https://github.com/iLambda/dotplot

A library which provides helpers to draw dotplots.
https://github.com/iLambda/dotplot

Last synced: 4 months ago
JSON representation

A library which provides helpers to draw dotplots.

• Host: GitHub
• URL: https://github.com/iLambda/dotplot
• Owner: iLambda
• License: mit
• Created: 2016-03-06T14:11:45.000Z (over 8 years ago)
• Default Branch: master
• Last Pushed: 2016-03-17T00:36:48.000Z (over 8 years ago)
• Last Synced: 2024-03-17T11:04:44.557Z (4 months ago)
• Language: JavaScript
• Size: 123 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

Lists

• repo-5916-awesome-genome-visualization - iLambda/Dotplot
• awesome-genome-visualization - iLambda/Dotplot

README

        
# 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](https://en.wikipedia.org/wiki/Dot_plot_(bioinformatics)))

## install

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

```sh

$ npm install dotplot --save

```

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

```html

```

## example

```js

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

```js

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](https://github.com/iLambda/sparse-binary-matrix), also [available on npm](https://www.npmjs.com/package/sparse-binary-matrix).

The output dotplot is square.

### correlation

```js

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](https://github.com/iLambda/sparse-binary-matrix), also [available on npm](https://www.npmjs.com/package/sparse-binary-matrix).

The output dotplot is not square.

### dataUri

```js

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](http://opensource.org/licenses/MIT)