Spatial patterns of red, purple, and blue colors due to plant pigments called anthocyanins appear in a wide variety of flower petals. Activator and inhibitor proteins involved in anthocyanin synthesis in Mimulus (monkeyflowers) have been identified, and an activator-inhibitor system based on the classic Gierer-Meinhardt system has been proposed as a mathematical model. Analysis in this paper provides a prediction for the critical value of a dimensionless parameter, the ratio of the degradation rate constants of the inhibitor and activator, for pattern formation to occur, and numerical simulations demonstrate the potential for this system to form disordered hexagonal or stripe patterns. We provide experimental evidence for spatial variation in total anthocyanin concentration and for concentration-dependent anthocyanin association. Extending the mathematical model to include anthocyanin transport and diffusion, a series of molecular transformations encompassing acid-base and hydration (speciation) reactions, and self association, we predict that spatial color patterns are accompanied by complex spatial variation in the degree of self association. An important consequence of these studies is a proposal that anthocyanin association allows for colored anthocyanin species to be present in large mole fractions in cell vacuoles despite the fact that the typical vacuolar pH range favors the formation of colorless species.