If there are loops in the topology, use Spanning Tree Protocol to break them and find the root node. But it seems your (unidirectional) graph is already loop-free.

Find the root node with no incoming links. Find the maximum depth for each node. Put the nodes on proper lines (3*depth or so). Assign columns opportunistically, depth first. You cannot avoid crossing links in general. For example, the diamond dependency 1->2; 1->3; 2->4; 2->5; 3->4; 3->5, is impossible to plot.