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 @@ <li> "Mean" - displays the mean</li> <li> "Minimum" - displays the minimum of all the points to be combined</li> </ul> <p> <strong>Smoothing window</strong>: 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".</p> <p> <strong>Negate values</strong>: 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 <strong>altColor</strong> not <strong>color</strong> as positive values -are.</p> +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.<br> +<img src="../../images/wig_negate-1.png" width="800px" > +</p> <p> <strong>Draw indicator lines (boxed in orange)</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. For example, in the image below, <strong>y=3</strong>.<br> <img src="../../images/wiggle_y-1.png" width="800px" > </li> </ul>