Circular/Radial Visualizations in Bioinformatics-2

02.10.2009 // Bioinformatics, Visual Analytics, Visualization // abhishektiwari // 7 Comments

Before we start exploring other case studies in this series (please check my previous post), I would like to bring your attention on “Focus+Context” methods.

Focus+Context

A family of methods such as fisheye view, document lens, perspective wall which allows user to focus on a special item, while preserving the broader context around it, all in a single display. In a “focus+context” view a subset of the data can be viewed at a higher resolution with the remaining contextual data still being in view, and it useful when data sets are too large to visualize on one screen. In general, fisheye approach employs a non-euclidean geometry such as hyperbolic space. In hyperbolic space circumference and area increase exponentially instead of geometrically, which enables allocation of more space for zoomed visualization.

Radial Clustergrams

Radial clustergram is an intuitive radial space-filling method for visualizing cluster hierarchies. Radial clustergram arranges the clusters into a series of layers, each representing a different level (depth) of the tree, and it can display both unpruned and pruned trees. Parent−child relationships are represented as adjacency of nodes. Further each layer is segmented for child nodes, where each segment can be color-coded based on user-defined property. A fisheye distortion view can be used to focus on areas of interest, without losing sight of the broader context around it. Radial clustergram is implemented using Shemanarev’s Anti-Grain Geometry (AGG) library in .Net environment. Radial clustergrams have been used to visualize diversity of chemical libraries and conformational space of small organic molecules.

ModelBrowser
ModelBrowser is interactive visualization system for biosimulation. ModelBrowser allows researcher to ask questions about a model through interaction with a graph of the mathematical model, particularly to understand and modify others’ code and debug their own. Model variables and equations appear as a directed graph of nodes and edges. Parameters (such as rate constants) and variables can be color-coded by scientific unit and clustered by module or hierarchies (see below).
ModelBrowser runs as a plugin to JSim, a Java-based simulation environment developed at NCR Washington. ModelBrowser can search, filter, color, cluster, or merge variables based on metadata associated with the model. During navigation model visualization can be expanded or contracted based on hierarchies or modules (see next image, fully expanded model). ModelBrowser approach to model visualization is different from other circular visualization as visualization depends on model metadata and ontologies.TreeDyn
TreeDyn is a powerful tool for editing and analyzing multiple trees. It makes extensive use of meta-information (or annotations) related to the entities under study such as taxonomic descriptions, geographic distribution or gene functions by using external annotation files in the form of key-values couples. These relationships are used by dynamic graphics operators, information visualization methods like projection, localization, labelization, reflection allowing an interaction from annotations to trees, from trees to annotations and from trees to trees through annotations. It is designed to use a standard 2D Euclidean space with feasibility for alternate layouts such as radial view, circular inside and outside.

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7 Responses to “Circular/Radial Visualizations in Bioinformatics-2”

1. 

   Abhishek Tiwari

   02.10.2009

   Circular/Radial Visualizations in Bioinformatics-2: Before we start exploring other case studies in this series .. http://tinyurl.com/aqgpqd
2. 

   Chris

   10.22.2009

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3. 

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   10.24.2009

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   06.02.2010

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   03.14.2011

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