Computational protocol: R-Based Software for the Integration of Pathway Data into Bioinformatic Algorithms

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[…] There are several packages available which focus primarily on the visualization of R graph data. Package pathRender provides plotting capabilities with preset parameters to quickly retrieve visualization of graphs. RedeR [] is a powerful tool, which implements plotting and remote interaction of graph objects of package igraph with a Java-based graphical user interface similar to Cytoscape, especially focused on visualizing extremely large networks. CePa provides preset plotting parameters for its supplied igraph objects. The packages NCIgraph, KEGGgraph, pathview and rBiopaxParser enable the user to plot pathways via Rgraphviz. Package pathview additionally provides a function to export native KEGG representations as PNG image files. The graphite package, which uses RCytoscape for visualization, as well as RCytoscape itself, visualize graphs via an active Cytoscape session. RCytoscape offers a multitude of well-documented parameters and functions to visualize, layout and modify R graph objects using Cytoscape.Furthermore, the user is free to extend and improve visualization, since all methods for visualization—Cytoscape, RedeR, Graphviz as well as common R plotting—allow for individual modifications of parameters, e.g., color, size of nodes, width of edges. […]

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