The figure was generated by (i) clustering the original networks observed at each time point; (ii) generating and clustering the bootstrap replicate networks for each time point; (iii) determining significance of the clustering for at each time point; and finally to reveal stories in the network data and connect the changes between time points (iv) generating an alluvial diagram.
The technology used to generate biological networks is not and can't be very accurate, "medium" accuracy -for yeast two-hybrid screening of protein-protein interactions, as an example, - is on the order of 50% false positives. A recent article in PNAS titled, "Missing and Spurious Interactions and the Reconstruction of Complex Networks" by Guimera et al. outlines a method to accurately analyze different types of complex networks. It strongly relies on the fact that the nodes in networks can be organized into groups. Group membership governs which nodes can interact.
Many other simpler data visualization tools and methods exist suitable to other specific data-rich applications. IBM's Many Eyes site provides a variety of ways to analyze text, maps, trends and relationships among data points.
Bubble diagrams (also known as bubble charts and spray diagrams) are centered around one (like mind maps) or more concepts. They can then be used to compare and contrast concepts, and identify the common ground and the areas of difference. Diagramic builds such diagrams from spreadsheets and text files.
World Wibe Web makes huge quantities of information readily available."How do you take a big collection of things and make sense out of it?" asks Gary Flake, founder and director of Microsoft Live Labs designing experimental Web tools. The lab's answer to this question is Pivot, a tool recently released to the public - see a demonstration Flake gave at the TED conference in Long Beach, CA.
AnyChart is a flexible Flash based solution that allows you to create interactive and great looking flash charts.
Axiis is a Data Visualization Framework for Flex. It has been designed to be a concise, expressive, and modular framework that let developers and designers create compelling data visualization solutions.
BirdEye is a community project to advance the design and development of a comprehensive open source information visualization and visual analytics library for Adobe Flex. The actionscript-based library enables users to create multi-dimensional data visualization interfaces for the analysis and presentation of information.
Degrafa is a declarative graphics framework for creating rich user interfaces, data visualization, mapping, graphics editing and more.
DojoX Data Chart
An addition in the Dojo 1.3 release is the new dojox.charting class. Its primary purpose is to make connecting a chart to a Data Store a simple process.
Dundas provides a wide range of data visualization solutions for Microsoft technologies. They offer a number of data visualization tools including: Chart, Gauge, Map and Calendar for .net and Dashboards for Silverlight.
Flex has built in chart controls: area, bar, bubble, candlestick, column, HLOCC, Line, Pie, Plot.
Flex uses FXG, a graphical interchange format developed by Adobe and is similar in many ways to SVG. Nice article here by James Whittaker looking at FXG and Degrafa. See quick tutorial and article on Creating Visual Experiences with Flex 3.0.
FlexMonster Pivot Table and Charts
Flexmonster provides Pivot table Flex/Flash components rich internet application (RIA) development services.
Animated flash charts for web apps.
Google Chart API
The Google Chart API lets you dynamically generate charts.
Enhance data visualization within Flex and AIR applications with IBM ILOG Elixir.
Creates charts such as bar charts, line charts, pie charts, time series charts, candlestick charts, high/low/open/close charts, wind plots, and meter charts. I wish these charts looked better out of the box, because the features and functionality are good, but the visual design really detracts from the graphs. JFreeChart guys- email me- together we can make the world of JFreeChart a prettier place.
The PHP graphing scripts provide a very easy way to embed dynamically generated graphs and charts into PHP applications and HTML web pages.
Kap IT Labs Diagrammer and Visualizer
Kap Lab's Diagrammer provides ready-to-use yet highly customizable multi-layout data visualization and diagramming for Adobe Flex and Air.
Visualizer displays data as graphs to better visualize connections. Kap Lab's Visualizer provides ready-to-use yet highly customizable multi-layout data visualization for Adobe Flex and Air.
A simple to use, yet robust library for transforming table data into a chart. This library uses the HTML5 tag and is only supported on browsers other than IE until ExCanvas gets proper text support.
Open Flash Charts
Open source Flash charts.
Protovis composes custom views of data with simple marks such as bars and dots. Unlike low-level graphics libraries that quickly become tedious for visualization, Protovis defines marks through dynamic properties that encode data, allowing inheritance, scales and layouts to simplify construction.
Microsoft Silverlight comes with the bar, line, pie, column, and scatter charts.
Telerik Charts for Silverlight, WFP, ASP.NET
Telerik Charts offers rich functionality and data presentation capabilities.
Visifire is a set of open source data visualization controls - powered by Microsoft® Silverlight™ & WPF.
yFiles for Ajax , .NET or Flex
The yFiles product family means state-of-the-art software components for the visualization of networks and diagrams. Unequaled automatic diagram layout, cutting edge graph analysis, and extraordinary visualization.
A few more resources:
Gephi, the open graph Viz platform
XML/SWF Charts is a simple, yet powerful tool to create attractive charts and graphs from XML data.
Bime, Browser-based business intelligence solution (based on Flex)
75+ tools to visualize your data
Flare is an ActionScript library for creating visualizations that run in the Adobe Flash Player
Microsoft Chart Controls, ASP.NET and Windows Forms Chart Controls for .NET Framework 3.5 SP1
Periodic table of visualization methods (data, information,concept, strategy, metaphor)
Popular and Creative visualization methods
Software FX has lots of great products for every platform.
Also check out MIT's SIMILE project
Google Vizualisation API with maps and magic-tables
InstantAtlas™ enables information analysts and researchers to create highly-interactive online reporting solutions that combine statistics and map data to improve data visualization, enhance communication, and engage people in more informed decision making.
Mindsetgeometrics allows to build custom charts using predefined SVG files or Adobe Catalyst models.
Seer is a lightweight, semantically rich Ruby on Rails wrapper that provides a seamless interface for the Google Visualization API . It allows to easily create a visualization of data in a variety of formats with a single line of code.
YUI Charts from Yahoo
Silverlight Pivot Grid
AmCharts is a set of Flash charts for your websites and Web-based products. AmCharts can extract data from simple CSV or XML files, or they can read dynamic data generated with PHP, .NET, Java, Ruby on Rails, Perl, ColdFusion, and many other programming languages.