Why in the heck are these rats living in your shared space and not in your roommate's bedroom? If she wants to have messy, caged pets (and not clean up after them) she should be dealing with the smell and — eek — rat feces solo. That's your first step. She's already proved herself not able or willing to do the necessary upkeep for these pets (which is NOT okay, owning a pet is a serious responsibility) so she should also deal with the unpleasantness of that decision.
If she doesn't agree, I think you need to start looking for a new living situation. In fact, based on the way she communicates (or, more accurately, DOESN'T communicate) you might want to consider it anyway. That's probably not what you want to hear because, well, moving sucks, but I don't see this roommate relationship getting much better. Since she owns the house, you may want to just give yourself a break and get out of there.