Directed assembly of an array of Ru nanoclusters (NCs) is achieved by deposition of Ru at around room temperature on a single layer of graphene supported on Ru(0001). In this system, directed assembly is guided by the periodic moir´e structure of the buckled graphene sheet. Behavior is analyzed utilizing both scanning tunneling microscopy and atomistic lattice-gas modeling together with kinetic Monte Carlo simulation. We elucidate the kinetics of NC nucleation and growth, specifically assessing the coverage dependence of the NC density and height distribution. In addition, we provide a detailed characterization of the development of short-range spatial order within the NC array, identifying a tendency for row formation.