Sounds like a cool project! If you are not specifically interested in static graphs, you can also use profilers (XDebug, xhprof) to capture calls as they happen and display them with KCacheGrind or something similar. That gives you call graphs which include information like percentage of time spent in a subgraph and are great for optimization.
Doxygen can also supposedly generate static call graphs, although I don't know how good it is at it (it's generally not very PHP-friendly).