Customizing feature colors with callbacks and plugins

If you have a color callback that has a lot of logic in it, then using jexl to express all that logic may be hard. Instead, you can make a small plugin which adds a function to the jexl language, and call that function in your jexl callback.

For example, create a file named "myplugin.js" (see also Footnote 1)

export default class MyPlugin {
  name = 'MyPlugin'
  version = '1.0.0'
  install() {}
  configure(pluginManager) {
    pluginManager.jexl.addFunction('colorFeature', feature => {
      let type = feature.get('type')
      if (type === 'CDS') {
        return 'red'
      } else if (type === 'exon') {
        return 'green'
      } else {
        return 'purple'
      }
    })
  }
}

Then put myplugin.js in the same folder as your config file, and then you can use the custom jexl function in your config callbacks as follows:

{
  "plugins": [
    {
      "name": "MyPlugin",
      "esmLoc": { "uri": "myplugin.js" }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "my_track",
      "name": "my track",
      "assemblyNames": ["hg19"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffLocation": {
          "uri": "volvox.filtered.gff"
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "mytrack-LinearBasicDisplay",
          "renderer": {
            "type": "SvgFeatureRenderer",
            "color1": "jexl:colorFeature(feature)"
          }
        }
      ]
    }
  ]
}

The feature in the callback is a "SimpleFeature" type object, and you can call feature.get('start'), feature.get('end'), feature.get('refName'), or feature.get('other_attribute') for e.g. maybe a field in a GFF3 column 9

See our no-build plugin tutorial for more info on setting up a simple plugin for doing these customizations.

Footnote 1

myplugin.js does not have to use the jbrowse-plugin-template if it is small and self-contained like this, and does not import other modules. If you import other modules from your plugin, then it can be worth it to use the jbrowse-plugin-template.

Footnote 2

If you are using embedded, there are also other methods of including plugins, see https://jbrowse.org/storybook/lgv/main/?path=/story/using-plugins--page