Pviz
JavaScript Other
Switch branches/tags
Nothing to show
Latest commit abd4197 Sep 13, 2016 @alexmasselot alexmasselot committed on GitHub Merge pull request #11 from lfrohman/master
add cursor position bubble

README.md

#pViz.js: a dynamic JavaScript & SVG library for visualization of protein sequence features

###Head straight for working examples, demo applications and code documentation here

##What is pViz.js? pViz.js is a protein sequence features viewer for modern browsers, based on a JavaScript library, SVG and css.

Given a sequence and a list of positioned features, it displays the sequence and aligns the features to the sequence. Features are layed out to not overlap each other, allowing zooming, interaction and customization.

Default sources can be explicitly defined in JavaScript (sky is the limit), DAS servers, PEFF (PSI extended Fasta format) or any combination of them.

Warning! pViz prefers modern browsers, such as Firefox, Chrome and Safari. Do not expect it to work on IE7, just upgrade.

##Hello World Creating a basic pViz application takes only three steps:

  1. Download two files from github.

    -pviz-bundle.min.js

    -pviz-core.css

  2. Create an HTML file in the directory, with the content shown below.

  3. Open the file in your browser.

.

<head>
  <link rel="stylesheet" type="text/css" href="pviz-core.css">
  <script src="pviz-bundle.min.js"></script>
</head>
<body>
  <div id="main"></div>
  <script>
    var pviz = this.pviz;
    var seqEntry = new pviz.SeqEntry({sequence : 'ABCDEFGIJKLMNOPQRSTUVWXYZ'});
    
    new pviz.SeqEntryAnnotInteractiveView({
      model : seqEntry,
      el : '#main'
      }).render();
      
    seqEntry.addFeatures([
      {category : 'foo', type : 'bar', start : 5, end : 12, text : 'hello'},
      {category : 'foo', type : 'bar', start : 9, end : 15, text : 'world'}]);
  </script>
</body>

Et voilĂ ...The rendered features. In practice, the widget is zoomable

##How does it work? ###Principles A SeqEntry object contains a sequence, a list of features (and whatever you may find convenient for later display).

###Structure

Features are added to the model (if the view is already instanciated, it will be updated once the features are received, thanks to backbone.js). A feature is a JavaScript object (a plain hashmap, though), containing several fields

  • groupSet [optional]: a group of categories which allows features with the same category name, to be grouped at first by groupSet;
  • category: all features from the same category will be handled in the same layer;
  • categoryType [optional]: has no grouping purpose, but allows to define properties among different categories (track height, css);
  • type: within a category, features can have different types, offering the possibility for custom render (default is just a rectangle) or interaction;
  • start: starting position (0 is the first amino acid of the sequence);
  • end: an inclusive end position;
  • text [optional]: text to be be displayed in the default rectangle;
  • Whatever you may need for customized display or interaction.

###Third parties dependencies pViz library uses D3 for SVG generation, backbone.js framework for the model/view framework, Twitter Bootstrap for the css, underscore.js library for convenient utilities, and require.js for dependency management.

But do not worry, including the packaged distribution bundles all of them for you.

##Examples ###The working examples and demo applications can be found here.

####Full documentation can be found here.

Easier than a full documentation, we bring some demonstration use cases:


2 categories, a few features and an interactive view

css depending on category and feature type

drawing special ideograms depending on the feature type

getting more of less extend tracks depending on the category

mouse over, click etc. some feature to see more happen

loading sequence & features from EBI/Uniprot DAS server in an interactive view

ebi/uniprot DAS server is used to populate the sequence, and Pride server to add features and customize the parsing

PSI Extended Fasta Format handles classic fasta information plus annotations

displaying features in a simple, non interactive ideogram (and potentially showing thousands of them on the same page)

the same ideogram, but showing multiple categories at once

NB: download the project locally, at least on your file system, to get javascript executed;

##And more ###A few comments on the code The JavaScript library relies on some "modern" language components. That said, you can either use the bundled library (with all dependencies) or created you own application using require.js and checked out source code.

####Unit testing Via Jasmine, either in the browser (test/index.html) or command line with phantom.js

####Continuous integration Testing, distribution etc. can be launched in a CI environment via grunt tasks grunt test, build...

####Build code documentation JsDoc3 annotations were used to document the library. To generate the doc (in examples/doc directory):

grunt jsdoc

####Build code documentation JsDoc3 annotations were used to document the library. To generate the doc (in examples/doc directory):

###Authors

This library was initiated by Alexandre Masselot (masselot.alexandre@gene.com) & Kiran Mukhyala (mukhyala.kiran@gene.com) within Genentech Bioinformatics & Computational Biology Department.

###Reference Please refer to this library via "Visualization of protein sequence features using JavaScript and SVG with pViz.js - Mukhyala K, Masselot A - Bioinformatics. 2014 Aug"

###License The library is distributed under a BSD license. Full description can be found in LICENSE.txt