6a1988273860acb652ac951a47562181560080a4 ccpowell Mon Apr 29 16:13:23 2019 -0700 Adding images to hgWiggleHelp.html, refs #23300 diff --git src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html index b61bb7e..99f9bd5 100755 --- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html +++ src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html @@ -1,150 +1,151 @@ <!DOCTYPE html> <!--#set var="TITLE" value="Genome Browser Wiggle Tracks" --> <!--#set var="ROOT" value="../.." --> <!-- Relative paths to support mirror sites with non-standard GB docs install --> <!--#include virtual="$ROOT/inc/gbPageStart.html" --> <!-- Graph-Based Track Help Page --> <a name="Topic5"></a><br> <h1>Configuring graph-based tracks</h1> <p> Genome Browser graph-based tracks may be configured in a variety of ways to highlight different aspects of the displayed information. Some track types, such as BAM tracks and certain gene tracks, offer dynamic calculation of items in the current window to display a density graph where the height is proportional to the number of items mapped to each genomic position. The following information explains each of the available configuration options.</p> <p> <strong>Overlay method</strong>: The default "transparent" setting displays the colored transparent graphs of multiple subtracks overlayed in the same vertical space. The "solid" setting displays the colored opaque graphs of multiple subtracks overlayed in the same vertical space. The "stacked" setting displays each graph stacked on top of each other where the high point of the graph is the sum of all the values. The "none" setting displays each graph in its own vertical space. Note that not all graph-based tracks include this option.</p> <p> <strong>Type of graph</strong>: The default "Bar" setting depicts the graph data using color-filled bars. To view the data as a series of points or lines, select the "Points" setting.</p> <p> +<img src="../../images/conf_encode.png" width="800px"> <strong>Track height</strong>: To change the default display height of the graph in pixels, type in a value from within the indicated range.</p> <p> <strong>Vertical viewing range</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>Data view scaling</strong>: The default "Use vertical viewing range setting" option displays the data using the parameters specified in the Vertical viewing range setting. To configure the graph to automatically scale to a range defined by the minimum and maximum data 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> <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> "Mean+whiskers" - displays the mean in a dark shade, one standard deviation around the mean in a medium shade, and the maximum/minimum in a light shade. For bar graphs only the mean, the mean plus a standard deviation, and the max are visible. This mode is not available if the Overlay method is stacked.</li> <li> "Maximum" - displays the maximum value of all the points to be combined</li> <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 e.</p> <p> <strong>Draw indicator lines</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.</li> </ul> <p> When you have finished making your configuration changes, click the <em>Apply</em> button to preview your changes, or click the <em>Submit</em> button to return to the annotation track display page.</p> <a name="TRACK_CONT"></a> <h3>Annotation track display modes</h3> <p> Each annotation track within the window may have up to five display modes: <p> <ul class="gbsNoBullet"> <li> <strong>Hide:</strong> the track is not displayed at all. To hide all the annotation tracks, click the <em>hide all</em> button. This mode is useful for restricting the display to only those tracks in which you are interested. For example, someone who is not interested in SNPs or mouse synteny may want to hide these tracks to reduce track clutter and improve speed. There are a few annotation tracks that pertain only to one specific chromosome, e.g. Sanger22, Rosetta. In these cases, the track and its associated controller will be hidden automatically when the track window is not open to the relevant chromosome.</li> <li> <strong>Dense:</strong> the track is displayed with all features collapsed into a single line. This mode is useful for reducing the amount of space used by a track when you don't need individual line item details or when you just want to get an overall view of an annotation. For example, by opening an entire chromosome and setting the RefSeq Genes track to dense, you can get a feel for the known gene density of the chromosome without displaying excessive detail. <br> <img src="../../images/wiggle_dense-1.png" width="800px"> </li> <li> <strong>Full:</strong> the track is displayed with each annotation feature on a separate line. It is recommended that you use this option sparingly, due to the large number of individual track items that may potentially align at the selected position. For example, hundreds of ESTs might align with a specified gene. When the number of lines within a requested track location exceeds 250, the track automatically defaults to a more tightly-packed display mode. In this situation, you can restore the track display to full mode by narrowing the chromosomal range displayed or by using a track filter to reduce the number of items displayed. On tracks that contain only hide, dense, and full modes, you can toggle between full and dense display modes by clicking on the track's center label.<br> <img src="../../images/wiggle_full-1.png" width="800px"> </li> <li> <strong>Squish:</strong> the track is displayed with each annotation feature shown separately, but at 50% the height of full mode. Features are unlabeled, and more than one may be drawn on the same line. This mode is useful for reducing the amount of space used by a track when you want to view a large number of individual features and get an overall view of an annotation. It is particularly good for displaying tracks in which a large number of features align to a particular section of a chromosome, e.g. EST tracks.<br> <img src="../../images/wiggle_squish-1.png" width="800px"> </li> <li> <strong>Pack:</strong> the track is displayed with each annotation feature shown separately and labeled, but not necessarily displayed on a separate line. This mode is useful for reducing the amount of space used by a track when you want to view the large number of individual features allowed by squish mode, but need the labeling and display size provided by full mode. When the number of lines within the requested track location exceeds 250, the track automatically defaults to squish display mode. In this situation, you can restore the track display to pack mode by narrowing the chromosomal range displayed or by using a track filter to reduce the number of items displayed. To toggle between pack and full display modes, click on the track's center label.<br> <img src="../../images/wiggle_pack-1.png" width="800px" > </li> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->