1. In this classroom, the teacher is in control. The teacher calls the shots, not the students.
2. The lawyer tried to take control of the courtroom, but the judge reminded him that it is the judge who calls the shots.

This idiom stems from use in sports that involve aiming. For example, in darts, the thrower might call out the exact spot he/she expects to hit on the target. Calling the shots well shows the player to be in control of the outcome.