Figure 6
From: LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB
Example drawings of a typical network. The network consists of three functional modules of P. aeruginosa PAO1 with totally 290 nodes. Nodes of the same modules are drawn in identical shapes and colors: red square = central metabolism; blue ellipse = lipid synthesis; green rectangle = nucleotide synthesis. For clarity, node labels are not shown. Panels A, B, and C correspond to common, compact, and stretched layout styles, respectively. Panel D shows a result when functional module information is supplied in advance. We added an extra positive value (= 10) to the weights w ij of any two nodes which belong to the same modules when graph distances L ij = 2 or 3. The running time for one layout is 6 sec on an AMD 5200+ desktop computer.