The hierarchical structure of option precedence ensures flexibility and control; settings defined in the configuration file override the default values coded within rNets, while CLI arguments take precedence over both configuration settings and defaults. This design allows users to establish a baseline configuration file reflecting their standard visualization preferences, with the flexibility to use CLI arguments for temporary or experiment-specific modifications. rNets rigorously checks the validity of user-defined values to maintain stability and reliability. The available configuration options are described in Tables S3-S5 and an example of a configuration file can be found in Note S5 and in the code repository. For advanced customization, the opts option enables the specification of Graphviz parameters for various elements of the network visualization. Additional details on utilizing this feature are available in Note S6.