fd1449d98ffc991fb02795bc3a5388a83d1d2d98 ccpowell Thu May 2 15:57:35 2019 -0700 editing typo & moving images, refs #23300 diff --git src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html index 8b586e3..920c8f8 100755 --- src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html +++ src/hg/htdocs/goldenPath/help/hgWiggleTrackHelp.html @@ -6,35 +6,35 @@

Configuring graph-based tracks

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.

Display settings

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Type of graph: 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.

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Track height (boxed in blue): To change the default display height of the graph in pixels, type in a value from within the indicated range.

Vertical viewing range (boxed in red): 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".

Data view scaling (boxed in red): 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".

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  • "Mean" - displays the mean
  • "Minimum" - displays the minimum of all the points to be combined

    • Smoothing window: 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".

    Negate values: 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 altColor not color as positive values -e.

    +are.

    Draw indicator lines (boxed in orange):