Wiggle SVG Plot Plugin

Provides the same visualization as the built in XYPlot and Density plot but renders the plot using HTML SVG which is better for PDF/SVG screenshots.

Install

For JBrowse 1.11.6+ in the JBrowse/plugins folder, type:
git clone https://github.com/bhofmei/jbplugin-wigglesvg.git WiggleSVGPlotPlugin

or

downloaded the latest release version at releases.
Unzip the downloaded folder, place in JBrowse/plugins, and rename the folder WiggleSVGPlotPlugin

Activate

Add this to jbrowse.conf under [GENERAL]:

[ plugins.WiggleSVGPlotPlugin ]
location = plugins/WiggleSVGPlotPlugin

If that doesn't work, add this to jbrowse_conf.json:

"plugins" : {
    "WiggleSVGPlotPlugin" : { "location" : "plugins/WiggleSVGPlotPlugin" }
}

DO NOT ADD THE PLUGIN TO BOTH!

Note: The plugin location folder can be named differently, i.e. svgwiggle, but the plugin ID MUST be jbplugin-wigglesvg for the plugin to work correctly.

Test

Sample data is included in the plugin to test that the plugin is working properly. With URL as the URL path to the JBrowse instance, navigate a web browser to URL/index.html?data=plugins/WiggleSVGPlotPlugin/test/data.

Using SVG Wiggle Plots

In general, it is recommended to use XYPlot and Density over the SVGXYPlot and SVGDensity when using the browser. The main purpose of these SVG tracks are for screenshots.

Use the same as normal for XYPlot an Density except change type to WiggleSVGPlotPlugin/View/Track/Wiggle/SVGXYPlot or WiggleSVGPlotPlugin/View/Track/Wiggle/SVGDensity.

Currently, masking of SVGXYPlots and SVGDensity do not work.

Example configuration of SVGXYPlot In trackList.json,

{  
  "key" : "SVG XY Plot",
  "label" : "track_svg_xy",
  "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
  "urlTemplate" : "path/to/bigwig_file.bw",
  "type" : "WiggleSVGPlotPlugin/View/Track/Wiggle/SVGXYPlot"
}

Example configuration of SVGDensity In trackList.json,

{  
  "key" : "SVG Density Plot",
  "label" : "track_svg_dens",
  "storeClass" : "JBrowse/Store/SeqFeature/BigWig",
  "urlTemplate" : "path/to/bigwig_file.bw",
  "type" : "WiggleSVGPlotPlugin/View/Track/Wiggle/SVGDensity"
}

Future plans

• add masking for SVG XY Plot and SVG Density