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IntroductionSpRay
DiscussionFuture Work
SpRayan R-based visual-analytics platform for large and
high-dimensional datasets
J. Heinrich1 J. Dietzsch1 D. Bartz2 K. Nieselt1
1Center for Bioinformatics, University of Tübingen
2ICCAS/VCM, University of Leipzig
August 12, 2008
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
Outline
1 Introduction
2 SpRay
3 Discussion
4 Future Work
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
High-Dimensional DataVisual AnalyticsRelated Work
Data Sets Become Increasingly Large
High-Throughput techniques yield a huge amount of dataMicroarraysCT scannerSimulation data
Many data sets are high-dimensionalTime series: 100 experiments, 5 replicates, 10000 oligos10000 rows × 500 columns = 5 · 106 data points
. . . and complexHeterogeneous data (categorical, metric)Invalid data (NA, NaN)
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
High-Dimensional DataVisual AnalyticsRelated Work
Knowledge Discovery Becomes Increasingly Difficult
Effects of Large and High-Dimensional Datasets for theAnalysis
Storage: obviousSpeed: time to read, locate, compute, render, display thedataQuality: errors, administrationComplexity: more variables, more detail, special cases. . .Visualization: Dimensionality, Occlusion, Identification
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
High-Dimensional DataVisual AnalyticsRelated Work
Visual Analytics with R
Analytical Reasoning
Gain insight into dataReveal underlying structure and modelExtract information contained
TechniquesData AnalysisVisualizationInteraction
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
High-Dimensional DataVisual AnalyticsRelated Work
Visual Analytics with RRelated Work
GGobi1 RGL2 iPlots3
- linked views - no linked views - linked views- CPU only - CPU/GPU - CPU/GPU- R optional - depends on R - depends on R
1[Swayne et al., 2003]2[Adler and Nenadic, 2003]3[Urbanek and Theus, 2003]
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
SpRayviSual exPloRation and anAlYsis of high-dimensional data
- linked views- CPU/GPU- R optional
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
SpRayObjectives
ObjectivesExtendableInteractivePortableStatistical BackendHigh-Performance
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
SpRayArchitecture
VisLibIndependent Visualization Library
Plugins
Implement the plugin-interfaceMake use of VisLib (optional)
Host ApplicationDefines the plugin-interfaceOrganizes communication
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
Plugins
Currently availableParallelCoordinatesScatterplotHistogramData TableTableLensR-ConsoleBrushing
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
Parallel Coordinates
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
Scatterplot
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
Data Table and R-Console
Data Table R-Console
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
TableLens
[Rao and Card, 1994]
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
Linking and Brushing
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
ImplementationPluginsPerformance
Performance
Depends onSize of the data setNumber of plugins loadedOperation in progressAvailable hardware (GPU?)
ResultsLower response times than GGobi/iPlots/RGL/MondrianGood performance for middle-sized datasets
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
Discussion
Objectives achievedExtendable Visual-Analytics-FrameworkIndependent Visualization LibraryHardware-accelerated GraphicsStatistical Backend using RInteractivityGood performance / Low response times
ProblemsRedundancy in frequently used calculationsVery basic interface to Rcategorical data only supported via the R-plugin
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
Future Work
Future WorkIncorporate meta-information into datamodel to avoidredundancy (e.g. maxima)Add/Improve plugins (Heatmap, 3D Plots, . . . )Extend interface to R (hot-linking, selections)Improve GPU-usage (textures, framebufferobjects . . . )
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
Thank You!
useR! 2008 SpRay - an R-based visual-analytics platform
IntroductionSpRay
DiscussionFuture Work
References I
Adler, D. and Nenadic, O. (2003).A Framework for an R to OpenGL Interface for Interactive 3D graphics.In Proc. of the 3rd International Workshop on Distributed Statistical Computing.
Rao, R. and Card, S. K. (1994).The table lens: merging graphical and symbolic representations in an interactive focus + context visualizationfor tabular i nformation.In Proc. of SIGCHI conference on Human factors in computing systems, pages 318–322, New York, NY,USA. ACM.
Swayne, D. F., Lang, D. T., Buja, A., and Cook, D. (2003).GGobi: evolving from XGobi into an extensible framework for interactive data visualization.Computational Statistics and Data Analysis, 43(4):423–444.
Urbanek, S. and Theus, M. (2003).iPlots - High Interaction Graphics for R.In Proc. of the 3rd International Workshop on Distributed Statistical Computing.
useR! 2008 SpRay - an R-based visual-analytics platform