Assuming the API supports it, the ability to customise the graph nodes’ colours and text would make it easier to separate what cards (markdown files) are used for what. For example, we may have front-matter indicating that the card relates to a person, and another to a concept/definition, another to Map of Concepts (MOC) etc. We could prefix each category by an icon, and change the node colour. Like the example below:
This could be realised by mapping a front-matter parameter (category) to a set of colours and optionally icons, or alternatively mapping to tags.