Go to Hyperdia.com.
Click on ‘More options’.
Tick/untick boxes like the figure below (if you’re using JR Pass).
Input your starting point and destination and then Search.
It will display different routes and other details.
If nothing is being shown, it means that you have to consider using Private lines. 
Just tick on ‘Private Railway’ then ‘Search’.
Note: You need to pay the cost of using Private lines separately.
Since Rinkai Line (based on the example figure above) is a private line, you will need to buy a separate train ticket from Osaki Station going to Tokyo Teleport Station which costs 330jpy. Osakajokitazume to Osaki station is covered by JR Pass.
You may also check this 9D10N detailed budget itinerary for Japan. It covers tourist spots in Nagoya, Osaka, Kyoto, Tokyo, Hiroshima and Fukuoka.
