Tag Archives: Biology

Visualization of Large, Time-Dependent, Abstract Data with Integrated Spherical and Parallel Coordinates

Parallel Coordinates with Spherical axisParallel coordinates is one of the most popular and widely used visualization techniques for large, high dimensional data. Often, data attributes are visualized on individual axes with polylines joining them. However, some data attributes are more naturally represented with a spherical coordinate system. We present a novel coupling of parallel coordinates with spherical coordinates, enabling the visualization of vector and multi-dimensional data. The spherical plot is integrated as if it is an axis in the parallel coordinate visualization. This hybrid visualization benefits from enhanced visual perception, representing vector data in a more natural spatial domain and also reducing the number of parallel axis within the parallel coordinates plot. This raises several challenges which we discuss and provide solutions to, such as, visual clutter caused by over plotting and the computational complexity of visualizing large abstract, time-dependent data. We demonstrate the results of our work-in-progress visualization technique using biological animal tracking data of a large, multi-dimensional, time-dependent nature, consisting of tri-axial accelerometry samples as well as several additional attributes. In order to understand marine wildlife behavior, the acceleration vector is reconstructed in spherical coordinates and visualized alongside with the other data attributes to enable exploration, analysis and presentation of marine wildlife behavior.

James Walker, Zhao Geng, Mark W. Jones, Robert S. Laramee.
Eurovis Short Papers, 43-47, 2012. [doi] [BibTex]

Smooth Graphs for Visual Exploration of Higher-Order State Transitions

Representing higher order paths with smooth linesIn this paper, we present a new visual way of exploring state sequences in large observational time-series. A key advantage of our method is that it can directly visualize higher-order state transitions. A standard first order state transition is a sequence of two states that are linked by a transition. A higher-order state transition is a sequence of three or more states where the sequence of participating states are linked together by consecutive first order state transitions. Our method extends the current state-graph exploration methods by employing a two dimensional graph, in which higher-order state transitions are visualized as curved lines. All transitions are bundled into thick splines, so that the thickness of an edge represents the frequency of instances. The bundling between two states takes into account the state transitions before and after the transition. This is done in such a way that it forms a continuous representation in which any subsequence of the timeseries is represented by a continuous smooth line. The edge bundles in these graphs can be explored interactively through our incremental selection algorithm. We demonstrate our method with an application in exploring labelled time-series data from a biological survey, where a clustering has assigned a single label to the data at each time-point. In these sequences, a large number of cyclic patterns occur, which in turn are linked to specific activities. We demonstrate how our method helps to find these cycles, and how the interactive selection process helps to find and investigate activities.

Jorik Blaas, Charl P. Botha, Ed Grundy, Mark W. Jones, Robert S. Laramee and Frits H. Post.
IEEE Transactions on Visualization and Computer Graphics 15(6), 969-976, 2009. [doi] [BibTeX]

Visualization of Sensor Data from Animal Movement

Accelerometry data visualized on a sphereA new area of biological research is identifying and grouping patterns of behaviour in wild animals by analysing data obtained through the attachment of tri-axial accelerometers. As these recording devices become smaller and less expensive their use has increased. Currently acceleration data are visualised as 2D time series plots, and analyses are based on summary statistics and the application of Fourier transforms. We develop alternate visualisations of this data so as to analyse, explore and present new patterns of animal behaviour. Our visualisations include interactive spherical scatterplots, spherical histograms, clustering methods, and feature-based state diagrams of the data. We study the application of these visualisation methods to accelerometry data from animal movement. The reaction of biologists to these visualisations is also reported.

Edward Grundy, Mark W. Jones, Robert S. Laramee, Rory P. Wilson and Emily L.C. Shepard
Eurovis 2009, Computer Graphics Forum 28(3), 815-822, 2009 [doi] [BibTeX]