483e785a1cef9c2bfe1f08030cbc781f353deffc
lrnassar
  Tue Jun 10 09:01:13 2025 -0700
Doc'ing logoMaf option, refs #34064

diff --git src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
index 2d255c8c9f9..dd1bfe45ed1 100644
--- src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
+++ src/hg/htdocs/goldenPath/help/trackDb/trackDbLibrary.shtml
@@ -2866,30 +2866,40 @@
     <pre>   transformFunc LOG</pre>
 </DIV>
 
 <DIV class="logo"><span class="types bigWig"></span>
 <div class="format"><code>logo on</code></div>
     <P>Enables <a target="_blank" href="https://kundajelab.github.io/dynseq-pages/">
     dynseq display</a>, which graphs the signal as reference base nucleotide letters 
     with their heights equal to the
     signal value within the bigWig track. If not sufficiently zoomed in, the bigWig will
     revert to bars instead of letters by default. See a working example of the <code>logo</code>
     dynseq display on the <a href="../bigWig.html#Ex4" target="_blank">bigWig</a> help page.</p>
     <P><B>Example:</B></P>
     <pre>   logo on</pre>
 </DIV>
 
+<DIV class="logoMaf"><span class="types bigWig"></span>
+<div class="format"><code>logoMaf &lt;url/relativePath&gt;</code></div>
+    <P>The argument to logoMaf is the path to a MAF alignment (either a table or bigMaf). 
+    If set and zoomed into base level the wiggle will be drawn as a sequence logo calculated 
+    by counting the number of each nucleotide aligned to that base which will be scaled by 
+    the value in the wiggle.</p>
+    <P><B>Example:</B></P>
+    <pre>   logoMaf https://hgdownload.soe.ucsc.edu/goldenPath/hg38/multiz470way/multiz470way.bigMaf</pre>
+</DIV>
+
 <DIV class="mouseOverFunction"><span class="types wig bigWig bedGraph"></span>
 <div class="format"><code>mouseOverFunction &lt;noAverage&gt;</code></div>
     <P>Limit mouse over value display to only display the fundamental values
     without any averaging of multiple data points.  Display will show
     "zoom in to see values" when fundamental individual values can not
     be shown.  Useful for tracks where averaging values together is not a
     valid operation.</P>
     <P><B>Example:</B></P>
     <pre>   mouseOverFunction noAverage</pre>
 </DIV>
 
 <DIV class="viewLimits"><span class="types wig bigWig bedGraph"></span>
 <div class="format">
     <code>viewLimits &lt;lower:upper&gt;</code><BR>
     <code>viewLimitsMax &lt;lower:upper&gt;</code></div>