README.md

NeatCanvasFeatures - a JBrowse plugin.

It applies intron hats and a gradient 'tubular' look to features and subfeatures of CanvasFeatures tracks.

What it does:

• draws intron hats and inverted hats for reverse direction features.
• it applies a gradient 'tubular' look to features and subfeatures, inheriting the feature colors and properties.
• modifies UTR to be a outlined box, inheriting the original color.
• generally functional in stand-alone JBrowse.

Install / Activate:

For JBrowse 1.11.6+, copy the NeatCanvasFeatures directory to the plugins directory. Add this to appropriate trackList.json under the plugins section (create one if it doesn't exist):

"plugins": [
     'NeatCanvasFeatures'
 ],

For Apollo 2.x, copy the NeatCanvasFeatures directory to the web-apps/jbrowse/plugins directory. Add this to web-apps/jbrowse/plugins/WebApollo/json/annot.json:

"plugins" : [
    {
       "location" : "./plugins/WebApollo",
       "name" : "WebApollo"
    },
    {
           "location" : "./plugins/NeatCanvasFeatures",
           "name" : "NeatCanvasFeatures"
    }
],

Config Options:

Gradient Features are ON for all Canvas tracks by default. They can be turned off globally in trackList.json file by setting gradient = 0 in the plugin definition, for example:

"plugins": [
     {
         "name": "NeatCanvasFeatures",
         "gradient": 0
     }
],