Version 0.2.8
The library provides web-based client-side JavaScript visualizations for the KBase project. It also includes a reference server that provides service endpoints for data exchange. The server both transforms data from the KBase API for direct use by the visualization modules and caches data for performance.
The library makes heavy use of the excellent D3.js library, although some novel visualizations are written using native HTML5 technologies such as Canvas and SVG. And just like almost every JavaScript library, it relies on jQuery.
The code is managed with RequireJS for Asynchronous Module Definition (AMD). This allows the separation of various modules and greatly helps in development.
The library includes a distribution mechanism that wraps all the renderers and external dependencies into a single library that can be dropped into any page (see below).
##Dependencies
##Installation Various external modules are managed either through NPM or as Git modules. They can be downloaded and installed by running:
make init
The client-side JavaScript libraries that drive all the visualizations are managed in separate module files using RequireJS, but they can be packaged into a single library that can be dropped into any page. To build that library, run
make dist
Which will, by default, create a minified library as 'dist/datavis.js'. To specify a different output file for the library, use the DISTLIB=/path/to/target.js. To avoid minification (useful for debugging), add MINIFY=0. For example, to create a non-optimized library as /tmp/foo.js, run:
make dist MINIFY=0 DISTLIB=/tmp/foo.js
##Server Deployment The provided server connecting to the KBase API can be started by
node app
This starts the web server at http://0:3000, which shows various widgets that make use of the visualization library. The startup script takes the following options:
--cache: Use a Redis cache for API endpoints (Redis must be running)--debug: Prints debug information, including RPC calls to the API--env: Run in eitherproductionordevelopmentmode (see below). If not set, will fall back on theNODE_ENVenvironment variable.--port: The network port to use
Run node app --help for information on other options.
###Use in Production
The app can be run in production mode, which has a different configuration and serves optimized client code. The optimized code is generated as a copy of the /public directory saved in /build. To generate the optimized code, run:
make build
To run the app in production mode, run
node app --env production
##Usage and Documentation The client-side library can be used on the browser as in the following example:
<!DOCTYPE html>
<head>
<link rel="stylesheet" href="kbase.css" type="text/css">
<script src="datavis.js" type="text/javascript"></script>
<script>
datavis.require(['charts/bar'], function (Chart) {
var chart = new Chart({
element: "body",
// other options
});
chart.setData([ /* Data here */ ]);
chart.render();
});
</script>
</head>
<body>
</body>
Please refer to the API documentation for more information on available renderers and options.
##Changelog ####v0.2.8
- Bug fixes and improvements.
####v0.2.6
- Fixes to distribution file and clean debug.
####v0.2.5
- Select by cluster
- User control of network dynamics
- Updated CSS, checkbox and slider utilities
####v0.2.4
- Network filters
- Network search
- Better integration and coexistence with non-AMD libraries
####v0.2.2
- Bootstrap 3
- Built library now compatible with external libraries
- Small improvements
####v0.1.1
- Minor fixes and improvements
####v0.1.0
- Server-side and client-side error handling.
- Inline help documentation for the workbench apps.
- Added KBase look-and-feel. Integrated FontAwesome for icons.
- Build an optimized distribution package of the library for external use.
- Production environment: Using separate configuration, optimized client-side assets (CSS, JS, HTML).
- Shared templates across apps.
- Network renderer: Hiding nodes, highlighting nodes, colored edges, node labels, performance improvements.
- Manhattan renderer: highlighting loci.
- Heatmap renderer: Axes.
- Various UI enhancements, including dragging of elements like the dock, HUDs, and viewports.
- Genotype Phenotype Workbench: Connected widgets for expression, networks, and function; Gene Pad for inputting custom list of genes, breadcrumbs for entity selection.
- Network Workbench: Defined user story — fetch clusters associated with docked genes, then add cluster members shared with the docked genes having multiple interactions ("co-neighbors"); added cluster table for hiding/unhiding clusters; internal network for docked genes.
- Added viewports with a customizable, auto-hidden toolbox for data export and window controls (rearrange, maximize)
- Improved progress indicators.
- Updated KBase APIs; endpoints managed in environment-specific configuration.
####v0.0.3
- Wrapping widgets in Viewports.
- Heatmap renderer: Auto-resizing based on parent dimensions.
- Manhattan renderer: Axes, labels
- GO Enrichment widget.
- Dropdowns for selection of genomes, experiments, traits.
- Pie and bar chart renderers.
- Handling of asynchronous requests.
- API functionality now maintained in kbase façade object.
- Web caching for API paths.
- Handling of chunked HTTP (Experimental).
####v0.0.2
- Network renderer: introduced dock for anchoring genes, double-clicking to add new nodes, info box on node click.
- Reusable renderer modules.
- Added Bootstrap.
Copyright (c) 2012-2013 Shiran Pasternak, <shiranpasternak at gmail.com>
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