Foamtree@reactome

New high level pathways overview visualisation based on Voronoi tessellation

1. Foamtree@Reactome Chuqiao Gong

2. Chuqiao Major in Computer science Visitor in Reactome team since January 2019

3. Motivation Fireworks show the entire Reactome pathway hierarchy, but Colour highlighting may be difficult to see, as there are not many pixels per node difficult to get a quick visual overview not printing well for figures in publications Links between duplicated pathways was a constraint in the implementation, but might not be needed

4. FoamTree is a JavaScript Voronoi treemap visualization innovative layout animated interactions customization Requires JavaScript and HTML5 canvas support. It works on any browser FoamTree supports hierarchies of any depth Commercial library Free version with FoamTree logo in one of the cells: https://carrotsearch.com/foamtree/

5. Foamtree example Showing java code coverage statistics gathered by Atlassian Clover

6. Reactome fireworks => foamtree DNA Replication Cell Cycle Double click cell to expose and go to next hierarchy Reactome fireworks

7. Human json data Top level h uman json data Get data model t o visualise Data model to visualize Data must be in the FoamTree data format Nodes: { dbId: 1640170 stId: R-HSA-16040170 Name: Cell Cycle Ratio: 0.05 } Edges{ From: dbId: 1640170 To:dbId : 1500620 }

8. Foamtree with Reactome data Get data and massage it Parse data in foamtree js and define the other fancy functionalities Show in Browser Visualization human data with Foamtree JS

9. Visualise data analysis result Support overrepresentation type data analysis Same process as visualise human data Get data analysis result through a Token and map two data sets to generate a new data set by matched stId Use the same fireworks color profile to recolor foamtree

10. Pros and Cons Pro Visually attractive Useful for figures, slides, etc Easy navigation Cons External, commercial library Unclear how well it integrates with Pathway Browser Pathway links not available

11. Future Development Move from prototype to production quality Link from Reactome to Foamtree as external visualisation tool

12. Future Development Move from prototype to production quality Link from Reactome to Foamtree as external visualisation tool Full integration with Pathway Browser (and all the other Reactome applications!) ?

13. A cknowledgements Henning Hermjakob Guilherme Viteri (project contributor)

14. DEMO TIME