If they are in a bag to avoid dangerous projections and oily parts from hitting other passengers then no problem, but no bag then don't think about it. At a pinch some big garbage bags and tape will suffice but remember to either fold the bike or disassemble it first.
I love seing other cyclist on the train. You give each other a nod maybe a wave and both smile as though you known a big secret! Maybe we do! The fountain of youth? Stress relief? Whatever you want! I love it! I have a nice bag from Ostrich that works nice. 6000yen