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

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

	RedeR	Cytoscape	Graphviz	igraph	graph
Software design
Hierarchical data structure^a	Yes^b	No	Yes^b	No	No
Data abstraction^a	Modular^b	Flat	Layered^b	Flat	Flat
Data encapsulation^a	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 language^c	C^d	-
Selected features
Scalability on nested networks^e	Yes	No^f	Yes	No^g	No^g
Interactive graph handling	Yes	Yes	No	Partially^h	No
Dynamic layouts	Yesⁱ	No	No	No	No
Comparison across multiple nested networks	Yes	No	No	No	No
Panels^j	Yes	No	No	No	No

^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.

ISSN: 1474-760X