RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of nested networks. Graph, node, and edge attributes are set either using graphical or command-line methods following igraph syntax rules. The RedeR/R package sets all details to initialize the R-to-Java interface, which uses an interactive force-directed layout algorithm, adjusting the graph layout to the hierarchical levels of a nested network. Supporting information is available from Castro et al. (2016).
RedeR 3.2.0
RedeR is an R-based package combined with a Java application for network analysis and visualization. RedeR is designed to deal with three key challenges in network analysis. Firstly, biological networks are modular and hierarchical, so network visualization needs to take advantage of such structural features. Secondly, network analysis relies on statistical methods, many of which are already available in resources like CRAN or Bioconductor. Thirdly, in larger networks user input is needed to focus the view of the network on the biologically relevant parts, rather than relying on an automatic layout function. The graphical user interface is depicted in Figure 1.