50879a38007a5d65c7212f08a4050b36addee76a jcasper Mon Apr 15 16:04:43 2019 -0700 Cleaning up a few HTML tags while trying to track down bug, refs #23323 diff --git src/hg/htdocs/inc/hgCollectionHelpInclude.html src/hg/htdocs/inc/hgCollectionHelpInclude.html index cbce744..eb9ebb1 100755 --- src/hg/htdocs/inc/hgCollectionHelpInclude.html +++ src/hg/htdocs/inc/hgCollectionHelpInclude.html @@ -11,31 +11,31 @@ <h6><a href="#GetStarted">Getting Started</a></h6> <ul> <li><a href="#AddCollection">Create a new collection</a></li> <li><a href="#AddTracks">Add tracks to a collection</a></li> <li><a href="#BrowserOptions">Browser viewing options</a></li> <li><a href="#Configure">Configure collection</a></li> <li><a href="#SaveAndShare">Saving and sharing collections</a></li> </ul> <h6><a href="#Support">Resources and Support</a></h6> <a name="Intro"></a> <h2>Introduction</h2> <p>The <a href="../cgi-bin/hgCollection">Track Collection Builder</a> (My Data > Track Collection Builder) is a tool that allows multiple tracks to be copied and grouped together into one composite -track</a> or "collection." A +track or "collection." A <a href="../goldenPath/help/trackDb/trackDbHub.html#compositeTrack" target="_blank" >composite track</a> can be thought of as a container for grouping a set of similar-type annotation tracks. </p> <a name="Video"></a> <h3> Quick video demo</h3> <p>Two-minute video demo of Track Collection Builder:</p> <p><iframe width="560" height="315" src="https://www.youtube.com/embed/2_RiIY07omY?rel=0" frameborder="0" allow="accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture" allowfullscreen></iframe> </p> <a name="SupportedData"></a> <h3>Supported Data Types</h3> <p> Only the following continuous-value graphing track types can be added to a collection:</p> <ul> <li><a href="../goldenpath/help/wiggle.html" target="_blank">Wiggle Track Format (WIG)</a></li> @@ -151,43 +151,43 @@ magnitude at the top of the subtracks in the collection where magnitude reflects the total number of pixels set when drawing each track. </p> </ul> <p> <strong>Tip:</strong> Displaying collection names in the browser:</p> <div class="row"> <!-- Left column --> <div class="col-md-4" > <p> <img src="../../images/hgCollectionMouseOver.jpg" alt="hgCollection Mouse-over in browser window.jpg"></p> </div> <!-- end left column --> <!-- Middle column --> - </br> + <br> <div class="col-md-4" style="background-color:#eef0f2;"> <p> Once a collection has been created and tracks have been added to it, click <button class="gbButtonGo" type="button">GO</button> (upper right) to view the collection in the browser window. In the browser, mouse-over the gray vertical buttons at the left window frame to - see the name of each collection.</p></br> + see the name of each collection.</p><br> </div> <!-- end middle column --> <!-- Right column --> <div class="col-md-4"> <p></p> </div> <!-- end right column --> -</div> <!-- end row --></br> +</div> <!-- end row --><br> <a name="Configure"></a> <h3>Step 4: Configure collection</h3> <ul> <li><strong>Track Color:</strong></li> <p> Track color for all subtracks in a collection can be set by double-clicking the collection folder in the right window of the Track Collection Builder, which will display a pop-up dialog box. In the pop-up, a color can be set for the subtracks in the collection. Color will be applied as a gradient to subtracks in the collection (e.g., if red is selected, the subtrack graphs will appear in varied shades of red within the browser window).</p> <p> To revert back to the original track color, change the color picker to '#000000'. To change the track color to black rather than any non-black original color, set the color picker to any shade of black besides '#000000', such as '#000001'. For example, if a track's original color is @@ -219,49 +219,49 @@ <dt>Subtract</dt> <dd>The first (top) subtrack is subtracted from the sum of the others. Note: Re-order collection subtracks in the 'Collected Tracks' pane to change which subtract is at the top. For this 'subtract' view, there is also the option to configure how missing data are treated (see section below).</dd> </dl> <div class="row"> <!-- Left column --> <div class="col-md-4" > <p> <img src="../../images/hgCollectionMergeMethod.jpg" alt="hgCollection drop-down options for Merge Method "></p> </div> <!-- end left column --> <!-- Middle column --> - </br> + <br> <div class="col-md-4" style="background-color:#eef0f2;"> <p>Tracks in collections can be displayed with <a href="/goldenpath/help/trackDb/trackDbHub.html#multiWig" target="_blank"> multiWig aggregate/overlay</a> "merge" methods (stacked, transparent, etc.) as well - as new add & subtract options.</p></br> + as new add & subtract options.</p><br> </div> <!-- end middle column --> <!-- Right column --> <div class="col-md-4"> <p></p> </div> <!-- end right column --> - </div> <!-- end row --></br> + </div> <!-- end row --><br> <li><strong>Missing data treatment:</strong></li> <dl> <dt>Missing=0</dt> <dd>Default setting. Missing data are replaced with a 0 (zero). Graphing will be drawn at the zero point for the x-axis and y-axis (0,0). - </br><i>Note: </i>Calculations (where 'Merge Method' = 'Add' or 'Subtract') will use a zero + <br><i>Note: </i>Calculations (where 'Merge Method' = 'Add' or 'Subtract') will use a zero in the arithmetic.</dd> <dt>Missing=missing</dt> <dd>Graphing will not be drawn for missing data points. Where data are missing for any point in the calculation, the calculated result for that position point will be missing.</dd> </dl> </ul> <a name="SaveAndShare"></a> <h3>Step 5: Saving and sharing collections</h3> <p> Collections will be available 48 hours before expiring. You must <a href="../goldenPath/help/hgSessionHelp.html#Create" target="_blank">save your session</a> to preserve collections long-term and to allow <a href="../goldenPath/help/hgSessionHelp.html#Share" target="_blank">sharing</a>. Even after saving collections and their configurations in a session, it is still highly recommended