Flowers appear at frequent intervals in the story and are important symbols. Joseph grows calla lilies in his basement. He also gets very angry as a child when another child picks the one stunted sunflower he is able to grow near the slum he lives in. He wants, an unusual desire for him, to kill that child.
The flowers are symbols of Joseph's patients. Joseph is a nurturer who gets plants and people to grow and blossom in unlikely places. His response to the sunflower shows how deeply he cares about his work.
Yellow is an important symbol as well and associated with Joseph. He wears an "off yellow" cardigan. He grows sunflowers. He is associated with the sun: the sun is needed to shine on flowers and make them grow, just as Joseph shines his light on people and helps them grow.
The sin eater Joseph talks about is a symbol of himself.
Joseph falling out the tree limb from far up the tree symbolizes how Joseph goes out on a limb too far to help his patients.
You might think too about how Joseph is like the Old Testament Joseph.