There is a good example of a metaphor right near the beginning of "Dr. Heidegger's Experiment"
Colonel Killigrew had wasted his best years, and his health and substance, in the pursuit of sinful pleasures, which had given birth to a brood of pains, such as the gout, and divers other torments of soul and body.
Colonel Killigrew's sinful pleasure could not have literally "given birth" to his various pains. Rather, Hawthorne means that the sinful life of overeating and loose morals had brought about the Colonel's ailments just like the process of birth brings about a new baby.
This is a classic example of metaphor: it compares two things without using the words "like" or "as."