paweł widera p a . ei w l r@ w s.e . t c n da o t u ak ....

Network visualisationsHow to tame the complexity?

Paweł Wideracd a .a t kuoe c nww l s. te r [email protected]

ICOS seminar

2013-06-13

Outline

1 Background and motivation

2 Network as a graph

3 Alternative visualisations

4 Hierarchical data

5 Summary

Paweª Widera Network visualisations - how to tame the complexity 2013-06-13 2 / 16

The problemWhat is gene/protein interaction network?

Network analysismeasure geneexpressioncorrelateexpression profilesconnect genes ifρ > thresholddiscover regulationmechanism

Example networkSeedNetgene interactions indormant and germinatingArabidopsis seeds


The problemWhat is gene/protein interaction network?

http://vseed.nottingham.ac.uk/

Network analysismeasure geneexpressioncorrelateexpression profilesconnect genes ifρ > thresholddiscover regulationmechanism

Example networkSeedNetgene interactions indormant and germinatingArabidopsis seeds



Network visual attributes

http://blog.visual.ly/network-visualizations/

Visual elementsnodesedges

Real-world exampleSCoPNetpredicted geneinteractions in dormantand germinatingArabidopsis seeds


http://blog.visual.ly/network-visualizations/

Network visual attributes


Visual elementsnodesedges

Real-world exampleSCoPNetpredicted geneinteractions in dormantand germinatingArabidopsis seeds



Manual positioningHow to make a network infographic?

"Coctails" infographic by Pop Chart Lab


http://www.fastcodesign.com/1668928/the-only-chart-you-need-to-mix-a-proper-cocktail

Layout algorithmsIn what situations they work well?

FruitNet (unpublished) — OpenOrd layout

Special casesfeature emphasissmall sizenatural ordere.g. time, flow



http://moviegalaxies.com/movies/660-Pulp-Fiction



http://moviegalaxies.com/movies/660-Pulp-Fiction


http://xkcd.com/657/



http://xkcd.com/657/


http://bost.ocks.org/mike/sankey/



http://bost.ocks.org/mike/sankey/

Circular layoutHow to reduce the visual clutter?

Examplesbasic layoutedge bindingCircos [Krzywinski et al., 2009]

A B C D

A 105 450 92 96B 20 46 78 33C 118 553 94 317D 100 18 108 104



http://mbostock.github.io/d3/talk/20111116/bundle.html


A B C D

A 105 450 92 96B 20 46 78 33C 118 553 94 317D 100 18 108 104


http://mbostock.github.io/d3/talk/20111116/bundle.html


http://circos.ca/intro/tabular_visualization/


A B C D

A 105 450 92 96B 20 46 78 33C 118 553 94 317D 100 18 108 104


http://circos.ca/intro/tabular_visualization/


http://mkweb.bcgsc.ca/tableviewer/samples/


A B C D

A 105 450 92 96B 20 46 78 33C 118 553 94 317D 100 18 108 104


http://mkweb.bcgsc.ca/tableviewer/samples/


http://web.williams.edu/Mathematics/devadoss/careerpath.html


A B C D

A 105 450 92 96B 20 46 78 33C 118 553 94 317D 100 18 108 104


http://web.williams.edu/Mathematics/devadoss/careerpath.html

Pivot graphHow to reduce the number of nodes?

[Wattenberg, 2006]nodes roll-upnetwork reduction

Communicationinside a company

between officesbetweendepartments


Hive plotHow to reduce the number of connections?

http://www.hiveplot.net/conference/vizbi2011/poster/krzywinski-hiveplot-poster.png

[Krzywinski et al., 2012]nodes on linearaxesflexible node → axisassignment andon-axis position

Network comparisonA) Escherichia Coli

gene transcription(1k nodes, 3k edges)

B) Linux function calls(12k nodes, 34k edges)




Hive plotHow to reduce the number of connections?

http://bost.ocks.org/mike/hive/

[Krzywinski et al., 2012]nodes on linearaxesflexible node → axisassignment andon-axis position

Network comparisonA) Escherichia Coli

gene transcription(1k nodes, 3k edges)

B) Linux function calls(12k nodes, 34k edges)


http://bost.ocks.org/mike/hive/

BioFabricHow to comb the hair ball?

http://www.biofabric.org/gallery/pages/SuperQuickBioFabric.html

[Longabaugh, 2012]each node is ahorizontal lineeach edge is avertical line


http://www.biofabric.org/gallery/pages/SuperQuickBioFabric.html

Hierarchical dataVisual ordering

http://bl.ocks.org/mbostock/1005873

ExamplesIcicleSunburst[Stasko et al., 2000]



Hierarchical dataVisual ordering


"Coffee flavour wheel" by Jason Davies

ExamplesIcicleSunburst[Stasko et al., 2000]



http://www.jasondavies.com/coffee-wheel/

Hierarchical dataVisual subdivision


http://mbostock.github.io/d3/talk/20111018/treemap.html

ExamplesTree mapCircle packing



http://mbostock.github.io/d3/talk/20111018/treemap.html

Hierarchical dataVisual subdivision


http://mbostock.github.io/d3/talk/20111116/pack-hierarchy.html

http://wimbledon.prcweb.co.uk/playerbubbles.html

ExamplesTree mapCircle packing



http://mbostock.github.io/d3/talk/20111116/pack-hierarchy.html

http://wimbledon.prcweb.co.uk/playerbubbles.html

Hierarchical dataInteractive exploration

http://wheredoesmymoneygo.org/bubbletree-map.html

ExamplesBubble treeSocial networkBlogosphere


http://wheredoesmymoneygo.org/bubbletree-map.html


http://www.quadrigram.com/action/exploring-your-social-network



http://www.quadrigram.com/action/exploring-your-social-network


http://linkfluence.com



http://linkfluence.com

Summary

Conclusionsnetwork visualisation is not just about nodes and edgesvisual aggregation improves readabilitychangeable point of view and interactive exploration

Ideas for the futurebubble based hierarchical browsercontext depended connections


Thank you!

AcknowledgementsThis work was supported by theEngineering and Physical SciencesResearch Council [EP/D061571/1].

Netvis TeamJames GilbertNatalio Krasnogor

Contactdl cs .ow re t k. i t@c u.e a anwpa .


http://creativecommons.org/licenses/by-sa/3.0/

References

Krzywinski, M., Birol, I., Jones, S. J., and Marra, M. A. (2012).Hive plots – rational approach to visualizing networks.Briefings in Bioinformatics, 13(5):627–644.

Krzywinski, M., Schein, J., Birol, I., Connors, J., Gascoyne, R., Horsman, D., Jones, S. J., and Marra, M. A. (2009).Circos: An information aesthetic for comparative genomics.Genome Research, 19(9):1639–1645.

Longabaugh, W. (2012).Combing the hairball with BioFabric: a new approach for visualization of large networks.BMC Bioinformatics, 13(1):275.

Stasko, J., Catrambone, R., Guzdial, M., and McDonald, K. (2000).An evaluation of space-filling information visualizations for depicting hierarchical structures.International Journal of Human-Computer Studies, 53(5):663–694.

Wattenberg, M. (2006).Visual Exploration of Multivariate Graphs.In Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, CHI ’06, pages 811–819, New York.


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