How to represent a conceptual framework?

My conceptual framework has several characteristics:

1. There is flow in the system means the order of active components per piece while running
2. There is a static structure.
3. There are dependencies
4. There are hierarchies
5. Different dimensions, for example, the hardware environment

The hierarchies make it complicated to use a directed graph with different arrows. Nevertheless, there are nodes and arrows between them. 

The solution is that a node in the directed can contain another directed graph. If an inner node has a dependency on a node that is not in the same parent-node, the parent-node gets an addiction to the other node on the same level on the hierarchy. 

How to display this? 

1. Zooming: Child-Graphs are not shown. I have to click on the parent first and get the child graph presented
2. Grouping: Within a node, there can be other nodes and edges.

It makes sense to split the declaration from the visualization and let, e.g., Graphviz handle the latter. I can think of a simple internal DSL to describe the conceptual framework and the Dot-file one output.

The graph cannot represent the dimensions. Do the techniques known from software architecture (e. g. the C4-model help here?

The conceptual framework and software architecture
I have the feeling that I simply can use software architecture as a boost for representing my conventional model. In the end software, architecture is also a conventional model that groups documents (source code files).