Martin Graham

A survey of multiple tree visualisation

This article summarises the current state of research into multiple tree visualisations. It discusses the spectrum of current representation techniques used on single trees, pairs of trees and finally multiple trees, in order to identify which representations are best suited to particular tasks and to find gaps in the representation space, in which opportunities for future multiple tree visualisation research may exist. The application areas from where multiple tree data are derived are enumerated, and the distinct structures that multiple trees make in combination with each other and the effect on subsequent approaches to their visualisation are discussed, along with the basic high-level goals of existing multiple tree visualisations.

A comparison of set-based and graph-based visualisations of overlapping classification hierarchies

The visualisation of hierarchical information sets has been a staple of Information Visualisation since the field came into being in the early 1990s. However, at present, support for visualising the correlations between multiple, overlapping sets of hierarchical information has been lacking. This is despite the realisation that for certain tasks this information is as important as the information that forms the individual hierarchies. In response to this, we have produced two early visualisation prototypes, one based on a graph visualisation, and the other on a set-based metaphor, that endeavour to display such information in a readily perceived form to potential users. The science of botanical taxonomy is used as an example of a field where such a visualisation would be useful, and also as a resource for example information sets that the prototypes can act upon. Technical and perceptual issues involved in the design and implementation of both prototypes are discussed. Following this, informal user testing on both prototypes is described, which utilised user observation techniques to elicit qualitative feedback from the taxonomists. These findings are then used to emphasise the shortcomings and advantages of each prototype, and from these probable issues for future prototyping and development are drawn.

Towards a methodology for developing visualizations

This paper presents a case study of the development of a visualization to represent and explore the relationships between multiple hierarchical structures, specifically botanical taxonomies. The case study outlines the visualizations development from initial meetings with taxonomists, through the early visual sketches of their activities, and through to the prototype as it exists now after two rounds of usability testing. Qualitative user feedback was elicited from taxonomists who used the system, using standard techniques, taken from traditional usability methodologies such as direct observation, concurrent verbal protocols, video recording and software logs. Some difficulties and differences in the testing and stages of development arising from the information visualization (IV) approach to the graphical display, as contrasted to a more standard graphical user interface (GUI), are noted and solutions proposed.

Exploring Multiple Trees through DAG Representations

We present a directed acyclic graph visualisation designed to allow interaction with a set of multiple classification trees, specifically to find overlaps and differences between groups of trees and individual trees. The work is motivated by the need to find a representation for multiple trees that has the space-saving property of a general graph representation and the intuitive parent-child direction cues present in individual representation of trees. Using example taxonomic data sets, we describe augmentations to the common barycenter DAG layout method that reveal shared sets of child nodes between common parents in a clearer manner. Other interactions such as displaying the multiple ancestor paths of a node when it occurs in several trees, and revealing intersecting sibling sets within the context of a single DAG representation are also discussed.

Combining linking and focusing techniques for a multiple hierarchy visualisation

Visualisations have previously combined linking and brushing operations successfully. However, none (to our knowledge) have combined linking and focusing techniques. We describe the motivation behind developing such a technique, and show how our visualisation takes advantage of inherent links in a set of multiple overlapping hierarchies to build a mechanism that can produce linked focus+context effects between these multiple hierarchies with a single user action. Previously, our visualisation had utilised linking only, using colour to highlight correlations between distinct but overlapping hierarchies.

Extending taxonomic visualisation to incorporate synonymy and structural markers

The visualisation of taxonomic hierarchies has evolved from indented lists of names to techniques that can display thousands of nodes and onto hundreds of thousands of nodes over multiple taxonomies. However, challenges remain within multiple hierarchy visualisation, and for taxonomic hierarchy visualisation in particular. Firstly, at present, there is no support for handling specific taxonomic information such as synonymy, with current visualisations matching solely on names. Synonymy is extremely important as it reflects expert opinion on the compatibility of data held in separate taxonomies, and is needed to produce an accurate picture of taxonomic overlap. Also, current techniques for exploring large hierarchies find it difficult to convey internal re-organisations between hierarchies, with most systems showing only addition, removal or wide-ranging fragmentation of information between taxonomies. Finding the source of changes that have occurred within an existing structure is currently only achievable through exhaustive drill-down exploration. This paper describes work that tackles these problems, incorporating synonymy information into a model for multiple hierarchy visualisation of large taxonomies, and also detailing techniques that aid navigation for discovering structural re-organisations between hierarchies and for revealing information about nodes that lie below the effective display resolution of the hierarchy layout. Two examples on real taxonomic data sets are annotated to show the effectiveness of these techniques in operation.

The challenge of visualising multiple overlapping classification hierarchies

Techniques for visualising hierarchies have concentrated on displaying static structures or, in the case of dynamic hierarchies, adding or deleting nodes from the hierarchy. However none have adequately dealt with the situation of visualising change occurring in the structure between existing nodes. We present initial work that outlines the difficulties of visualising such an event, with specific regard to the multiple classifications of information that are produced in botanical taxonomy.

Helium: visualization of large scale plant pedigrees

BackgroundPlant breeders use an increasingly diverse range of data types to identify lines with desirable characteristics suitable to be taken forward in plant breeding programmes. There are a number of key morphological and physiological traits, such as disease resistance and yield that need to be maintained and improved upon if a commercial variety is to be successful. Computational tools that provide the ability to integrate and visualize this data with pedigree structure, will enable breeders to make better decisions on the lines that are used in crossings to meet both the demands for increased yield/production and adaptation to climate change.ResultsWe have used a large and unique set of experimental barley (H. vulgare) data to develop a prototype pedigree visualization system. We then used this prototype to perform a subjective user evaluation with domain experts to guide and direct the development of an interactive pedigree visualization tool called Helium.ConclusionsWe show that Helium allows users to easily integrate a number of data types along with large plant pedigrees to offer an integrated environment in which they can explore pedigree data. We have also verified that users were happy with the abstract representation of pedigrees that we have used in our visualization tool.

VIPER: a visualisation tool for exploring inheritance inconsistencies in genotyped pedigrees

BackgroundPedigree genotype datasets are used for analysing genetic inheritance and to map genetic markers and traits. Such datasets consist of hundreds of related animals genotyped for thousands of genetic markers and invariably contain multiple errors in both the pedigree structure and in the associated individual genotype data. These errors manifest as apparent inheritance inconsistencies in the pedigree, and invalidate analyses of marker inheritance patterns across the dataset. Cleaning raw datasets of bad data points (incorrect pedigree relationships, unreliable marker assays, suspect samples, bad genotype results etc.) requires expert exploration of the patterns of exposed inconsistencies in the context of the inheritance pedigree. In order to assist this process we are developing VIPER (Visual Pedigree Explorer), a software tool that integrates an inheritance-checking algorithm with a novel space-efficient pedigree visualisation, so that reported inheritance inconsistencies are overlaid on an interactive, navigable representation of the pedigree structure.Methods and resultsThis paper describes an evaluation of how VIPER displays the different scales and types of dataset that occur experimentally, with a description of how VIPERs display interface and functionality meet the challenges presented by such data. We examine a range of possible error types found in real and simulated pedigree genotype datasets, demonstrating how these errors are exposed and explored using the VIPER interface and we evaluate the utility and usability of the interface to the domain expert.Evaluation was performed as a two stage process with the assistance of domain experts (geneticists). The initial evaluation drove the iterative implementation of further features in the software prototype, as required by the users, prior to a final functional evaluation of the pedigree display for exploring the various error types, data scales and structures.ConclusionsThe VIPER display was shown to effectively expose the range of errors found in experimental genotyped pedigrees, allowing users to explore the underlying causes of reported inheritance inconsistencies. This interface will provide the basis for a full data cleaning tool that will allow the user to remove isolated bad data points, and reversibly test the effect of removing suspect genotypes and pedigree relationships.

Visual exploration of alternative taxonomies through concepts

Abstract A graphical user interface is presented that allows users of taxonomic data to explore concept relationships between conflicting but related taxonomic classifications. Ecological analyses that use taxonomic metadata depend on accurate naming of specimens and taxa, and if the metadata involves several taxonomies, care has to be taken to match concepts between them. To perform this accurately requires expert-defined concept relationships, which are more complex yet more representative than the simple one-to-one mappings found through simple name matching, and can accommodate nomenclatural changes and differences in classification technique (cf ‘lumpers’ versus ‘splitters’). In the SEEK-Taxon (Scientific Environment for Ecological Knowledge) project we aim to help users of taxonomic datasets untangle and understand these relationships through a prototype visual interface which graphically displays these relationship structures, allowing users to comprehend such information and more accurately name their data.