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Client-Side Visualization of Cancer Pathway Data

Client-Side Visualization of Cancer Pathway Data. Philip Heller Winter 2019. Agenda. Visualization philosophy ErbB2 pathway Demo Future directions. 2 Branches of Visualization. Scientific Viz Typically engineering data Measurement Simulation High degree of spatial context

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Client-Side Visualization of Cancer Pathway Data

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  1. Client-Side Visualization of Cancer Pathway Data Philip Heller Winter 2019

  2. Agenda • Visualization philosophy • ErbB2 pathway • Demo • Future directions

  3. 2 Branches of Visualization • Scientific Viz • Typically engineering data • Measurement • Simulation • High degree of spatial context • Information Viz • No x/y/z/t

  4. Scientific Visualization • f ( 2D / 2D+t, 3D, 3D+t ) = scalar / vector / tensor • Regularity -> Best practices • Natural spatial context -> easier interpretation

  5. Scientific Viz: Fluid Dynamics Source: http://img.directindustry.com/images_di/photo-g/ fluid-dynamics-and-thermal-transfer-simulation-software-387217.jpg

  6. Scientific Viz: Jupiter Source: http://www.mps.mpg.de/projects/planetary-dynamics/JupiterSim.gif

  7. Info Viz • f ( patient / gene / organism ) = scalar / record “You can’t overlook the lack, Jack, Of any other highway to ride. It’s got no signs or dividing lines, And very few rules to guide” -- Robert Hunter, New Speedway Boogie

  8. Possibly the worst info viz ever Source: http://www.math.yorku.ca/SCS/Gallery/

  9. Formalizing Info Viz • A few “don’ts” • Even fewer “do’s” • Start with Edward Tufte • All quotes from presentation 12/10/2009

  10. Complicated Data, Simple Interactions • “The information is the interface.” • “Be content-driven, not process-driven.” • “Local optimizing of interface elements leads to global pessimizing of the interface.” • “No matter how beautiful your UI is, it would be better if there were less of it.”

  11. ErbB2 • Proto-oncogene • Cell surface receptor • Overexpressed in ~ 20% of breast cancer patients • 20% * 1.3 million new cases / yr worldwide = 260,000 new patients/yr with overexpressed ErbB2 (Source: ACS) • Under investigation at UCSC by Haussler & Stuart Labs

  12. The ErbB2 Pathway Source: Zack Sanborn

  13. How to study a pathway:For each gene… Hundreds of patients

  14. Convert to heat map

  15. Repeat for each gene & cram onto diagram

  16. Solution: Circle Graphs • Developed at UCSC by Steve Benz and Zack Sanborn • Wrap table around central spindle, compress as needed

  17. Source: Zack Sanborn

  18. My Contribution:Circle graphs meet client-side analysis • What are the measurement values behind the heats? • What information in hiding in the white? • How does one ring correlate with others? • Let’s see …

  19. Future Development • Multiple circles, plus relationship lines • Ad-hoc grouping • Ring re-ordering • Canonical layout … • MaGnET …

  20. Source: http://www.biocarta.com/pathfiles/h_her2Pathway.asp

  21. pheller@soe.ucsc.edu

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