When visualizing graphs, it is essential to communicate the meaning of each graph object via text or graphical labels.
For instance, one may use this technique to visualize graph data better as the large cliques can be combined to reveal other important structural properties [21, 22].
The desktop version of Cytoscape is optimized for rendering node-link, or ball-stick network diagrams, which is only one way to visualize graph data while Cytoscape 3 supports multiple-rendering engines and if developers can implement new rendering engines for new visualizations, such as Treemaps or Chord Diagrams, they can add new visualizations on Cytoscape.
For instance, the R package igraph (Csardi & Nepusz, 2006) or the standalone program Cytoscape (Shannon et al., 2003) can be used to analyse and visualize graphs.
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily) is a tool for visualizing assembly graphs with connections.
Vizify helped its users better visualize and graph their social lives in the format of a personal website of sorts.
Nicolás Parziale has created a very cool flash app inspired by They Rule that visualizes the graph of connections throughout CrunchBase.
The ISS is a human-centric system to enable value cognition and follows the following process: (1) visualized scenario graph generation, (2) human value cognition, (3) value co-creation based on shared knowledge, and (4) emerging chances evaluation.
Not only could they search through storylines by keywords and their combinations, but also visualize the graph of storylines to find other terms associated with the tweets from which those terms are extracted.
A hierarchical organization of nodes according to some authority or centrality measure allows to visualize the graph at different levels of details, eliminating the need to display all nodes and edges at once [60].
