Module structure and network connections in the expression data can be visualized in several different ways. For example, the co-expression module structure can be visualized by heatmap plots of gene-gene connectivity that can be produced using the function TOMplot. Examples are presented in Figures 2C and 4B. An alternative is a multi-dimensional scaling plot; an example is presented in Figure 2B. Relationships among modules can be summarized by a hierarchical clustering dendrogram of their eigengenes, or by a heatmap plot of the corresponding eigengene network (function labeledHeatmap), illustrated in Figures 3C, D, and 4C, D. The package includes several additional functions designed to aid the user in visualizing input data and results. These functions rely on basic plotting functions provided in R and the packages sma [35] and fields [36].
