README.md

graphgenomeviewer

Install

The graphgenomeviewer NPM module is a React component that can be installed with yarn or npm

yarn add graphgenomeviewer

Usage with React

import {Graph} from 'graphgenomeviewer'

function App() {
  return (
    <Graph
      graph={{
        nodes: [
          { id: 'id1', length: 5000 },
          { id: 'id2', length: 10000 },
        ],
        links: [{ source: 'id1', target: 'id2', id: 'edge1' }],
      }}
      width={800}
      height={600}
    />
  )
}

or with helper that fetches a GFA file and parses it

import {GFAGraph} from 'graphgenomeviewer'

function App() {
  return (
    <GFAGraph
      url="myfile.gfa"
      width={800}
      height={600}

    />
  )
}

API

Here are all the props for the Graph component

function Graph({
  graph,
  drawPaths = false,
  drawLabels = false,
  colorScheme = 'Rainbow',
  chunkSize = 1000,
  linkSteps = 10,
  sequenceThickness = 10,
  linkThickness = 2,
  theta = 0.9,
  strengthCenter = -50,
  width = 2000,
  height = 1000,
  onFeatureClick = () => {},
}: {
  graph: Graph
  drawPaths?: boolean
  drawLabels?: boolean
  colorScheme?: string
  width?: number
  height?: number
  chunkSize?: number
  linkSteps?: number
  sequenceThickness?: number
  linkThickness?: number
  theta?: number
  strengthCenter?: number
  onFeatureClick?: (arg?: Record<string, unknown>) => void
}) {
  /*...*/
}

The GFAGraph everything is the same except you use either

• a url to a GFA file supplied to the url prop
• a string of GFA data supplied to the data prop

function GFAGraph({
  url,
  data,
  drawPaths = false,
  drawLabels = false,
  colorScheme = 'Rainbow',
  chunkSize = 1000,
  linkSteps = 10,
  sequenceThickness = 10,
  linkThickness = 2,
  theta = 0.9,
  strengthCenter = -50,
  width = 2000,
  height = 1000,
  onFeatureClick = () => {},
}: {
  url: string
  data: string
  drawPaths?: boolean
  drawLabels?: boolean
  colorScheme?: string
  width?: number
  height?: number
  chunkSize?: number
  linkSteps?: number
  sequenceThickness?: number
  linkThickness?: number
  theta?: number
  strengthCenter?: number
  onFeatureClick?: (arg?: Record<string, unknown>) => void
}) {
  /*...*/
}

the Graph type (used by the "Graph" component and not "GFAGraph" since GFAGraph just builds this internally is as follows

export interface Path { name: string path: string }

export interface Node { id: string sequence?: string tags?: Record<string, unknown> cigar?: string length?: number }

export interface Graph { nodes: Node[] links: Link[] paths?: Path[] }