Graphviz and Dynagraph — Static and Dynamic Graph Drawing Tools

Ellson, J.; Gansner, Emden R.; Koutsofios, Eleftherios; North, Stephen C.; Woodhull, Gordon

doi:10.1007/978-3-642-18638-7_6

Cited by 294 publications

(241 citation statements)

References 21 publications

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“…We chose the widely used Fruchterman-Reingold (FR) algorithm to lay out our graphs. All layouts were generated by an FR implementation as provided by the GraphViz graph visualization software [7].…”

Section: Graph Layoutmentioning

confidence: 99%

An extended evaluation of the readability of tapered, animated, and textured directed-edge representations in node-link graphs

Holten

Isenberg

Wijk

et al. 2011

2011 IEEE Pacific Visualization Symposium

102

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Section: Graph Layoutmentioning

confidence: 99%

An extended evaluation of the readability of tapered, animated, and textured directed-edge representations in node-link graphs

Holten

Isenberg

Wijk

et al. 2011

2011 IEEE Pacific Visualization Symposium

102

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“…This method is based on the routines for plotting 'BinaryTree' objects in package party (Hothorn, Hornik, and Zeileis 2006). For Weka learners implementing the Drawable interface, i.e., providing a graph() method, it is also possible to use write_to_dot() to create DOT language representations of the built classifiers for processing via the dot program of Graphviz (Ellson, Gansner, Koutsofios, North, and Woodhull 2003). These approaches are illustrated in the code below, yielding the visualizations shown in Figure 1.…”

Section: R> Print(foo)mentioning

confidence: 99%

Open-source machine learning: R meets Weka

2008

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Two of the prime open-source environments available for machine/statistical learning in data mining and knowledge discovery are the software packages Weka and R which have emerged from the machine learning and statistics communities, respectively. To make the different sets of tools from both environments available in a single unified system, an R package RWeka is suggested which interfaces Weka's functionality to R. With only a thin layer of (mostly R) code, a set of general interface generators is provided which can set up interface functions with the usual "R look and feel", re-using Weka's standardized interface of learner classes (including classifiers, clusterers, associators, filters, loaders, savers, and stemmers) with associated methods.

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“…1). The system maintains the pathway structure information in a flat file format written with the DOT language that can be processed by the Graphviz program (Ellson et al, 2003). Information regarding the relationship between pathways and genes/metabolites, gene annotations and sequences, and the user-uploaded data sets, including project information, are stored in the back-end MySQL database for efficient manipulation.…”

Section: Description Of the Plant Metgenmap Systemmentioning

confidence: 99%

“…edu), respectively. The pathway structure information was extracted from these files using a custom python script and then converted to the DOT language, a plain text graph description language that can be processed by the Graphviz package for visualization (Ellson et al, 2003), using an in-house Perl script. Synonyms for each metabolite in the pathways were also collected from these pathway databases and stored in the system.…”

Section: Collection and Processing Of Biochemical Pathway And Gene Anmentioning

confidence: 99%

Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology

et al. 2009

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The information and resources generated from diverse "omics" technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti.cornell.edu/tool/MetGenMAP.

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Graphviz and Dynagraph — Static and Dynamic Graph Drawing Tools

Cited by 294 publications

References 21 publications

An extended evaluation of the readability of tapered, animated, and textured directed-edge representations in node-link graphs

An extended evaluation of the readability of tapered, animated, and textured directed-edge representations in node-link graphs

Open-source machine learning: R meets Weka

Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology

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