"You're" is rife with similes and metaphors as its purpose is to compare the titular character to all of the things which remind Plath of him/her. This poem is about an unborn child--a baby still in the womb--which helps to identify the various comparisons Plath makes.
The first metaphor appears in the first line--"Clownlike"--which she then supports with imagery by suggesting that the character, like a clown, is most comfortable on his hands with feet in the air. Plath is referencing the baby's position, head down and facing the birth canal. She suggests the baby is "Gilled like a fish" because he/she is swathed in amniotic fluid. Plath then compares the baby to a turnip, "Mute as a turnip from the Fourth/Of July to All Fools' Day," which might imply the timing of the baby's birth or might simply be a comparison to the fact that the baby won't speak or make itself much known during that time.
She makes many comparisons in the second verse to the baby as a compact, contained entity--"bent-backed Atlas," "traveled prawn," "snug as a bug," and so forth. There is also, in this verse, the suggestion that the child seems far off--in the distance in terms of time, or perhaps even slightly emotionally, as something "vague" and "foggy" to her yet, but at the same time something for which she is searching.
The reference to her "little loaf" is taken straight from the colloquialism "bun in the oven" and there are multiple food-based comparisons in the poem. Generally, in American slang, terms of endearment are based on food, so this helps to indicate her affection for the baby.