R for graphs with nested subgraphs?

I'm looking for an r-package for graphs / grids that can handle nested subgraphs. Graphviz does this, but only provides visualization - I need classes or some way to represent the data structures themselves. The igraph has subgraphs, but they cannot be nested as far as I can see.

To clarify, I already use DiagrammeR and Rgraphviz to draw networks, but I want to analyze and manipulate, for example

(pseudocode)

newnet = oldnet + myAddedNode 

      

        
        
        
      

    

add node to oldnet to create a new network named newnet.