Table 1

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

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


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.

Castro et al. Genome Biology 2012 13:R29   doi:10.1186/gb-2012-13-4-r29

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