Graphviz is a family of tools and a file format. Being text based it is easily manipulable and readily scalable to many nodes. It also supports subgraphs. I a

Graphviz is a family of tools and a file format. Being text based it is easily manipulable and readily scalable to many nodes. It also supports subgraphs. I am surprised at being downvoted when suggesting what is quantifiably the most mature tool in the space. PDF is a presentation format, and has nothing to do with graphs in the sense of data structures. The fact that the original question references photoshop shows that the person asking is not approaching the problem from a formal standpoint. This is asking for trouble. Frankly, I am not sure a graph is the right data structure for this problem. It is more likely that a general purpose database would fulfil current and future requirements more effectively. Graphs could be generated from that trivially as representations.