Using JRPass within the city

We are arriving in Japan in 5 days and purchased the 7 day JRPass. It is a 10 day vacation but 4-5 days will just be in Tokyo so when we do activate the pass, we plan to visit places like Kyoto, Mt Fuji, and Osaka.

My question is for the JRPass, besides going from one city to another, can the JRPass also be used within the city itself such as public transport/buses/subway/trains or is that a separate purchase that is required.

Thanks.