> How do you add nodes to a graph without connecting from to others via an edge?

Use a different file format that supports disconnected edges. Pajek 
(https://gephi.org/users/supported-graph-formats/pajek-net-format/) or GML 
(https://gephi.org/users/supported-graph-formats/gml-format/) are probably the 
easiest to create.

T.

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