README.md

WashU Epigenome Browser embedding code boilerplate

Installation

yarn add wuepgg

or

npm install --save wuepgg

Basic Example

Render some tracks with URLs

import { GenomeViewer } from "wuepgg";

<GenomeViewer
  viewRegion="chr7:27181545-27245617"
  tracks={[
    {
      url: "https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/combined.hic",
      name: "hictest",
      type: "hic",
    },
    {
      url: "https://vizhub.wustl.edu/hubSample/hg19/bam1.bam",
      name: "bamtest",
      type: "bam",
    },
    {
      name: "gencodeV47",
      type: "geneannotation",
    },
  ]}
  genomeName="hg19"
/>

See below for the full list of supported parameters.

Render the entire browser as a react component

import { GenomeHub } from "wuepgg";

<GenomeHub />

Render the browser's landing page where user can choose a genome to view

API Reference

GenomeViewer

A React component for visualizing genomes

Props:

• genomeName (string, required)
  Name of the genome to display (e.g., "hg38", "mm10").
  Example: "hg38"

• tracks (TracksProps[], required)
  An array of track configuration objects. Each object describes a data track to display in the viewer.

  TypeScript interface:

  interface TracksProps {
    url?: string; // Optional: Data file URL, (track types such as geneannotation, ruler do not need a URL)
    name?: string; // Optional: Legend display name
    options?: { [key: string]: any }; // Optional: Track-specific options (e.g., color)
    type: string; // Required: Track type (e.g., "ruler", "bam", "hic", "geneannotation", "bigwig", "longrange"...)
  }

  Example:

  [
    {
      "type": "track_type1",
      "name": "track_name1",
      "url": "track_url1",
      "options": {}
    },
    {
      "type": "track_type2",
      "name": "track_name2",
      "url": "track_url2",
      "options": {}
    }
  ]

  For more details on track formatting, see the Epigenome Gateway Datahub documentation.

• viewRegion (string, optional)
  Genomic region to display, as a string.

  Template:

  "chr<chromosome>:<start>-<end>"
  

  Example:

  "chr7:27053397-27373765"
  

  Default: Uses the genomeConfig’s default region if not provided.

• windowWidth (number, optional)
  Width of the genome viewer in pixels.
  Default: 1200

• customGenome (any, optional)
  Optional custom genome object if the user created their own genome matching the current formatting.

GenomeHub

A React component that renders the full genome browser interface.
No props are required.
Future updates will add options for customizing the appearance and behavior of the browser.