This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
First, I recommend converting the data to some simplistic format like XML so it can be made uniform and easy to read. For Java graphing, there's a ton of SourceForge projects as well as proprietary chart programs, and some are better than others.
The reason I recommend the XML is that at least if you pick a particular format you can more easily migrating it to something else later.