When using VT Graph quota is consumed from your VirusTotal account. The quota consumed is mainly API quota but there is certain functionality that consumes VirusTotal Intelligence quota.
In the lower right corner of the screen you can see an API requests counter:
Basically API requests are consumed by:
- The initial resource search.
- Every parent node type.
- Each time you click on a file to retrieve the additional information shown on the left side.
Also note that if you use the "Expand using new intelligence search" it will consume from your VirusTotal Intelligence quota.