Specialization of $F$-Zips

In \cite{MW}, B. Moonen and the author defined a new invariant, called $F$-Zips, of certain varieties in positive characteristics. We showed that the isomorphism classes of these invariants can be interpreted as orbits of a certain variety $Z$ with an action of a reductive group $G$. In loc. cit. we gave a combinatorial description of the set of these orbits. In this manuscript we give an explicit combinatorial recipe to decide which orbits are in the closure of a given orbit. We do this by relating $Z$ to a semi-linear variant of the wonderful compactification of $G$ constructed by de Concini and Procesi. As an application we give an explicit criterion of the closure relation for Ekedahl-Oort strata in the moduli space of principally polarized abelian varieties.