 920c8f8..282c654 100755 --- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html +++ src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html @@ -55,31 +55,36 @@

"Mean" - displays the mean

"Minimum" - displays the minimum of all the points to be combined

Smoothing window: When set to a numerical value, this option determines the size, in pixels, of a smoothing window to be passed over the plot to smooth the edges of the bars or lines. This is equivalent to a trend line calculation on the graph. The default setting is "OFF".

Negate values: When checked, all values in the wiggle are negated, meaning that positive values become negative and vice-versa. This is useful for wiggles representing transcription or other activities on the Crick strand. Be aware that wiggles with negative values are drawn in altColor not color as positive values -are.

+are.The below image shows ENCODE RNA-seq data around two genes on different strands, SIRT1 and +HERC4, with a minus signal track using Negate values to flip the wiggle display to emphasize HERC4 +expresses on the minus strand. This image also displays the signal graphed in points and a +smoothing window of 16 pixels.
+

Draw indicator lines (boxed in orange):

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. For example, in the image below, y=3.