jbrowse-plugin-bedfeaturecoloring

Simple "no-build" ESM plugin for Jbrowse 2, which defines a jexl callback function colorFeature to harness the score and itemRgb columns in a BED file FeatureTrack for enhanced visualisation.

itemRgb is a string containing a comma-separated list of three integer values representing red, green and blue, each in the range 0-255. e.g. "255,0,0" for red.

score is an integer value between 0-1000, which is scaled to a float in the range 0-1 for the alpha component of the color.

Each feature line in the BED file will have its color rendered using these two values.

Quick start

1. Create a local jbrowse-web instance

npx @jbrowse/cli create jbrowse-web
cd jbrowse-web

2. Launch local instance

npx serve . -p 3000

3. Navigate to http://localhost:3000/?config=https://unpkg.com/@haessar/jbrowse-plugin-bedfeaturecoloring@latest/test_config.json in browser to use a test config.json from the latest version of the plugin.

Defining custom tracks

The following template config.json shows how to define a custom BED FeatureTrack to utilise the colorFeature function in its display:

{
  "plugins": [
    {
      "name": "BedFeatureColoring",
      "url": "https://unpkg.com/@haessar/jbrowse-plugin-bedfeaturecoloring"
    }
  ],
  "assemblies": [...],
  "tracks": [
    {
      "type": "FeatureTrack",
      "name": "Colored BED Track",
      "adapter": {
        "type": "BedAdapter",
        "bedLocation": { "uri": "path/to/file.bed" }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "renderer": {
            "type": "SvgFeatureRenderer",
            "color1": "jexl:colorFeature(feature)"
          }
        }
      ]
    }
  ]
}

Contributors

• @haessar
• @tobyweir