Analyzing large, multivariate graphs is an important problem in many domains, yet such graphs are challenging to visualize. In this paper, we introduce a novel, scalable, tree-table multivariate graph visualization technique, which makes many tasks related to multivariate graph analysis easier to achieve. The core principle we follow is to selectively query for nodes or subgraphs of interest and visualize these subgraphs as a spanning tree of the graph. The tree is laid out linearly, which enables us to juxtapose the nodes with a table visualization where diverse attributes can be shown. We also use this table as an adjacency matrix, so that the resulting technique is a hybrid node-link adjacency matrix technique. We implement this concept in Juniper and complement it with a set of interaction techniques that enable analysts to dynamically grow, restructure, and aggregate the tree, as well as change the layout or show paths between nodes. We demonstrate the utility of our tool in usage scenarios for different multivariate networks: a bipartite network of scholars, papers, and citation metrics and a multitype network of story characters, places, books, etc.
@cite_18: Pathway maps are an important source of information when analyzing functional implications of experimental data on biological processes. However, associating large quantities of data with nodes on a pathway map and allowing in depth-analysis at the same time is a challenging task. While a wide variety of approaches for doing so exist, they either do not scale beyond a few experiments or fail to represent the pathway appropriately. To remedy this, we introduce enRoute, a new approach for interactively exploring experimental data along paths that are dynamically extracted from pathways. By showing an extracted path side-by-side with experimental data, enRoute can present large amounts of data for every pathway node. It can visualize hundreds of samples, dozens of experimental conditions, and even multiple datasets capturing different aspects of a node at the same time. Another important property of this approach is its conceptual compatibility with arbitrary forms of pathways. Most notably, enRoute works well with pathways that are manually created, as they are available in large, public pathway databases. We demonstrate enRoute with pathways from the well-established KEGG database and expression as well as copy number datasets from humans and mice with more than 1,000 experiments. We validate enRoute using case studies with domain experts, who used enRoute to explore data for glioblastoma multiforme in humans and a model of steatohepatitis in mice.
@cite_3: Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways, multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists' use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.
@cite_6: Social networks collected by historians or sociologists typically have a large number of actors and edge attributes. Applying social network analysis (SNA) algorithms to these networks produces additional attributes such as degree, centrality, and clustering coefficients. Understanding the effects of this plethora of attributes is one of the main challenges of multivariate SNA. We present the design of GraphDice, a multivariate network visualization system for exploring the attribute space of edges and actors. GraphDice builds upon the ScatterDice system for its main multidimensional navigation paradigm, and extends it with novel mechanisms to support network exploration in general and SNA tasks in particular. Novel mechanisms include visualization of attributes of interval type and projection of numerical edge attributes to node attributes. We show how these extensions to the original ScatterDice system allow to support complex visual analysis tasks on networks with hundreds of actors and up to 30 attributes, while providing a simple and consistent interface for interacting with network data.
@cite_43: The analysis of paths in graphs is highly relevant in many domains. Typically, path-related tasks are performed in node-link layouts. Unfortunately, graph layouts often do not scale to the size of many real world networks. Also, many networks are multivariate, i.e., contain rich attribute sets associated with the nodes and edges. These attributes are often critical in judging paths, but directly visualizing attributes in a graph layout exacerbates the scalability problem. In this paper, we present visual analysis solutions dedicated to path-related tasks in large and highly multivariate graphs. We show that by focusing on paths, we can address the scalability problem of multivariate graph visualization, equipping analysts with a powerful tool to explore large graphs. We introduce Pathfinder, a technique that provides visual methods to query paths, while considering various constraints. The resulting set of paths is visualized in both a ranked list and as a node-link diagram. For the paths in the list, we display rich attribute data associated with nodes and edges, and the node-link diagram provides topological context. The paths can be ranked based on topological properties, such as path length or average node degree, and scores derived from attribute data. Pathfinder is designed to scale to graphs with tens of thousands of nodes and edges by employing strategies such as incremental query results. We demonstrate Pathfinder's fitness for use in scenarios with data from a coauthor network and biological pathways.
@cite_51: 
works by adjusting the layout so that a direct association between the nodes edges and their attributes can be established. This is a broad category that includes placing the nodes in a scatterplot defined by two attributes as in GraphDice @cite_6 or aggregating nodes into bar charts as in GraphTrail @cite_51 . Another strategy is to linearize (parts of) a node-link layout so that it can be easily juxtaposed with a table visualizing node or edge attributes. Examples of this approach include Pathline @cite_3 , where a whole network including cycles and branching is linearized and juxtaposed with an attribute visualization; enRoute @cite_18 , which linearizes a user-chosen path; and Pathfinder @cite_43 , which queries for paths in networks and juxtaposes those paths with attribute visualizations. All these approaches make compromises between the readability of the topology of the graph and the association of the attributes to the network.