When you are new to Japan, there might be lots of things you will be surprised about Japanese behavior.
But the golden rule is, not to disturb others. THAT’S IT!
 
I am Japanese raised up by Japanese parents and grew up in Tokyo,
and this golden rule “don’t disturb others” had been taught everywhere.
From my parents, kindergarten teachers, elementary school teachers, and else,
I’ve heard a lot of times that they say “you can do whatever you want to, as long as you do not disturb others”.

 
The rules based on that golden rule are, for example,
 

To Walk the right side while walking
No smoking while walking
To Wait till ppl get off the train before you get in
No talking on the phone while you are in a train….. etc.
 

You can see that all these kind of (hidden) rules are basically from the idea “don’t disturb others”.
 
When you can’t judge if you are doing right or not, remember this golden rule and enjoy Tokyo! 🙂