198c9b8daecc44fbda6a6494c566c723920f030a lrnassar Wed Mar 11 18:25:21 2026 -0700 Fixing a few hundred clear typos with the help of Claude. Some are less important in code comments, but majority of them are in user-facing places. I manually approved 60%+ of the changes and didn't see any that were an incorrect suggestion, at worst it was potentially uncessesary, like a code comment having cant instead of can't. No RM. diff --git src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html index 26bcfaeab4e..680bc44a5c2 100755 --- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html +++ src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html @@ -32,45 +32,45 @@ points in the current view, select the "Auto-scale to data view" option. To keep the y=0 value in view at all times when Auto-scale is selected, set "Always include zero" to "ON".</p> <ul> <li>When viewing signal tracks within a composite group use "group auto-scale" to enable having all tracks scaled against the one track in the group that has the highest maximum data points in the current view. For example, below is a side-by-side image of two views of the same data from a selection of cell lines within a composite of related RNA-seq experiments. On the left is the original "auto-scale to data view" setting, where each track is auto-scaled to appear at each track's highest value. And on the right is the new "group auto-scale" setting for the same RNA-seq data where all tracks are scaled against the one track in the region that has the highest value (67215 for IMR9 cell TAP + 1).<br> <img src="../../images/groupAutoScale.png" width='600' alt="Auto-scale comparison"><br> Click this <a href="/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.autoScale" - target="_blank">link</a> to interact with the original "auto-scale to data view" on + target="_blank">link</a> to interact with the original "auto-scale to data view" on the left, and to contrast the results with the new "group auto-scale" click this <a href="/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.groupAutoScale" target="_blank">link</a>. - <li>Note that the "group auto-scale" setting is meant to be turned on and off at the + <li>Note that the "group auto-scale" setting is meant to be turned on and off at the composite group track set level, but you can toggle individual tracks. For instance, click the second "group auto-scale" session <a href="/cgi-bin/hgTracks?hgS_doLoadUrl=submit&hgS_loadUrlName=http://genome.ucsc.edu/goldenPath/help/examples/sessions/session.groupAutoScale" target="_blank">link</a> that has all tracks adjusted to the highest value (67215 for IMR9 cell TAP + 1). If you right-click that individual highest track and instead of configuring the track set, select to configure only the subtrack IMR9 cell TAP + 1 from "group auto-scale" to "auto-scale to data view" and select OK and then refresh your browser window (or click one of the "refresh" buttons on the screen) you will see all the tracks adjust to the next-highest track within all tracks - still tagged to display "group auto-scale" (39320 for IMR9 cell + 1).</li> + still tagged to display "group auto-scale" (39320 for IMR9 cell + 1).</li> </ul> <p> <strong>Vertical viewing range (boxed in red)</strong>: The min and max values specify the vertical portion of the graph that is displayed (default range is 30-70). These numbers can be used to set data threshold indicators. For example, to display only those GC values greater than 50 percent, set the min value to "50".</p> <p> <strong>Transform function</strong>: Transforms the data points by the function selected in the drop-down menu. Usually the default setting is "None".</p> <p> <strong>Windowing function</strong>: When a view is too large to show individual data values, the values must be combined to produce a plot point. This option specifies the combining function to be used (default is "Mean"):</p> <ul> <li> @@ -146,36 +146,36 @@ histogram-like image. <br> <img src="../../images/wiggle_full-1.png" width="800px"> </dd> <dt>Hide</dt> <dd>The track is not displayed at all. To hide all the annotation tracks, click the <em>hide all</em> button.</dd> </dl> <h3>Overlay method</h3> <p> Note that not all graph-based tracks include the Overlay options.</p> <dl class="gbsNoBullet"> <dt>Transparent</dt> <dd>This setting displays the colored - transparent graphs of multiple subtracks overlayed in the same vertical space.<br> + transparent graphs of multiple subtracks overlaid in the same vertical space.<br> <img src="../../images/trans_encode-1.png" width="800px" height="100px"> </dd> <dt>Solid</dt> <dd>This setting displays the colored opaque graphs of multiple subtracks - overlayed in the same vertical space.<br> + overlaid in the same vertical space.<br> <img src="../../images/encode_solid-1.png" width="800px" height="100px"> </dd> <dt>Stacked</dt> <dd>This setting displays each graph stacked on top of each other where the high point of the graph is the sum of all the values.<br> <img src="../../images/encode_stack-1.png" width="800px" height="100px"> </dd> <dt>None</dt> <dd>This setting displays each graph in its own vertical space. <br> <img src="../../images/encode_none-1.png" width="800px" height="130px"> </dd> </dl>