Browsing by Subject "Graph Visualization"

Now showing 1 - 8 of 8

Open Access
A circular layout algorithm for clustered graphs
(2009) Belviranlı, Mehmet Esat
Visualization of information is essential for comprehension and analysis of the acquired data in any field of study. Graph layout is an important problem in information visualization and plays a crucial role in the drawing of graph-based data. There are many styles and ways to draw a graph depending on the type of the data. Clustered graph visualization is one popular aspect of the graph layout problem and there have been many studies on it. However, only a few of them focus on using circular layout to represent clusters. We present a new, elegant algorithm for layout of clustered graphs using a circular style. The algorithm is based on traditional force-directed layout scheme and uses circles to draw each cluster in the graph. In addition it can handle non-uniform node dimensions. It is the first algorithm to properly address layout of the quotient graph while considering inter-cluster relations as well as intra-cluster edge crossings. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has been successfully implemented as part of Chisio, version 1.1. Chisio is an open source general purpose graph editor developed by i-Vis (information visualization) Research Group of Bilkent University.
Open Access
A framework for complexity management in graph visualization
(Springer, Berlin, Heidelberg, 2002) Doğrusöz, Uğur; Genç, Burkay
We present a comprehensive framework for development of complexity management techniques in graph visualization tools. The presented architecture is capable of managing multiple associated graphs with navigation links and nesting of graphs as well as ghosting, folding and hiding of unwanted graph elements. The theoretical analyses show that the involved data structures and algorithms are quite effcient, and an implementation in a graph drawing tool has proven to be successful. Our architecture is based on dynamic interactive compound graphs. The definition of compound graphs is extended to efficiently handle the graph editing and complexity management operations. A navigation forest is used to keep track of navigational links among nodes and graphs, and a nesting forest is used to keep track of nesting (inclusion) relations.
Open Access
Improvements on pathwaymapper: a collaborative pathway curation tool
(2018-07) Dervishi, Leonard
Information visualization focuses on visually representing abstract data to amplify human cognition. Graph visualization is one of the most common types in the eld of information visualization because of its capabilities to present huge amount of data in a clear and meaningful manner. A graph is a suitable data structure for representing relational information and for this reason graph visualization has a wide usage in biological pathway visualization as well. In this thesis, we focus on collaborative construction of cancer pathways and visualization of cancer genomics data overlaid over such networks. Several biological pathway visualization tools have been developed to help biologists analyze cancer genomics data, using various formats, including standard formats like SBGN, in the past. Nevertheless, most biologists prefer curated pathway diagrams like the ones featured in The Cancer Genome Atlas (TCGA) manuscripts, using a simpler notation. These pathway diagrams outline the alterations occurring in pathways for di erent cancer types. To address this need, a web-based tool called PathwayMapper was previously developed. PathwayMapper can be used to view pre-curated cancer pathways or to create new pathways from scratch. It has many features including overlay of genomic alteration data from the cBioPortal. It also includes a collaborative mode so that the users can interactively create and modify the cancer pathways. With this thesis, we improve PathwayMapper in several ways to make it a more complete and powerful editor with a better user interface. New features include complexity management operations, edge bend support, interactive node resize, and various highlighting capabilities. Furthermore, the user interface has been improved to be more user friendly with the addition of a toolbar.
Open Access
A layout algorithm for graphs with overlapping clusters = Kesişen kümelenmiş çizgeler için bir yerleştirme algoritması
(2014) Cengiz, Can Çağdaş
Graphs are often used for visualizing relational data such as social or biological networks. Numerous methods have been proposed for automatic layout of simple graphs. However, simple graphs are usually insufficient in displaying relational information, since relational information is often clustered. Clustering models traditionally assume that each data point belongs to one and only one cluster; however, in complex networks, these clusters often overlap. For effective visualization of clustered graphs, the nodes in the same cluster should be placed together, respecting general graph drawing criteria such as avoiding node-node overlaps, minimizing edge crossings, and minimizing the total drawing area. Clustered graph layout problem becomes even more challenging when cluster overlaps are allowed. Here, we present a new algorithm for automatic layout of graphs with overlapping clusters based on force directed layout approach. The graph is first divided into zones according to clusters and their intersections, and new additional forces are introduced to the traditional spring embedder algorithm to keep nodes in the same cluster together, trying to keep neighboring nodes in separate clusters at a safe distance. Spring constants had to be fine-tuned to achieve a fast and effective layout operation. The algorithm was implemented and validated within a new layout style named Cluster Layout in the layout module of ChiEd visualization tool.
Open Access
A layout algorithm for undirected compount graphs
(2005) Giral, Erhan
Graph layout is an important problem in information visualization. All datadriven graph-based information visualization systems require some sort of an automatic geometry generation mechanism, as it is generally not directly available from the data being modeled. This is why graph layout problem has been studied extensively. However, for the case of compound graphs, there are still important gaps in this area. We present a new, elegant algorithm for undirected compound graph layout. The algorithm is based on the traditional force-directed layout scheme with extensions to handle nesting, varying node sizes, and possibly other application-specific constraints. Experimental results show that the execution time and quality of the produced drawings with respect to commonly accepted layout criteria are quite satisfactory. The algorithm has also been successfully implemented as part of a pathway integration and analysis toolkit named Patika for drawing complicated biological pathways with compartmental constraints and arbitrary nesting relations to represent molecular complexes and various types of pathway abstractions.
Open Access
Methods and tools for synchronized visualization of evolving networks
(2018-07) Safarli, Ilkin
Graph visualization is a powerful tool to convey and analyze relational information in the form of networks such as biological networks, social networks, and computer networks. Abundant research has been conducted on the automatic layout of static graphs and numerous tools have been developed to visualize them. However, in many applications, graphs are not static; they change or evolve over time. To void this gap, we designed two new dynamic graph layout methods, implemented a dynamic graph layout library and developed a web-based application to visualize and contrast dynamic graphs effectively. Cytoscape.js-synched is a library that implements three different dynamic graph layout algorithms, two of which are proposed by us. In the layout of dynamic graphs, the main criteria is to keep the mental map and minimize the total distance among different versions of the same graphs. It is also important to minimize general layout metrics such as node to node overlaps, number of edge crossing, total area, and total edge length. Proposed and implemented algorithms address both of these conflicting criteria to a satisfactory level and result in aesthetically pleasing layouts. EVEN, which is based on Cytoscape.js graph library, is a highly customizable, open source, web-based, and interactive application for visualization of dynamic graphs. It supports visualization and automatic synchronized layout of two or more dynamic graphs. EVEN makes analysis of dynamic graphs more practical by providing synchronized graph exploration features. It also has basic support for constructing and editing dynamic graph.
Open Access
Methods and tools for visualization and management of SBGN process description maps
(2014) Sarı, Mecit
Graphs are commonly used to model relational information in many areas such as relational databases, software engineering, biological and social networks. In visualization of graphs, automatic layout, interactive editing and complexity management of crowded graphs are essential for effective utilization of underlying information. Advances in graphical user interfaces have given rise and value to interactive editing and diagramming techniques in graph visualization. As the size of the information to be visualized vastly increased, it became harder to analyze such networks, making use of relational information needed to be acquired. To overcome this problem, sophisticated and domain-specific complexity management techniques should be provided. The Systems Biology Graphical Notation (SBGN) has been developed over a number of years by biochemists and computer scientists to standardize visual representation of biochemical and cellular processes. SBGN introduces a concrete, detailed set of symbols for scientists to represent network of interactions, in a way that is not open to more than one interpretation. It also describes the manner, in which such graphical information should be interpreted. The SBGN Process Description (PD) language shows how entities are influenced by processes, which are represented by several reaction types in a biological pathway. It can be used to show all the molecular interactions taking place in a network of biochemical entities, with the same entity appearing multiple times in the same diagram. We developed methods and tools to effectively visualize and manage SBGNPD diagrams. Specifically, we introduced new algorithms for proper management of complexity of large SBGN-PD diagrams. These algorithms strive to keep SBGN-PD diagrams intact as complexity management takes places. In addition, we provided software components and web-based tools that implement these methods. These tools use state-of-the-art web technologies and libraries.
Open Access
Two-dimensional packing algorithms for layout of disconnected graphs
(Elsevier, 2002) Dogrusoz, U.
We present and contrast several efficient two-dimensional packing algorithms for specified aspect ratio. These near-linear algorithms are based on strip packing, tiling, and alternate-bisection methodologies and can be used in the layout of disconnected objects in graph visualization. The parameters that affect the performance of these algorithms as well as the circumstances under which they perform well are analyzed. © 2002 Elsevier Science Inc. All rights reserved.