Donjon are basically really big yagura that evolved to 3 or more levels. Especially, in eastern Japan many castles built a large 3 level yagura in place of a donjon. Such donjon were also called gosankai yagura. The donjon of Hirosaki Castle and Marugame Castle are actually 3 level yagura. At Edo Castle, the 3 level Fujimi Yagura was used in place of the donjon after it burned down too.

Typical 3 level yagura
Edo Castle	Takamatsu Castle	Fukuyama Castle	Nagoya Castle	Hikone Castle

Gosankai Yagura
Hirosaki Castle	Kakegawa Castle	Shiroishi Castle	Shirakawa Castle

All Pictures...