Naval vessels infrastructures are evolving towards increasingly connected and automatic systems. Such accelerated complexity boost to search for more adapted and useful navigation devices may be at odds with cybersecurity, making necessary to develop adapted analysis solutions for experts. This paper introduces a novel process to visualize and analyze naval Cyber-Physical Systems (CPS) using oriented graphs, considering operational constraints, to represent physical and functional connections between multiple components of CPS. Rapid prototyping of interconnected components is implemented in a semi-automatic manner by defining the CPS's digital and physical systems as nodes, along with system variables as edges, to form three layers of an oriented graph, using the open-source Neo4j software suit. The generated multi-layer graph can be used to support cybersecurity analysis, like attacks simulation, anomaly detection and propagation estimation, applying existing or new algorithms.