Now,I have two separate projects in visual studio namely client1 and client2. And there are some places where client1 project refers client2 project. I'm going to generate separate code map for client1 and client2 and link them together. So that I will get complete flow of my application.

Is it possible to do this above requirement using visual studio enterprise 2017?

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Yes, you can start from an empty code map and then drag and drop each project form the Solution Explorer. You can also drag one project and show its dependencies.