Bioinformatics Advance Access originally published online on March 17, 2008
Bioinformatics 2008 24(9):1210-1211; doi:10.1093/bioinformatics/btn091
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Celestial3D: a novel method for 3D visualization of familial data
1Laboratory for Genetic Epidemiology, Western Australian Institute for Medical Research and UWA Centre for Medical Research and 2General Practice, School of Primary, Aboriginal & Rural Health Care, The University of Western Australia, Perth, Australia
*To whom correspondence should be addressed.
 |
ABSTRACT |
|---|
 TOP ABSTRACT ACKNOWLEDGEMENTSREFERENCE |
|---|
Summary: Traditional two-dimensional (2D) software programs for drawing pedigrees are limited when dealing with extended pedigrees. In successive generations, the number of individuals grows exponentially, leading to an unworkable amount of space required in the horizontal direction for 2D displays. In addition, it is not always possible to place closely related individuals near each other due to the lack of space in 2Ds. To address these issues we have developed three-dimensional (3D) pedigree drawing techniques to enable clearer visualization of extended pedigrees. Currently no other methods are available for displaying extended pedigrees in 3Ds. We have made freely available a software tool—‘Celestial3D’—that implements these novel techniques.
Availability: Freely available to non-commercial users
Contact: celestial3d{at}genepi.org.au
Supplementary information: www.genepi.org.au/celestial3d
With the ever-growing size and popular usage of genealogical and family-based datasets around the world, there is a concomitant need for software tools that can graphically display immense pedigree structures in a clear and interpretable fashion. This is particularly crucial given the growing number of biobanks being developed internationally. Traditional methods for drawing pedigrees in two dimensions (2D) are implemented in software programs such as Progeny (www.progenygenetics.com), PViN (Wernert and Lakshmipathy, 2005) and Cyrillic (www.cyrillicsoftware.com).1 When displaying large families, 2D methods are bound by a number of inherent limitations including:
- Horizontal space is used up rapidly by expanding generations, which leads to a lack of discernible detail.
- It may not be possible to place closely related individuals near each other, or easily interpret relationships (Fig. 1b).
- It is difficult to display families or individuals of interest in the context of the entire population.
- It is difficult to avoid long lines or crossed lines.
|
Celestial3D is a tool that has been developed to implement three dimensional (3D) pedigree visualization techniques which alleviate each of these problems. To our knowledge, there is no other tool able to display extensive pedigrees in 3D. Recent advances in consumer graphics technology have allowed the development of such a tool, suitable for use on most personal computers. Celestial3D is freely available to non-commercial users and has cross-platform support.
The underlying principle for the use of 3D space in Celestial3D is illustrated in Figure 1a. The top row shows two families displayed using conventional 2D techniques. The bottom row illustrates how these families can be displayed using 3D; the children are positioned radiating outward from the parents in the generation level below. This allows many more individuals to be placed in a given viewing area, and closely related individuals to be placed near each other (Figs 1c and d), making trends within families more visible. Navigation tools allow users to manipulate the display such that individuals of interest are seen clearly. Each individual's ID number is displayed below his or her icon.
Celestial3D employs sophisticated, specifically developed visualization techniques including layout algorithms that avoid screen clutter, and shadows that demarcate clades (individuals descended from a common ancestor), so that extensive pedigrees (such as shown in Fig. 1e) are readily interpretable. Multiple families can be displayed in a unique spiral view as illustrated in Figure 1f. In this view, each distinct family is represented by a sphere, with the pedigree structure visible inside. The spiral view allows the user to zoom in and focus on any particular family or individual without losing the context. The 3D spiral layout allows the families to be ordered along the axis into the screen, and helps to avoid spheres occluding each other. Sphere colour summarizes clinical phenotypes recorded for each family (for example, incidence of disease).
Celestial3D showcases novel 3D methods, and as it is further developed, will incorporate a comprehensive set of features to make it a valuable tool for research involving large pedigrees.
|
ACKNOWLEDGEMENTS |
|---|
|
TOPABSTRACTACKNOWLEDGEMENTSREFERENCE |
|---|
This work was funded by the Asthma Foundation of Western Australia. We would like to thank Brenda Powell, Ingrid Nilsson, Gabrielle Reid, Kylie Hewitt, Darren Twomey, Marion Macnish and Rebecca Webster for their helpful comments.
Conflict of Interest: none declared.
|
FOOTNOTES |
|---|
Associate Editor: Martin Bishop
1A more extensive list of software tools appears in the Supplementary Material. 
Received on October 5, 2007; revised on March 5, 2008; accepted on March 5, 2008
|
REFERENCE |
|---|
|
TOPABSTRACTACKNOWLEDGEMENTSREFERENCE |
|---|
Wernert EA, Lakshmipathy J. PViN – A Scalable and Flexible System for Visualizing Pedigree Databases. ( (2005) ) Proceedings of the 2005 ACM Symposium on Applied Computing: Santa Fe, New Mexico. 115–122..
CiteULike 
Connotea 
Del.icio.us What's this?
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||