README.md

sequencelogo.js - simple sequence logo visualization in Javascript

Description

This is a simple Javascript library that renders a sequence logo into an HTML canvas element, given a PSSM. Advantages:

• small
• cross-browser
• no dependencies on other Javascript libraries
• renders graphics on the fly
• default color sets for nucleotide and peptide sequences

Installation

Simply include the script in your pages with the script tag.

Node.js/NPM

This library is also available as an npm package:

  npm install --save @baliga-lab/sequencelogo.js

Documentation

Official documentation at http://baliga-lab.github.io/sequencelogo.js/

Usage

seqlogo.makeLogo(id, pssm, options);

Parameters

• id: the id of a DOM element. This will be replaced with a canvas element
• pssm: a Javascript object that represents a PSSM. The following format is used:
  • alphabet: list of single character strings
  • values: pssm values, columns correspond to the alphabet characters
• options: a Javascript object containing the following attributes
  • width: canvas width
  • height: canvas height
  • glyphStyle: font used to display the motif characters

Example

seqlogo.makeLogo('mylogo',
                 {
                   alphabet: ['A', 'G', 'C', 'T'],
                   values: [[0.0, 0.1, 0.8, 0.1],
                            ...]
                 },
                 {
                   width: 100, height: 100,
                   glyphStyle: '20pt Helvetica'
                 });