Logtalk (which supports 12 Prolog systems) provides a diagrams tool that can generate several kinds of diagrams, including cross-referencing diagrams. It can also be used with some limitations, depending on the Prolog system, to create diagrams for Prolog code. For example:
http://logtalk.org/diagrams/swi_prolog_library_entity_diagram.svg
An example of a cross-referencing diagram (generated using an old version of tool) is:
http://logtalk.org/diagrams/pengines_module_xref_diagram.pdf
This tool may be a viable option (it's default output is GraphViz .dot files) in your case depending on the Prolog system that you're using and how you organize your code. Maybe you can update your post with some more details?