node package manager
Painless code sharing. npm Orgs help your team discover, share, and reuse code. Create a free org »

dotplot

dotplot

This library allows you to create and draw dotplots. In bioinformatics, a dot plot is a graphical method that allows the comparison of two biological sequences and identify regions of close similarity between them. It is a type of recurrence plot. (Source : wikipedia)

install

If you're using node.js and npm, type into a terminal :

$ npm install dotplot --save

If you're using the browser, add to the beginning of your file:

<script src="dotplot.js"></script>

example

var dotplot = require('dotplot')
 
// creates a dotplot for a DNA sequence 
var plot = dotplot.pattern("ATCGATCGCGATCATCGGG".split(''))
// return its data uri 
var uri = dotplot.dataURI(plot)

api

The following methods are available:

pattern

var plot = dotplot.pattern(sequence)

Returns a dotplot of the given sequence. The data returned is formatted to be able to be used with sparse-binary-matrix, also available on npm.

The output dotplot is square.

correlation

var plot = dotplot.pattern(sequence)

Returns a dotplot of correlation between two sequences. The data returned is formatted to be able to be used with sparse-binary-matrix, also available on npm.

The output dotplot is not square.

dataUri

dotplot.dataUri(plot)

Returns a graphic representation of the dotplot in the form of a data URI.

release History

  • 0.1.0 Initial release

license

MIT