Developer guide

In this guide, will introduce the JBrowse 2 ecosystem from the developer's point of view. We'll examine the core concepts of how code is packaged and structured, and then go over how to create new plugins and pluggable elements.

Introduction and overview

Let's get a high-level view of the JBrowse 2 ecosystem.

Products and plugins

The JBrowse 2 ecosystem has two main type of top-level artifacts that are published on their own: products and plugins.

Figure: Architecture diagram of JBrowse 2, showing how plugins encapsulate views (e.g. LinearGenomeView, DotplotView etc.), tracks (AlignmentsTrack, VariantTrack, etc.), adapters (BamAdapter, VcfTabixAdapter, etc.) and other logic like mobx state tree autoruns that add logic to other parts of the app (e.g. adding context menus)

A "product" is an application of some kind that is published on its own (a web app, an electron app, a CLI app, etc). jbrowse-web, jbrowse-desktop, and jbrowse-cli are products.

A "plugin" is a package of functionality that is designed to "plug in" to a product at runtime to add functionality. These can be written and published by anyone, not just the JBrowse core team. Not all of the products use plugins, but most of them do.

Also, most of the products are pretty standard in the way they are constructed. For example, jbrowse-web is a React web application that is made with Create React App (CRA), and jbrowse-cli is a command-line tool implemented with OCLIF.

Figure: This figure summarizes the general architecture of our state model and React component tree

Example plugins

You can follow this guide for developing plugins, but you might also want to refer to working versions of plugins on the web now

This repo contains a template for creating new plugins https://github.com/GMOD/jbrowse-plugin-template.

Here are some examples of working plugins.

• jbrowse-plugin-ucsc-api - probably the simplest plugin example, it demonstrates accessing data from UCSC REST API
• jbrowse-plugin-gwas - a custom plugin to display manhattan plot GWAS data
• jbrowse-plugin-biothings-api - demonstrates accessing data from mygene.info, part of the "biothings API" family
• jbrowse-plugin-msaview - demonstrates creating a custom view type that doesn't use any conventional tracks
• jbrowse-plugin-gdc - demonstrates accessing GDC cancer data GraphQL API, plus a custom drawer and track type for coloring variants by impact score

You can use these to see how plugins are generally structured, and can use the pluggable elements in them as templates for your own pluggable elements.

We will go over what plugins do and what is in them now

What's in a plugin

A plugin is an independently distributed package of code that is designed to "plug in" to a JBrowse application.

It's implemented as a class that extends @jbrowse/core/Plugin. It gets instantiated by the application that it plugs into, and it has an install method and a configure method that the application calls. This class is distributed as a webpack bundle that exports it to a namespace on the browser's window object specifically for JBrowse plugins¹.

It's common for a plugin to use its configure method to set up mobx autoruns or reactions that react to changes in the application's state to modify its behavior.

Plugins often also have their install method add "pluggable elements" into the host JBrowse application. This is how plugins can add new kinds of views, tracks, renderers, and so forth.

Pluggable elements

Pluggable elements are pieces of functionality that plugins can add to JBrowse. Examples of pluggable types include:

• Adapters
• Track types
• Renderer types
• Widgets
• RPC calls
• Display types
• View types

In additional to creating plugins that create new adapters, track types, etc. note that you can also wrap the behavior of another track so these elements are composable

For example we can have adapters that perform calculations on the results of another adapter, views that contains other subviews, and tracks that contain other tracks, leading to a lot of interesting behavior. Details and examples below

Adapters

Adapters basically are parsers for a given data format. We will review what adapters the alignments plugin has (to write your own adapter, see creating adapters)

Example adapters: the @jbrowse/plugin-alignments plugin creates multiple adapter types

• BamAdapter - This adapter uses the @gmod/bam NPM module, and adapts it for use by the browser.
• CramAdapter - This adapter uses the @gmod/cram NPM module. Note that CramAdapter also takes a sequenceAdapter as a subadapter configuration, and uses getSubAdapter to instantiate it
• SNPCoverageAdapter - this adapter takes a BamAdapter or CramAdapter as a subadapter, and calculates feature coverage from it

Displays

A display is a method for displaying a particular track in a particular view

For example, we have a notion of a synteny track type, and the synteny track type has two display models

• DotplotDisplay, which is used in the dotplot view
• LinearSyntenyDisplay, which is used in the linear synteny view

This enables a single track entry to be used in multiple view types e.g. if I run jbrowse add-track myfile.paf, this automatically creates a synteny track that can be opened in both a dotplot and a linear synteny view.

Most track types only have a "linear" display available, but one more example is the VariantTrack, which has two display methods

• LinearVariantDisplay - used in linear genome view
• ChordVariantDisplay - used in the circular view

Renderers

Renderers are a new concept in JBrowse 2, and are related to the concept of server side rendering (SSR), but can be used not just on the server but also in contexts like the web worker (e.g. the webworker can draw the features to an OffscreenCanvas). For more info see creating renderers

Example renderers: the @jbrowse/plugin-alignments exports several renderer types

• PileupRenderer - a renderer type that renders Pileup type display of alignments fetched from the BamAdapter/CramAdapter
• SNPCoverageRenderer - a renderer that draws the coverage. Note that this renderer derives from the wiggle renderer, but does the additional step of drawing the mismatches over the coverage track

Track types

Track types are a high level type that controls how features are drawn. In most cases, a track combines a renderer and an adapter, and can do additional things like

• Control what widget pops up on feature click
• Add extra menu items to the track menu
• Create subtracks (See AlignmentsTrack)
• Choose "static-blocks" rendering styles, which keeps contents stable while the user scrolls, or "dynamic-blocks" that update on each scroll

Example tracks: the @jbrowse/plugin-alignments exports multiple track types

• SNPCoverageTrack - this track type actually derives from the WiggleTrack type
• PileupTrack - a track type that draws alignment pileup results
• AlignmentsTrack - combines SNPCoverageTrack and PileupTrack as "subtracks"

Widgets

Widgets are custom info panels that can show up in side panels, modals, or other places in an app

Widgets can do multiple types of things including

• Configuration widget
• Feature detail widget
• Add track widget
• Add connection widget
• etc.

These widgets can be extended via plugins, so for example, the @jbrowse/plugin-alignments extends the BaseFeatureDetailWidget to have custom display of the alignments

• AlignmentsFeatureDetailWidget - this provides a custom widget for viewing the feature details of alignments features that customizes the basic feature detail widget

View types

Creating view types is one of the most powerful features of JBrowse 2, because it allows us to put entirely different visualizations in the same context as the standard linear-genome-view.

We have demonstrated a couple new view types in JBrowse 2 already including

• LinearGenomeView - the classic linear view of a genome
• CircularView - a Circos-like circular whole genome view
• DotplotView - a comparative 2-D genome view
• SvInspectorView - superview containing CircularView and SpreadsheetView subviews
• And more!

We think the boundaries for this are just your imagination, and there can also be interplay between view types e.g. popup dotplot from a linear view, etc.

RPC methods

Plugins can register their own RPC methods, which can allow them to offload custom behaviors to a web-worker or server side process. The Wiggle track for example registers WiggleGetGlobalStats and WiggleGetMultiRegionStats

MenuItems

You can add menus or add items to existing menus in several places.

A MenuItem object defines the menu item's text, icon, action, and other attributes.

Types of MenuItems:

• Normal: a standard menu item that performs an action when clicked
• Checkbox: a menu item that has a checkbox
• Radio: a menu item that has a radio button icon
• Divider: a horizontal line (not clickable) that can be used to visually divide menus
• SubHeader: text (not clickable) that can be used to visually label a section of a menu
• SubMenu: contains menu items, for making nested menus

Name	Description
type	Options are 'normal', 'radio', 'checkbox', 'subMenu', 'subHeader', or 'divider'. If not provided, defaults to 'normal', unless a subMenu attribute is present, in which case it defaults to 'subMenu'.
label	The text for the menu item. Not applicable to 'divider', required for all others.
subLabel	Additional descriptive text for the menu item. Not applicable to 'divider' or 'subHeader', optional for all others.
icon	An icon for the menu item. Must be compatible with Material-UI's Icons. Not applicable to 'divider' or 'subHeader', optional for all others.
disabled	Whether or not the menu item is disabled (meaning grayed out and not clickable). Not applicable to 'divider' or 'subHeader', optional for all others.
checked	Whether or not the checkbox or radio button are selected. Only applicable to 'radio' and 'checkbox'
onClick	Callback of action to perform on click. Function signature is (session) => undefined. Required for 'normal', 'radio', and 'checkbox', not applicable to any others.
subMenu	An array of menu items. Applicable only to 'subMenu'.

As an example, the here is an array of MenuItems and the resulting menu:

;[
  {
    label: 'Normal menu item',
    icon: AddIcon,
    onClick: () => {},
  },
  {
    label: 'Normal',
    subLabel: 'with subLabel',
    icon: AddIcon,
    onClick: () => {},
  },
  {
    label: 'Disabled menu item',
    disabled: true,
    icon: AddIcon,
    onClick: () => {},
  },
  {
    type: 'radio',
    label: 'Radio checked',
    checked: true,
    onClick: () => {},
  },
  {
    type: 'radio',
    label: 'Radio unchecked',
    checked: false,
    onClick: () => {},
  },
  {
    type: 'checkbox',
    label: 'Checkbox checked',
    checked: true,
    onClick: () => {},
  },
  {
    type: 'checkbox',
    label: 'Checkbox unchecked',
    checked: false,
    onClick: () => {},
  },
  { type: 'divider' },
  { type: 'subHeader', label: 'This is a subHeader' },
  {
    label: 'SubMenu',
    subMenu: [
      {
        label: 'SubMenu item one',
        onClick: () => {},
      },
      {
        label: 'SubMenu item two',
        onClick: () => {},
      },
    ],
  },
]

Figure: This screenshot shows all the various track menu options, generated by the code listing

Adding a top-level menu

These are the menus that appear in the top bar of JBrowse Web and JBrowse Desktop. By default there are File and Help menus. You can add your own menu, or you can add menu items or sub-menus to the existing menus and sub-menus.

Figure: In the above screenshot, the `File` menu has several items and an `Add` sub-menu, which has more items. You can have arbitrarily deep sub-menus.

You add menus in the configure method of your plugin. Not all JBrowse products will have top-level menus, though. JBrowse Web and JBrowse Desktop have them, but something like JBrowse Linear View (which is an just a single view designed to be embedded in another page) does not. This means you need to check whether or not menus are supported using isAbstractMenuManager in the configure method. This way the rest of the plugin will still work if there is not a menu. Here's an example that adds an "Open My View" item to the File -> Add menu.

import Plugin from '@jbrowse/core/Plugin'
import { isAbstractMenuManager } from '@jbrowse/core/util'
import InfoIcon from '@material-ui/icons/Info'

class MyPlugin extends Plugin {
  name = 'MyPlugin'

  install(pluginManager) {
    // install MyView here
  }

  configure(pluginManager) {
    if (isAbstractMenuManager(pluginManager.rootModel)) {
      pluginManager.rootModel.appendToSubMenu(['File', 'Add'], {
        label: 'Open My View',
        icon: InfoIcon,
        onClick: session => {
          session.addView('MyView', {})
        },
      })
    }
  }
}

This example uses rootModel.appendToSubMenu. These are all the menu-manipulation methods available on the root model:

appendMenu

Add a top-level menu

Parameters

Name	Description
menuName	Name of the menu to insert.

Return Value

The new length of the top-level menus array

insertMenu

Insert a top-level menu

Parameters

Name	Description
menuName	Name of the menu to insert.
position	Position to insert menu. If negative, counts from the end, e.g. insertMenu('My Menu', -1) will insert the menu as the second-to-last one.

Return Value

The new length of the top-level menus array

appendToMenu

Add a menu item to a top-level menu

Parameters

Name	Description
menuName	Name of the top-level menu to append to.
menuItem	Menu item to append.

Return Value

The new length of the menu

insertInMenu

Insert a menu item into a top-level menu

Parameters

Name	Description
menuName	Name of the top-level menu to insert into.
menuItem	Menu item to insert.
position	Position to insert menu item. If negative, counts from the end, e.g. insertMenu('My Menu', -1) will insert the menu as the second-to-last one.

Return Value

The new length of the menu

appendToSubMenu

Add a menu item to a sub-menu

Parameters

Name	Description
menuPath	Path to the sub-menu to add to, starting with the top-level menu (e.g. ['File', 'Insert']).
menuItem	Menu item to append.

Return value

The new length of the sub-menu

insertInSubMenu

Insert a menu item into a sub-menu

Parameters

Name	Description
menuPath	Path to the sub-menu to add to, starting with the top-level menu (e.g. ['File', 'Insert']).
menuItem	Menu item to insert.
position	Position to insert menu item. If negative, counts from the end, e.g. insertMenu('My Menu', -1) will insert the menu as the second-to-last one.

Return value

The new length of the sub-menu

Adding menu items to a custom track

If you create a custom track, you can populate the track menu items in it using the trackMenuItems property in the track model. For example:

types
  .model({
    // model
  })
  .views(self => ({
    trackMenuItems() {
      return [
        {
          label: 'Menu Item',
          icon: AddIcon,
          onClick: () => {},
        },
      ]
    },
  }))

Note that it is also common to use this scenario, because the base display may implement track menu items so this is like getting the superclasses track menu items

types
  .model({
    // model
  })
  .views(self => {
    const { trackMenuItems: superTrackMenuItems } = self
    return {
      get trackMenuItems() {
        return [
          ...superTrackMenuItems(),
          {
            label: 'Menu Item',
            icon: AddIcon,
            onClick: () => {},
          },
        ]
      },
    }
  })

Adding track context-menu items

When you right-click in a linear track, a context menu will appear if there are any menu items defined for it. It's possible to add items to that menu, and you can also have different menu items based on if the click was on a feature or not, and based on what feature is clicked. This is done by extending the contextMenuItems view of the display model. Here is an example:

class SomePlugin extends Plugin {
  name = 'SomePlugin'

  install(pluginManager) {
    pluginManager.addToExtensionPoint(
      'Core-extendPluggableElement',
      pluggableElement => {
        if (pluggableElement.name === 'LinearPileupDisplay') {
          const { stateModel } = pluggableElement
          const newStateModel = stateModel.extend(self => {
            const superContextMenuItems = self.contextMenuItems
            return {
              views: {
                contextMenuItems() {
                  const feature = self.contextMenuFeature
                  if (!feature) {
                    // we're not adding any menu items since the click was not
                    // on a feature
                    return superContextMenuItems()
                  }
                  return [
                    ...superContextMenuItems(),
                    {
                      label: 'Some menu item',
                      icon: SomeIcon,
                      onClick: () => {
                        // do some stuff
                      },
                    },
                  ]
                },
              },
            }
          })

          pluggableElement.stateModel = newStateModel
        }
        return pluggableElement
      },
    )
  }
}

Configuration model concepts

Configuration slot types

Our configuration system is "typed" to facilitate graphical editing of the configuration. Each configuration has a "schema" that lists what "configuration slots" it has. Each configuration slot has a name, description, a type, and a value.

Here is a mostly comprehensive list of config types

• stringEnum - allows assigning one of a limited set of entries, becomes a dropdown box in the GUI
• color - allows selecting a color, becomes a color picker in the GUI
• number - allows entering any numeric value
• string - allows entering any string
• integer - allows entering a integer value
• boolean
• frozen - an arbitrary JSON can be specified in this config slot, becomes textarea in the GUI
• fileLocation - refers to a URL, local file path on desktop, or file blob object in the browser
• text - allows entering a string, becomes textarea in the GUI
• stringArray - allows entering a list of strings, becomes a "todolist" style editor in the GUI where you can add or delete things
• stringArrayMap - allows entering a list of key-value entries

Let's examine the PileupRenderer configuration as an example.

Example config with multiple slot types

This PileupRenderer config contains an example of several different slot types

import { types } from 'mobx-state-tree'
export default ConfigurationSchema('PileupRenderer', {
  color: {
    type: 'color',
    description: 'the color of each feature in a pileup alignment',
    defaultValue: `jexl:get(feature,'strand') == - 1 ? '#8F8FD8' : '#EC8B8B'`,
    contextVariable: ['feature'],
  },
  displayMode: {
    type: 'stringEnum',
    model: types.enumeration('displayMode', ['normal', 'compact', 'collapse']),
    description: 'Alternative display modes',
    defaultValue: 'normal',
  },
  minSubfeatureWidth: {
    type: 'number',
    description: `the minimum width in px for a pileup mismatch feature. use for
        increasing mismatch marker widths when zoomed out to e.g. 1px or
        0.5px`,
    defaultValue: 0,
  },
  maxHeight: {
    type: 'integer',
    description: 'the maximum height to be used in a pileup rendering',
    defaultValue: 600,
  },
})

Accessing config values

So instead of accessing config.displayMode, we say

readConfObject(config, 'displayMode')

You might also see in the code like this

getConf(track, 'maxHeight')

Which would be equivalent to calling

readConfObject(track.configuration, 'maxHeight')`

Using config callbacks

Config callbacks allow you to have a dynamic color based on some function logic you provide. All config slots can actually become config callback. The arguments that are given to the callback are listed by the 'contextVariable' but must be provided by the calling code (the code reading the config slot). To pass arguments to the a callback we say

readConfObject(config, 'color', { feature })

That implies the color configuration callback will be passed a feature, so the config callback can be a complex function determining the color to use based on various feature attributes

Example of a config callback

We use Jexl to express callbacks. See https://github.com/TomFrost/Jexl for more details.

If you had an variant track in your config, and wanted to make a custom config callback for color, it might look like this

{
  "type": "VariantTrack",
  "trackId": "variant_colors",
  "name": "volvox filtered vcf (green snp, purple indel)",
  "category": ["VCF"],
  "assemblyNames": ["volvox"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "vcfGzLocation": {
      "uri": "volvox.filtered.vcf.gz",
      "locationType": "UriLocation"
    },
    "index": {
      "location": {
        "uri": "volvox.filtered.vcf.gz.tbi",
        "locationType": "UriLocation"
      }
    }
  },
  "displays": [
    {
      "type": "LinearVariantDisplay",
      "displayId": "volvox_filtered_vcf_color-LinearVariantDisplay",
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'type')=='SNV'?'green':'purple'"
      }
    }
  ]
}

This draws all SNV (single nucleotide variants) as green, and other types as purple (insertion, deletion, other structural variant).

Configuration internals

A configuration is a type of mobx-state-tree model, in which leaf nodes are ConfigSlot types, and other nodes are ConfigurationSchema types.

       Schema
    /     |     \
   Slot  Schema  Slot
         |    \
         Slot  Slot

Configurations are all descendants of a single root configuration, which is root.configuration.

Configuration types should always be created by the ConfigurationSchema factory, e.g.

import { ConfigurationSchema } from '@jbrowse/core/utils/configuration'
const ThingStateModel = types.model('MyThingsState', {
  foo: 42,
  configuration: ConfigurationSchema('MyThing', {
    backgroundColor: {
      defaultValue: 'white',
      type: 'string',
    },
  }),
})

An example of a config schema with a sub-config schema is the BamAdapter, with the index sub-config schema

ConfigurationSchema(
  'BamAdapter',
  {
    bamLocation: {
      type: 'fileLocation',
      defaultValue: { uri: '/path/to/my.bam', locationType: 'UriLocation' },
    },
    // this is a sub-config schema
    index: ConfigurationSchema('BamIndex', {
      indexType: {
        model: types.enumeration('IndexType', ['BAI', 'CSI']),
        type: 'stringEnum',
        defaultValue: 'BAI',
      },
      location: {
        type: 'fileLocation',
        defaultValue: {
          uri: '/path/to/my.bam.bai',
          locationType: 'UriLocation',
        },
      },
    }),
  },
  { explicitlyTyped: true },
)

Reading the sub-config schema is as follows

const indexType = readConfObject(config, ['index', 'indexType'])

Alternatively can use

const indexConf = readConfObject(config, ['index'])
indexConf.indexType

However, this may miss default values from the slot, the readConfObject has special logic to fill in the default value

Creating adapters

What is an adapter

An adapter is essentially a class that fetches and parses your data and returns it in a format JBrowse understands.

For example, if you have some data source that contains genes, and you want to display those genes using JBrowse's existing gene displays, you can write a custom adapter to do so. If you want to do a custom display of your data, though, you'll probably need to create a custom display and/or renderer along with your adapter.

What types of adapters are there

• Feature adapter - This is the most common type of adapter. Essentially, it takes a request for a region (a chromosome, starting position, and ending position) and returns the features (e.g. genes, reads, variants, etc.) that are in that region. Examples of this in JBrowse include adapters for BAM and VCF file formats.
• Regions adapter - This type of adapter is used to define what regions are in an assembly. It returns a list of chromosomes/contigs/scaffolds and their sizes. An example of this in JBrowse is an adapter for a chrome.sizes file.
• Sequence adapter - This is basically a combination of a regions adapter and a feature adapter. It can give the list of regions in an assembly, and can also return the sequence of a queried region. Examples of this in JBrowse include adapters for FASTA and .2bit file formats.
• RefName alias adapter - This type of adapter is used to return data about aliases for reference sequence names, for example to define that "chr1" is an alias for "1". An example of this in JBrowse is an adapter for (alias files)[http://software.broadinstitute.org/software/igv/LoadData/#aliasfile]
• Text search adapter - This type of adapter is used to search through text search indexes. Returns list of search results. An example of this in JBrowse is the trix text search adapter.

Note about refname alias adapter: the first column must match what is seen in your FASTA file

Skeleton of a feature adapter

A basic feature adapter might look like this (with implementation omitted for simplicity):

class MyAdapter extends BaseFeatureDataAdapter {
  constructor(config) {
    // config
  }
  async getRefNames() {
    // return refNames used in your adapter, used for refName renaming
  }
  getFeatures(region) {
    // return features from your adapter, using rxjs observable
  }
  freeResources(region) {
    // can be empty
  }
}

So to make a feature adapter, you implement the getRefNames function (optional), the getFeatures function (returns an rxjs observable stream of features, discussed below) and freeResources (optional)

Example feature adapter

To take this a little slow let's look at each function individually

This is a more complete description of the class interface that you can implement

import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
import SimpleFeature from '@jbrowse/core/util/simpleFeature'
import { readConfObject } from '@jbrowse/core/configuration'
import { ObservableCreate } from '@jbrowse/core/util/rxjs'

class MyAdapter extends BaseFeatureDataAdapter {
  // your constructor gets a config object that you can read with readConfObject
  // if you use "subadapters" then you can initialize those with getSubAdapter
  constructor(config, getSubAdapter) {
    const fileLocation = readConfObject(config, 'fileLocation')
    const subadapter = readConfObject(config, 'sequenceAdapter')
    const sequenceAdapter = getSubAdapter(subadapter)
  }

  // use rxjs observer.next(new SimpleFeature(...your feature data....) for each
  // feature you want to return
  getFeatures(region, options) {
    return ObservableCreate(async observer => {
      try {
        const { refName, start, end } = region
        const response = await fetch(
          'http://myservice/genes/${refName}/${start}-${end}',
          options,
        )
        if (response.ok) {
          const features = await result.json()
          features.forEach(feature => {
            observer.next(
              new SimpleFeature({
                uniqueID: `${feature.refName}-${feature.start}-${feature.end}`,
                refName: feature.refName,
                start: feature.start,
                end: feature.end,
              }),
            )
          })
          observer.complete()
        } else {
          throw new Error(`${response.status} - ${response.statusText}`)
        }
      } catch (e) {
        observer.error(e)
      }
    })
  }

  async getRefNames() {
    // returns the list of refseq names in the file, used for refseq renaming
    // you can hardcode this if you know it ahead of time e.g. for your own
    // remote data API or fetch this from your data file e.g. from the bam header
    return ['chr1', 'chr2', 'chr3'] /// etc
  }

  freeResources(region) {
    // optionally remove cache resources for a region
    // can just be an empty function
  }
}

What is needed from a feature adapter

getRefNames

Returns the refNames that are contained in the file, this is used for "refname renaming" and is optional but highly useful in scenarios like human chromosomes which have, for example, chr1 vs 1.

Returning the refNames used by a given file or resource allows JBrowse to automatically smooth these small naming disparities over. See reference renaming

getFeatures

A function that returns features from the file given a genomic range query e.g.

getFeatures(region, options)

The region parameter contains

interface Region {
  refName: string
  start: number
  end: number
  originalRefName: string
  assemblyName: string
}

The refName, start, end specify a simple genomic range. The "assemblyName" is used to query a specific assembly if your adapter responds to multiple assemblies e.g. for a synteny data file or a REST API that queries a backend with multiple assemblies.

The "originalRefName" are also passed, where originalRefName is the queried refname before ref renaming e.g. in BamAdapter, if the BAM file uses chr1, and your reference genome file uses 1, then originalRefName will be 1 and refName will be chr1

The options parameter to getFeatures can contain any number of things

interface Options {
  bpPerPx: number
  signal: AbortSignal
  statusCallback: Function
  headers: Record<string, string>
}

• bpPerPx - number: resolution of the genome browser when the features were fetched
• signal - can be used to abort a fetch request when it is no longer needed, from AbortController
• statusCallback - not implemented yet but in the future may allow you to report the status of your loading operations
• headers - set of HTTP headers as a JSON object

We return an rxjs Observable from getFeatures. This is similar to a JBrowse 1 getFeatures call, where we pass each feature to a featureCallback, tell it when we are done with finishCallback, and send errors to errorCallback, except we do all those things with the Observable

Here is a "conversion" of JBrowse 1 getFeatures callbacks to JBrowse 2 observable calls

• featureCallback(new SimpleFeature(...)) -> observer.next(new SimpleFeature(...))
• finishCallback() -> observer.complete()
• errorCallback(error) -> observer.error(error)

freeResources

This is uncommonly used, so most adapters make this an empty function

Most adapters in fact use an LRU cache to make resources go away over time instead of manually cleaning up resources

Writing your own plugin

JBrowse 2 plugins can be used to add new pluggable elements (views, tracks, adapters, etc), and to modify behavior of the application by adding code that watches the application's state. For the full list of what kinds of pluggable element types plugins can add, see the pluggable elements page.

The first thing that we have is a src/index.js which exports a default class containing the plugin registration code

src/index.js

import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
import Plugin from '@jbrowse/core/Plugin'
import { AdapterClass, configSchema } from './UCSCAdapter'

export default class UCSCPlugin extends Plugin {
  name = 'UCSCPlugin'
  install(pluginManager) {
    pluginManager.addAdapterType(
      () =>
        new AdapterType({
          name: 'UCSCAdapter',
          configSchema,
          AdapterClass,
        }),
    )
  }
}

src/UCSCAdapter/index.ts

import {
  ConfigurationSchema,
  readConfObject,
} from '@jbrowse/core/configuration'
import { ObservableCreate } from '@jbrowse/core/util/rxjs'
import { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
import SimpleFeature from '@jbrowse/core/util/simpleFeature'
import stringify from 'json-stable-stringify'

export const configSchema = ConfigurationSchema(
  'UCSCAdapter',
  {
    base: {
      type: 'fileLocation',
      description: 'base URL for the UCSC API',
      defaultValue: {
        uri: 'https://cors-anywhere.herokuapp.com/https://api.genome.ucsc.edu/',
        locationType: 'UriLocation',
      },
    },
    track: {
      type: 'string',
      description: 'the track to select data from',
      defaultValue: '',
    },
  },
  { explicitlyTyped: true },
)

export class AdapterClass extends BaseFeatureDataAdapter {
  constructor(config) {
    super(config)
    this.config = config
  }

  getFeatures(region) {
    const { assemblyName, start, end, refName } = region
    return ObservableCreate(async observer => {
      const { uri } = readConfObject(this.config, 'base')
      const track = readConfObject(this.config, 'track')
      try {
        const result = await fetch(
          `${uri}/getData/track?` +
            `genome=${assemblyName};track=${track};` +
            `chrom=${refName};start=${start};end=${end}`,
        )
        if (result.ok) {
          const data = await result.json()
          data[track].forEach(feature => {
            observer.next(
              new SimpleFeature({
                ...feature,
                start: feature.chromStart,
                end: feature.chromEnd,
                refName: feature.chrom,
                uniqueId: stringify(feature),
              }),
            )
          })
          observer.complete()
        }
      } catch (e) {
        observer.error(e)
      }
    })
  }

  async getRefNames() {
    const arr = []
    for (let i = 0; i < 23; i++) {
      arr.push(`chr${i}`)
    }
    return arr
  }

  freeResources() {}
}

Adding this track to our configuration

We can create a track.json like this

track.json

{
  "type": "FeatureTrack",
  "trackId": "genehancer_ucsc",
  "name": "UCSC GeneHancer",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "UCSCAdapter",
    "track": "geneHancerInteractionsDoubleElite"
  }
}

Then use the jbrowse CLI tool add-track-json

jbrowse add-track-json file.json

This will automatically add this track to the tracks array of our config.json

Alternatively, we can manually edit this JSON into the config.json.

When we open this track, we should see the GeneHancer regions are drawn as orange blocks.

Creating a custom renderer type

Let's say we want to create a track that connects a gene to it's enhancer. On UCSC the GeneHancer tracks do exactly this. An instance of the UCSC with the GeneHancer tracks is here.

We can see data that we can get for the GeneHancer interactions from the UCSC API like this

curl 'https://api.genome.ucsc.edu/getData/track?genome=hg19;\
track=geneHancerInteractionsDoubleElite;chrom=chr1;start=750000;\
end=505700000'|less

Given that the functionality of rendering arcs is so distinct from UCSC API adaptation, we can actually make this a new plugin. Let's imagine starting a new plugin from scratch again

src/index.js

import Plugin from '@jbrowse/core/Plugin'
import PluginManager from '@jbrowse/core/PluginManager'

import ArcRenderer, {
  configSchema as ArcRendererConfigSchema,
  ReactComponent as ArcRendererReactComponent,
} from './ArcRenderer'

export default class ArcRendererPlugin extends Plugin {
  name = 'ArcPlugin'
  install(pluginManager) {
    pluginManager.addRendererType(
      () =>
        new ArcRenderer({
          name: 'ArcRenderer',
          ReactComponent: ArcRendererReactComponent,
          configSchema: ArcRendererConfigSchema,
          pluginManager,
        }),
    )
  }
}

src/ArcRenderer/index.js

import React from 'react'
// prettier-ignore
import {
  ServerSideRendererType
} from '@jbrowse/core/pluggableElementTypes/renderers/ServerSideRendererType'
import {
  ConfigurationSchema,
  readConfObject,
} from '@jbrowse/core/configuration'

import { PrerenderedCanvas } from '@jbrowse/core/ui'
import { bpSpanPx } from '@jbrowse/core/util'
import {
  createCanvas,
  createImageBitmap,
} from '@jbrowse/core/util/offscreenCanvasPonyfill'

// Our config schema for arc track will be basic, include just a color
export const configSchema = ConfigurationSchema(
  'ArcRenderer',
  {
    color: {
      type: 'color',
      description: 'color for the arcs',
      defaultValue: 'darkblue',
    },
  },
  { explicitlyTyped: true },
)

// This ReactComponent is the so called "rendering" which is the component
// that contains the contents of what was rendered.
export const ReactComponent = props => {
  return (
    <div style={{ position: 'relative' }}>
      <PrerenderedCanvas {...props} />
    </div>
  )
}

// Our ArcRenderer class does the main work in it's render method
// which draws to a canvas and returns the results in a React component
export default class ArcRenderer extends ServerSideRendererType {
  async render(renderProps) {
    const { features, config, regions, bpPerPx, highResolutionScaling } =
      renderProps
    const region = regions[0]
    const width = (region.end - region.start) / bpPerPx
    const height = 500
    const canvas = createCanvas(
      width * highResolutionScaling,
      height * highResolutionScaling,
    )
    const ctx = canvas.getContext('2d')
    ctx.scale(highResolutionScaling, highResolutionScaling)
    for (const feature of features.values()) {
      const [left, right] = bpSpanPx(
        feature.get('start'),
        feature.get('end'),
        region,
        bpPerPx,
      )

      ctx.beginPath()
      ctx.strokeStyle = readConfObject(config, 'color', { feature })
      ctx.lineWidth = 3
      ctx.moveTo(left, 0)
      ctx.bezierCurveTo(left, 200, right, 200, right, 0)
      ctx.stroke()
    }
    const imageData = await createImageBitmap(canvas)
    const reactElement = React.createElement(
      this.ReactComponent,
      {
        ...renderProps,
        width,
        height,
        imageData,
      },
      null,
    )
    return { reactElement, imageData, width, height }
  }
}

The above code is relatively simple but it is fairly quirky. Here are some notes:

• renderers can be run in offscreen or even a node.js canvas, so we do not assume the document.createElement exists to create our canvas, instead using a utility function that makes a OffscreenCanvas or node-canvas (depends on context, e.g. webworker or node.js)
• the "rendering" component contains the results of our renderer. in this case it delegates to the PrerenderedCanvas component, a component we use in other places throughout the codebase

Bringing the two together

We can bring these two contexts together with a new track in our config.json. Remember our previous track.json? Now we can edit it to use our own ArcRenderer

track.json

{
  "type": "BasicTrack",
  "trackId": "genehancer_ucsc",
  "name": "UCSC GeneHancer",
  "assemblyNames": ["hg38"],
  "adapter": {
    "type": "UCSCAdapter",
    "track": "geneHancerInteractionsDoubleElite"
  },
  "renderer": {
    "type": "ArcRenderer"
  }
}

Then add the track

jbrowse add-track-json track.json --update

Creating custom renderers

What is a renderer

In JBrowse 1, a track type typically would directly call the data parser and do it's own rendering. In JBrowse 2, the data parsing and rendering is offloaded to a web-worker or other RPC. This allows things to be faster in many cases. This is conceptually related to "server side rendering" or SSR in React terms.

Figure: Conceptual diagram of how a track calls a renderer using the RPC

Important note: you can make custom tracks types that do not use this workflow, but it is a built in workflow that works well for the core track types in JBrowse 2.

How to create a new renderer

The fundamental aspect of creating a new renderer is creating a class that implements the "render" function. A renderer is actually a pair of a React component that contains the renderer's output, which we call the "rendering" and the renderer itself

class MyRenderer implements ServerSideRendererType {
  render(props) {
    const { width, height, regions, features } = props
    const canvas = createCanvas(width, height)
    const ctx = canvas.getContext('2d')
    ctx.fillStyle = 'red'
    ctx.drawRect(0, 0, 100, 100)
    const imageData = createImageBitmap(canvas)
    return {
      reactElement: React.createElement(this.ReactComponent, { ...props }),
      imageData,
      height,
      width,
    }
  }
}

In the above simplified example, our renderer creates a canvas using width and height that are supplied via arguments, and draw a rectangle. We then return a React.createElement call which creates a "rendering" component that will contain the output

Note that the above canvas operations use an OffscreenCanvas for Chrome, or in other browsers serialize the drawing commands to be drawn in the main thread

What are the props passed to the renderer

The typical props that a renderer receives

export interface PileupRenderProps {
  features: Map<string, Feature>
  layout: { addRect: (featureId, leftBp, rightBp, height) => number }
  config: AnyConfigurationModel
  regions: Region[]
  bpPerPx: number
  height: number
  width: number
  highResolutionScaling: number
}

The layout is available on BoxRendererType renderers so that it can layout things in pileup format, and has an addRect function to get the y-coordinate to render your data at

The features argument is a map of feature ID to the feature itself. To iterate over the features Map, we can use an iterator or convert to an array

class MyRenderer extends ServerSideRendererType {
  render(props) {
    const { features, width, height } = props
    // iterate over the ES6 map of features
    for (const feature in features.values()) {
      // render each feature to canvas or output SVG
    }

    // alternatively
    const feats = Array.from(features.values())
    feats.forEach(feat => {})
  }
}

Adding custom props to the renderer

Note that track models themselves can extend this using their renderProps function

For example the WiggleTrack has code similar to this, which adds a scaleOpts prop that gets passed to the renderer

const model = types
  .compose(
    'WiggleTrack',
    blockBasedTrack,
    types.model({
      type: types.literal('WiggleTrack'),
    }),
  )
  .views(self => {
    const { renderProps: superRenderProps } = self
    return {
      renderProps() {
        return {
          ...superRenderProps(),
          scaleOpts: {
            domain: this.domain,
            stats: self.stats,
            autoscaleType: getConf(self, 'autoscale'),
            scaleType: getConf(self, 'scaleType'),
            inverted: getConf(self, 'inverted'),
          },
        }
      },
    }
  })

Rendering SVG

Our SVG renderer is an example, where it extends the existing built in renderer type with a custom ReactComponent only

export default class SVGPlugin extends Plugin {
  install(pluginManager: PluginManager) {
    pluginManager.addRendererType(
      () =>
        new BoxRendererType({
          name: 'SvgFeatureRenderer',
          ReactComponent: SvgFeatureRendererReactComponent,
          configSchema: svgFeatureRendererConfigSchema,
          pluginManager,
        }),
    )
  }
}

Then, we have our Rendering component just be plain React code. This is a highly simplified SVG renderer just to illustrate

export default function SvgFeatureRendering(props) {
  const { width, features, regions, layout, bpPerPx } = props
  const region = regions[0]

  const feats = Array.from(features.values())
  const height = readConfObject(config, 'height', { feature })
  return (
    <svg>
      {feats.map(feature => {
        // our layout determines at what y-coordinate to
        // plot our feature, given all the other features
        const top = layout.addRect(
          feature.id(),
          feature.get('start'),
          feature.get('end'),
          height,
        )
        const [left, right] = bpSpanPx(
          feature.get('start'),
          feature.get('end'),
          region,
          bpPerPx,
        )
        return <rect x={left} y={top} height={height} width={right - left} />
      })}
    </svg>
  )
}

Notes:

• The above SVG renderer is highly simplified but serves an example, but it shows that you can have a simple React component that leverages the existing BoxRendererType, so that you do not have to necessarily create your own renderer class
• The renderers receive an array of regions to render, but if they are only equipped to handle one region at a time then they can select only rendering to regions[0]

Overriding the renderer's getFeatures method

Normally, it is sufficient to override the getFeatures function in your dataAdapter

If you want to drastically modify the feature fetching behavior, you can modify the renderer's getFeatures call

The base ServerSideRendererType class has a built-in getFeatures function that, in turn, calls your adapter's getFeatures function, but if you need tighter control over how your adapter's getFeatures method is called then your renderer. The Hi-C renderer type does not operate on conventional features and instead works with contact matrices, so the Hi-C renderer has a custom getFeatures function

import { toArray } from 'rxjs/operators'
class HicRenderer extends ServerSideRendererType {
  async getFeatures(args) {
    const { dataAdapter, regions } = args
    const features = await dataAdapter
      .getFeatures(regions[0])
      .pipe(toArray())
      .toPromise()
    return features
  }
}

Creating custom track types

At a high level the track types are just "ReactComponents" that contain rendered track contents. Oftentimes, for custom drawing, we create a renderer instead of a track, but here are some reasons you might want a custom track

• Drawing custom things over the rendered content (e.g. drawing the Y-scale bar in the wiggle track)
• Implementing custom track menu items (e.g. Show soft clipping in the alignments track)
• Adding custom widgets (e.g. custom VariantFeatureWidget in variant track)
• You want to bundle your renderer and adapter as a specific thing that is automatically initialized rather than the BasicTrack (which combines any adapter and renderer)

For examples of custom track types, refer to things like

• HicTrack, which uses a custom HicRenderer to draw contact matrix
• GDCPlugin, which has a custom track type that registers custom feature detail widgets
• VariantTrack, which also registers custom widgets, and has ChordVariantDisplay and LinearVariantDisplay
• SyntenyTrack, which can be displayed with DotplotDisplay or LinearSyntenyDisplay

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1. This means it's only possible to have one version of a particular plugin loaded on any given webpage, even if multiple products are loaded and using it on the same page.↩