Interactive graphics for high-dimensional genetic data

Karl Broman

Biostatistics & Medical Informatics, University of Wisconsin – Madison

kbroman.org
github.com/kbroman
@kwbroman

slides: bit.ly/Bro2014-11

Why aren’t all of our graphs interactive?

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1994

Bandwidth = 1.00

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1987

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1987

Becker & Cleveland (1987)

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1987

Becker & Cleveland (1987)

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1984

wikipedia.org

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Why?   summary + details

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Inbred mice

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Human vs mouse

daviddeen.com

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Intercross

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Genome scan for QTL

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Genome scan for QTL

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Genome-scale phenotypes

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Why?   summary + details

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Why?   people are busy

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Why?   reports to collaborators

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Why?   teaching

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Why?   teaching

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Why not?

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Why not?

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JASA Oct, 2014

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JASA Oct, 2014

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JASA Oct, 2014

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JASA Oct, 2014

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JASA Oct, 2014

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JASA Oct, 2014

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JASA Oct, 2014

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An alternative to tables

Carr & Pickle (2010) Visualizing data patterns with Micromaps.

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D3 is awesome!

You just need to learn html, css, svg, and javascript.

And don’t forget .enter()

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

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JSFiddle is awesome!

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Coffeescript is awesome!

blob.attr("x", (d) -> d.x)

height = options?.height ? 500

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Coffeescript is awesome!

blob.attr("x", (d) -> d.x)

height = options?.height ? 500

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Other options

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Trade-offs

Easy or flexible?

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Interactive eQTL plot

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R/qtlcharts   kbroman.org/qtlcharts

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R/qtlcharts   panels

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Summary

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Acknowledgments: Data

Alan Attie
Mark Keller
Biochemistry, UW–Madison
Brian Yandell Statistics and Horticulture, UW–Madison
Christina Kendziorski
Aimee Teo Broman
Biostatistics & Medical Informatics, UW–Madison
Eric Schadt Mount Sinai
Danielle Greenawalt
Amit Kulkarni
Merck & Co., Inc.
Edgar Spalding
Candace Moore
Logan Johnson
Botany, UW-Madison

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Acknowledgments: Code

D3 and stack.js by

D3 tutorials by Scott Murray

CoffeeScript by Jeremy Ashkenas

Eloquent JavaScript by Marijn Haverbeke

CoffeeScript book by Trevor Burnham

d3-tip by Justin Palmer

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slides:   bit.ly/Bro2014-11  

kbroman.org

github.com/kbroman

@kwbroman

kbroman.org/qtlcharts

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