Browsing by Subject "Compound graphs"

Now showing 1 - 8 of 8

Open Access
Chisio : a visual framework for compound graph editing and layout
(2007) Küçükkeçeci, Cihan
Graphs are data models, widely used in many areas from networking to biology to computer science. Visualization, interactive editing ability and layout of graphs are critical issues when analyzing the underlying relational information. There are many commercial and non-commercial graph visualization tools. However, overall support for compound or hierarchically organized graph representations is very limited. We introduce a new open-source editing and layout framework named Chisio for compound graphs. Chisio is developed as a free, easy-to-use and powerful academic graph visualization tool, supporting various automatic layout algorithms. It is written in Java and based on Eclipse’s Graphical Editing Framework (GEF). Chisio can be used as a finished generic compound graph editor with standard graph editing facilities such as zoom, scroll, add or remove graph objects, move, and resize. Object property and layout options dialogs are provided to modify existing graph object properties and layout options, respectively. In addition, printing or saving the current drawing as a static image and persistent storage facilities are supported. Saved graphs or GraphML formatted files created by other tools can be loaded into Chisio. Furthermore, a highlight mechanism is provided to emphasize subgraphs of users interest. The framework has an architecture suitable for easy customization of the tool for end-users’ specific needs as well. Also Chisio offers several layout styles from the basic spring embedder to hierarchical layout to compound spring embedder to circular layout. Furthermore, new algorithms are straightforward to add, making Chisio an ideal test environment for layout algorithm developers.
Open Access
Chisio Web : a web-based framework for customizable visualization of relational information
(2012) Sümer, Selçuk Onur
Graphs are widely used to represent complex relational information. Graph visualization is crucial for effective analysis of information. In simple graphs, nodes are generally considered as uniform-sized components and they cannot be nested. This is often not sufficient to visualize complex relationships, because relational information is often clustered or hierarchically organized into groups or nested structures. There exist many free, open source software in the field of web-based graph visualization. However, none fully supports compound or clustered graphs. Moreover, customization provided by such software is often limited to the basic visual properties of nodes and edges. It requires a lot of effort to build an advanced customization of visual properties and interactive functionality with these software. In this thesis, we introduce a free, open source, general-purpose, web-based graph visualization framework, named Chisio Web (ChiWeb). ChiWeb supports visualization, interactive editing and layout of both simple and compound graphs. ChiWeb is implemented in ActionScript language and based on Flare, which is an open source ActionScript library designed for data visualization. ChiWeb is specifically designed for easy customization with respect to visualization and functionality. ChiWeb can be used as a library to create a custom graph visualization with an advanced application behavior for particular needs of a specific domain. The elements and functionality that can be easily customized with ChiWeb are: visual styles, controls for interactive events such as node creation, key and mouse functionality, context menus, toolbars, and inspector windows. Furthermore, ChiWeb’s architecture allows easy integration of new graph layout algorithms.
Open Access
A compound graph layout algorithm with support for ports
(2020-10) Okka, Alihan
Information visualization is a eld of study that aims to represent abstract data in an aesthetically pleasing and easy to comprehend visual manner. Various approaches and standards have been created to reinforce the discovery of unstructured insights that are limited to human cognition via visual depictions. Complex systems and processes are often modelled as graphs since it would be di cult to describe in text. A type of visualization, graph drawing, addresses the notion of creating geometric representations of graphs. There are plentiful research directed to designing automatic layout algorithms for visualizing graphs. Nevertheless, a limited number of studies utilize ports, which are dedicated connection points on the locations where edge ends link to their incident nodes. We propose a new automatic layout algorithm named CoSEP supporting port constraints on compound nodes used for nested levels of abstractions in data. The CoSEP algorithm is based on a force-directed algorithm, Compound Spring Embedder (CoSE). Additional heuristics and force types are introduced on top of existing physical model. Using CoSE's layout structure as a baseline enables CoSEP to handle non-uniform node sizes, arbitrary levels of nesting, and intergraph edges that may span multiple levels of nesting. Our experiments show that CoSEP signi cantly improves the quality of the layouts for compound graphs with port constraints with respect to commonly accepted graph drawing criteria, while running in at most a few seconds, suitable for use in interactive applications for small to medium sized graphs. The CoSEP algorithm is implemented in JavaScript as a Cytoscape.js extension, and the sources along with a demo are available on the associated GitHub repository.
Open Access
CoSEP: a compound spring embedder layout algorithm with support for ports
(Sage Publications, 2021-07-01) Okka, Alihan; Doğrusöz, Uğur; Balcı, Hasan
This paper describes a new automatic layout algorithm named CoSEP for compound graphs with port constraints. The algorithm works by extending the physical model of a previous algorithm named CoSE by defining additional force types and heuristics for constraining edges to connect to certain user-defined locations on end nodes. Similar to its predecessor, CoSEP also accounts for non-uniform node dimensions and arbitrary levels of nesting via compound nodes. Our experiments show that CoSEP significantly improves the quality of the layouts for compound graphs with port constraints with respect to commonly accepted graph drawing criteria while running reasonably fast, suitable for use in interactive applications for small to medium-sized (up to 500 nodes) graphs. A complete JavaScript implementation of CoSEP as a Cytoscape.js extension along with a demo page is freely available at https://github.com/iVis-at-Bilkent/cytoscape.js-cosep.
Open Access
Fast compound graph layout with constraint support
(2022-08) Balcı, Hasan
Visual analysis of relational data becomes more challenging in today's world as the amount of data increases exponentially. Effective visual display of such data is therefore a key requirement to simplify the analysis process. Compound graphs present a practical structure for both representing the relational data with varying levels of groupings or abstractions and managing its complexity. In addition, a good automatic layout of these graphs lets users understand relationships, uncover new insights and find important patterns hidden in the data. To this end, we introduce a new layout algorithm named fCoSE (fast Compound Spring Embedder) for compound graphs with support for user-specified placement constraints. fCoSE combines the speed of spectral layout with the aesthetics and quality of force-directed layout while satisfying specified constraints and properly displaying compound structures. The algorithm first generates a draft layout with the help of a spectral approach, then enforces placement constraints by using newly introduced heuristics and finally polishes the layout via a force-directed layout algorithm modified to maintain enforced constraints. Our experiments performed on both real-life and randomly generated graphs verify that fCoSE outperforms its competitors in terms of both speed and generally accepted graph layout criteria and is fast enough to be used in interactive applications with small to medium-sized graphs.
Open Access
fCoSE: A fast compound graph layout algorithm with constraint support
(IEEE, 2021-07-07) Balcı, Hasan; Doğrusöz, Uğur
Visual analysis of relational information is vital in most real-life analytics applications. Automatic layout is a key requirement for effective visual display of such information. This paper introduces a new layout algorithm named fCoSE for compound graphs showing varying levels of groupings or abstractions with support for user-specified placement constraints. fCoSE builds on a previous compound spring embedder layout algorithm and makes use of the spectral graph drawing technique for producing a quick draft layout, followed by phases where constraints are enforced and compound structures are properly shown while polishing the layout with respect to commonly accepted graph layout criteria. Experimental evaluation verifies that fCoSE produces quality layouts and is fast enough for interactive applications with small to medium-sized graphs by combining the speed of spectral graph drawing technique with the quality of force-directed layout algorithms while satisfying specified constraints and properly displaying compound structures. An implementation of fCoSE along with documentation and a demo page is freely available on GitHub.
Open Access
A layout algorithm for undirected compound graphs
(Elsevier, 2009-03-15) Doğrusöz, Uğur; Giral, Erhan; Çetintaş, Ahmet; Civril, Ali; Demir, Emek
We present an algorithm for the layout of undirected compound graphs, relaxing restrictions of previously known algorithms in regards to topology and geometry. The algorithm is based on the traditional force-directed layout scheme with extensions to handle multi-level nesting, edges between nodes of arbitrary nesting levels, varying node sizes, and other possible 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. © 2008 Elsevier Inc. All rights reserved.
Open Access
An orthogonal layout algorithm for small compound graphs
(2021-09) Zaman, Mubashira
Information visualization is the study of diﬀerent approaches that aid in the visualization and examination of data. Among the broad variety of diﬀerent op-tions and techniques available in this ﬁeld is “Graph Drawing”, which is regarded as the algorithmic foundation of relational information or graph visualization. Graph drawing fuses graph theory and visualization for presenting data as geo-metric shapes and for laying them out in a 2-D or 3-D space. There exist many diﬀerent types of automatic graph layouts. One such layout is the orthogonal graph layout in which edges are made up of horizontal and vertical segments. A specialized version of graphs called compound graphs are used to represent grouping or clustering of graph objects. Many orthogonal layout approaches have been presented for simple graphs but there is considerably less research available for orthogonal layout algorithms for compound graphs. In this thesis, we present C-TSM, which takes the already existing Topology-Shape-Metrics (TSM) approach and extends it to cater to 4-degree small compound graphs with uniform node sizes. First, compound graphs are converted to simple graphs and then the TSM approach is applied to it. The resulting output is compacted again in a post-processing step and then the graph is converted back to a compound graph. The results of performance tests on our algorithm show that C-TSM works considerably well on small-sized graphs and gives the output in up to a few seconds. This algorithm has been implemented in Javascript and Python and is available as a Cytoscape.js extension. The source code and a demo application are available on a GitHub repository.