Graphs illustrating complex scientific relationships require students to integrate multiple concepts and visual features into a coherent understanding. We investigate ways to support students in integrating their understanding of density concepts through a graph that is linked to a simulation depicting the relationship between mass, volume, and density. We randomly assigned 325 8th-grade students to 1 of 2 graphing activities. In the "analyze" condition, students plotted a set of data points selected to help clarify the relationship between mass, volume, and buoyancy, and then interacted with a guided simulation to improve their plotting accuracy. In the "generate" condition, students chose their own data points, and then interacted with a guided simulation to test and revise their choices. We found that, although "analyze" participants were more likely to construct accurate graphs, "generate" participants were more likely to develop a coherent understanding of density and buoyancy. Analyses of process data and interviews suggest that "generate" participants grappled with the mass-volume ratio by deliberately testing points and identifying patterns as they updated their understanding of science concepts. In contrast, "analyze" participants displayed less deliberate exploration of the graph space. We discuss how activities that integrate graph interpretation and concept refinement can deepen science learning.