jbrowse-plugin-ideogram

jbrowse-plugin-ideogram

Jbrowse 2 plugin for displaying an ideogram

Screenshot

Note

Uses the great https://eweitz.github.io/ideogram/ library for rendering

Usage

In JBrowse Web

Development

git clone https://github.com/cmdcolin/jbrowse-plugin-ideogram
cd jbrowse-plugin-ideogram
yarn
yarn start

Then open JBrowse Web to (assuming it is running on port 3000):

http://localhost:3000/?config=http://localhost:9080/config.json

Production

Add to the "plugins" of your JBrowse Web config:

{
  "plugins": [
    {
      "name": "Ideogram",
      "url": "https://unpkg.com/jbrowse-plugin-ideogram/dist/jbrowse-plugin-ideogram.umd.production.min.js"
    }
  ]
}

Annotations

To annotate features on the ideogram as in the screenshot above, data must be uploaded via the setup screen's open file interface.

• annotations must be uploaded as a TSV with column headers
• enforced location data must be under a heading called 'genome location' and be in the format of 'chromosomeNumber:start-end', e.g. '1:39895426-39902013'
• alternatively, annotation files provided without genome location data will attempt to be cross referenced with a remote file of gene locations
• each row of data must include name
• any external links that wish to be formatted on the widget properly must be in the following format:
  • under a header 'external links'
  • a json string appearing as "[{"name": "MYLINK", "link": "https://my-link.com/"}]"
  • each annotation that you wish to have external links to must have this json string
  • multiple external links are permitted
• annotations can be categorized into two categories if the 'tier' header is within the TSV
  • tier 1 is annotated in blue
  • tier 2 is annotated in red
  • this field is to be provided as a 1 or a 2

examples

TSV with only required headers

name
note1
note2

TSV with optional headers

name  genomeLocation  tier externalLinks
note1 1:39895426-39902013 1 [{"name":"MYLINK","link":"https://my-link.com/note1"}]
note2 1:157573749-157598080 2 [{"name":"MYLINK", "link":"https://my-link.com/note2"}]

Any additional data will be parsed out and displayed in the widget that can be brought out by clicking an annotation on the ideogram.

If these formatting rules are not obeyed the annotations will not be displayed.