A result of Haglund implies that the
(q,t)-bigraded Hilbert series of the space of diagonal harmonics is a
(q,t)-Ehrhart function of the flow polytope of a complete graph with netflow vector
(-n,1,\ldots ,1). We study the
(q,t)-Ehrhart functions of flow polytopes of threshold graphs with arbitrary netflow vectors. Our results generalize previously known specializations of the mentioned bigraded Hilbert series at
t=1,
0, and
q^{-1}. As a corollary to our results, we obtain a proof of a conjecture of Armstrong, Garsia, Haglund, Rhoades, and Sagan about the
(q,q^{-1})-Ehrhart function of the flow polytope of a complete graph with an arbitrary netflow vector.