d92fae77c81b3969405c288413a30f675ec324c3 brianlee Wed Jul 7 09:54:40 2021 -0700 Adding a note about altColor on the wiggle.html page from MLQ input refs #27753 diff --git src/hg/htdocs/goldenPath/help/wiggle.html src/hg/htdocs/goldenPath/help/wiggle.html index 3a60bd1..538ea71 100755 --- src/hg/htdocs/goldenPath/help/wiggle.html +++ src/hg/htdocs/goldenPath/help/wiggle.html @@ -171,31 +171,33 @@ <strong>smoothingWindow=</strong>off|2-16</em></code></pre> <p> The track type with version is REQUIRED, and it currently must be <em>wiggle_0</em>:</p> <pre><code><strong>type wiggle_0</strong></code></pre> <p> The remaining values are OPTIONAL:</p> <pre><code><strong>name </strong><em><trackLabel> </em> # default is "User Track" <strong>description </strong><em><centerLabel> </em> # default is "User Supplied Track" <strong>visibility </strong><em><full|dense|hide> </em> # default is hide <strong>color </strong><em><RRR,GGG,BBB> </em> # default is 255,255,255 <strong>altColor </strong><em><RRR,GGG,BBB> </em> # default is 128,128,128 <strong>priority </strong><em><N> </em> # default is 100</code></pre> <p> For a list of additional options, see the <a href="bigWig.html#optional">bigWig format</a> page. Note that bigWig files created from bedGraph cannot be converted to wiggle using <code>bigWigToWig</code> -and instead will be reverted back to their original bedGraph format.</p> +and instead will be reverted back to their original bedGraph format. Also, for tracks using <code>altColor</code> +with the windowing function "mean+whiskers" the shading of colors will be impacted with lighter shades for values +a standard deviation around the mean, most noticeable when zoomed out and average calculations are taking place.</p> <h2>Examples</h2> <p> This example specifies 19 separate data points in <b>two tracks</b> (the first is <code>name="variableStep"</code> and the second is <code>name="fixedStep"</code> where <code>priority=</code> orders them) in the region chr19:49,304,200-49,310,700. To view this example as a custom track in the Genome Browser, copy the <a href="examples/wiggleExample.txt">text</a> and paste it into the "Add Custom Tracks" text box.</p> <p> <pre><code>browser position chr19:49304200-49310700 browser hide all # 150 base wide bar graph at arbitrarily spaced positions, # threshold line drawn at y=11.76 # autoScale off viewing range set to [0:25] # priority = 10 positions this as the first graph