Unfortunately most of the trains in Japan do not have luggage spaces near the doors. Therefore you have to carry your suitcase to the seat.
Shinkansen trains have wide overhead racks which large size suitcases can be fitted. However, most of the local trains do not have wide overhead racks which you can put your suitcases.
Then, some limited express trains have overhead bin similar to aircraft. However, as same as the aircraft, you can not put your large suitcase in it.
If you encounter with a train with narrow overhead rack or bin, please keep eye on the suitcase and let it allow not to bother other passengers.
Especially it is quite normal in Prague that passenger is carrying a large backpack on his/her back inside the crowded metro. However, this behavior is not allowed in Japan, and please kindly put down your backpack on the floor, near to your legs.