I believe I was primarily using Architexa (https://github.com/i3labs/architexa), but it was a number of years ago when I was working exclusively in Java.

JetBrains also provides a few diagramming plugins, but I've never used them.

I haven't yet come across tooling that does the same for C, C++, or D. This response inspired me to take a look though, and I did find something for Python (https://stackoverflow.com/questions/45238329). Thinking about it, the instrumentation approach taken there might actually work fairly well for most systems languages assuming you don't have any dead (or rarely called) code. Graphviz could be combined with the "-finstrument-functions" GCC flag and a few supporting data structures. Templated code would be tricky to deal with though.

Edit: Just came across CppDepend (https://www.cppdepend.com/). It's proprietary, but appears to be incredibly powerful at first glance. See its dependency analysis in particular (https://www.cppdepend.com/dependenciesview).