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Table 1 RedeR in the context of gold-standard network visualization software and R

From: RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations

  RedeR Cytoscape Graphviz igraph graph
Software design      
   Hierarchical data structurea Yesb No Yesb No No
   Data abstractiona Modularb Flat Layeredb Flat Flat
   Data encapsulationa Yes Yes No No No
   Core engine Java Java DOT C R
   R interface R <-> Java R -> Java R <- DOT R <- C Pure R
   Deployment to R Embedded External External Embedded Embedded
   Plugin coding language R Java DOT languagec Cd -
Selected features      
   Scalability on nested networkse Yes Nof Yes Nog Nog
   Interactive graph handling Yes Yes No Partiallyh No
   Dynamic layouts Yesi No No No No
   Comparison across multiple nested networks Yes No No No No
   Panelsj Yes No No No No
  1. aFor further definitions, please see the Implementation section and Figure 2. bIn RedeR, the hierarchy is encapsulated, so users deal with methods. In Graphviz users implement methods by themselves in DOT language. This difference has an important effect on the ability of the software to deal with modular structures, such as recycling data objects used in subnetworks. cThe plugin infrastructure is available for Graphviz. dProvides a C library to be used in third-party applications. eAble to accommodate increasing amounts of nested objects. fIn Cytoscape, nested networks are represented as images inside nodes. For each nested network one image is required. Images are not scalable, so the hierarchy cannot be extended to other levels. gIn these applications, modules can be represented by layering images, which is essentially a drawing process. hAccording to the authors, the interactive features are not very well developed at this stage. iIn RedeR, the dynamic layout is also extensible to the nested structures. jThis feature provides support for multiple panels in the same graph, representing subnetworks, and so on.