R for Data Visualizaiton and Graphics

Rob Kabacoff, Ph.D.Vice President of Research

Source code for presentation: http://tinyurl.com/Kabacoff-CS20

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R is a Statistical and Graphical Platform

• Free• Open source• State-of-the-art data analysis• Platform for programming new methods• Runs on Windows, Linux, Mac OS X• Enormous user base• Reproducible research

R Homepage - http://www.r-project.org/CRAN Mirrors – http://cran.r-project.org/

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Data Input

R

Statistical Packages

Database Management Systems

Keyboard

OtherText Files

SAS SPSS Stata

ExcelnetCDF

SQL MySQL Oracle Access

ASCII

XMLHDF5Webscraping

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Statistical Methods

Classical Test TheoryItem Response TheoryCorrespondence AnalysisMultidimensional ScalingMeta AnalysisStructural Equation ModelingComplex Survey DesignTime Series AnalysisLongitudinal AnalysisSocial Network AnalysisStudy of Mediation and ModerationPower AnalysisClinical Trials

Descriptive StatisticsExperimental DesignLinear , Generalized, Nonlinear, and Hierarchical ModelsAnalysis of Categorical DataNonparametric AnalysisSurvival AnalysisLatent Variable ModelsBayesian ModelsMissing Values Analysis Cluster AnalysisDecision TreesData Mining

and …

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Graphs!

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Theoretical

Applied

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A Topographic Map of Maunga Whau

Meters North

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Wes

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10 Meter Contour Spacing

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Sinc( r )

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lat

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Given : depth

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14.3

Pearsonresiduals:

p-value =<2e-16

Survival on the Titanic

Age

Sex

Surv

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ale

Yes

No

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Child Adult

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No

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A High Level Tour

• General Systems– base– lattice– ggplot2

• Interactive– iplots– rggobi– googleVis– Shiny

• Specialized– vcd (categorical data)– VIM (missing data)– likert (likert data)– scatterplot3d (3-D

scatterplot)– car (regression)– corrplot (correlations)– (decision trees)– (dendograms)– effects (glm/ANOVA)

Lattice Graphics

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ggplot2 Graphics

Base Graphics

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3 completegraphics systems

BASE GRAPHICS

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histogramsHistogram with Rug plot

Salary (dollars)

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sity

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+00

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-06

8.0e

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Histogram of Kernal Density Curve

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Histogram with Normal Curve

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bar charts

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box plots

Bass 2

Bass 1

Tenor 2

Tenor 1

Alto 2

Alto 1

Soprano 2

Soprano 1

60 65 70 75

Singer Height by Voice Part

Heights in Inches

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line chartsMonthly Airline Passengers

Time

Pas

seng

ers

(K)

1950 1952 1954 1956 1958 1960

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200

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400

500

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Monthly Airline Passengers

Time

Pas

seng

ers

(K)

1950 1952 1954 1956 1958 1960

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200

300

400

500

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UK Lung Cancer Deaths

year

1974 1975 1976 1977 1978 1979 1980

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TotalMaleFemale

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time series

Season Decomposition of a Time Series

Monthly Air Passengers

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data

Season Decomposition of a Time Series

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seas

onal

Season Decomposition of a Time Series

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Season Decomposition of a Time Series

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rem

aind

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time

SeasonDecomposition

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scatterplots

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Iris Data

Sepal Length (cm)

Pet

al L

engt

h (c

m)

-5 0 5 10

-10

-50

510

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High Density Scatterplot (n=10,000)

X

Y

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scatterplot matrix

Sepal.Length

2.0 2.5 3.0 3.5 4.0 0.5 1.0 1.5 2.0 2.5

4.5

5.5

6.5

7.5

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Sepal.Width

Petal.Length

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4.5 5.5 6.5 7.5

0.5

1.5

2.5

1 2 3 4 5 6 7

Petal.Width

Anderson's Iris Data -- 3 species

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dot plot

Cadillac FleetwoodLincoln ContinentalCamaro Z28Duster 360Chrysler ImperialMaserati BoraMerc 450SLCAMC JavelinDodge ChallengerFord Pantera LMerc 450SEMerc 450SLMerc 280CValiantHornet SportaboutMerc 280Pontiac FirebirdFerrari DinoMazda RX4Mazda RX4 WagHornet 4 DriveVolvo 142EToyota CoronaDatsun 710Merc 230Merc 240DPorsche 914-2Fiat X1-9Honda CivicLotus EuropaFiat 128Toyota Corolla

10 15 20 25 30

MPG by Automobile

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contour plots

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A Topographic Map of Maunga Whau

Meters North

Met

ers

Wes

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10 Meter Contour Spacing

LATTICE GRAPHICS

lattice graphs

• expands base graphics to include trellis plots• seeks to improve in graph defaults (symbols, axes, labels) over base

gaphics• grouping

– color, fill, line type can be mapped to variable values• facets

– subgroups can be plotted in an array based on the levels of (usually) one or two variables

• customizable panel functions allow you fine grained control of what is plotted in each facet

• comments– clean and fast– high degree of customization possible

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3D graphs with faceting

lattice graph with faceting and a customized panel function

GGPLOT2 GRAPHICS

ggplot2

• Grammar of Graphics• graphs built up in layers by plotting "geoms"• grouping

– color, fill, shape, size can be mapped to variable values• facets

– subgroups can be plotted in an array based on the levels of (usually) one or two variables

• comments– allows you to create novel plots– can be slow for large problems– no 3D graphs– HOT!

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kernel density plots with grouping

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histogram with faceting

Theoretical Applied

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boxplotsTheoretical Applied

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jittered plots

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scatter plot with smooth line

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scatterplot with fit lines, grouping, and faceting

SPECIALIZED GRAPHS

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visualizing missing dataN

umbe

r of m

issi

ngs

02

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1214

Bod

yWgt

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inW

gt

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Exp

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bina

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VIMpackage

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scatterplot matrices

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yrs.since.phd

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yrs.service

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salary

carpackage

33-1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4 0.6 0.8 1

cyl

disp

wt

hp

carb

qsec

gear

am

drat

vs

disp

wt

hp

carb

qsec

gear

am

drat

vs

mpg

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-59

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visualizing correlations

variables reorderedto find clusters

non-significant (.05)correlations indicatedwith an X

corrplot package

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cyl

am vs

carb w

t

drat

gear

qsec

mpg hp

disp

Specification Variables

Maserati BoraChrysler ImperialLincoln ContinentalCadillac FleetwoodHornet SportaboutPontiac FirebirdFord Pantera LCamaro Z28Duster 360ValiantHornet 4 DriveAMC JavelinDodge ChallengerMerc 450SLCMerc 450SEMerc 450SLHonda CivicToyota CorollaFiat X1-9Fiat 128Ferrari DinoMerc 240DMazda RX4Mazda RX4 WagMerc 280CMerc 280Lotus EuropaMerc 230Volvo 142EDatsun 710Porsche 914-2Toyota Corona

Car

Mod

els

Heatmapstats

package

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visualizing categorical data

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Male Female

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No Yes

Survived

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1st 2nd3rd

Class

vcdpackage

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visualizing effects (linear models)

2 x 3 ANCOVA

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rank*sex effect plot

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: sex Female

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rank by sex interaction (means)adjusting for other variables

effectspackage

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visualizing effects (generalized linear models)

Logistic regression with 8 predictors

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rating effects (prob) by gender adjustingfor other variables

effectspackage

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3D ScatterplotAutomobile Data

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1

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Displacement (cu. in.)

Wei

ght (

lb/1

000)

Mile

s/(U

S)

Gal

lon

Mazda RX4Mazda RX4 Wag

Datsun 710Hornet 4 Drive

Hornet SportaboutValiant

Duster 360

Merc 240D

Merc 230

Merc 280

Merc 280C Merc 450SEMerc 450SL

Merc 450SLC

Cadillac FleetwoodLincoln Continental

Chrysler Imperial

Fiat 128

Honda Civic

Toyota Corolla

Toyota Corona

Dodge ChallengerAMC Javelin

Camaro Z28

Pontiac Firebird

Fiat X1-9Porsche 914-2

Lotus Europa

Ford Pantera L

Ferrari Dino

Maserati Bora

Volvo 142E

scatterplot3dpackage

INTERACTIVE GRAPHICS

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iplots hold [Ctrl] and mouse over graph for info

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rggobi

• GGobi is an open source visualization program for exploring high-dimensional data

• rggobi provides R command line interface to GGobi

Installation1. install GGobi: download from www.ggobi.org2. in R: install.packages("rggobi")

see:http://www.ggobi.org/rggobi/introduction.pdf

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Display toopen newwindows

Interactionto select,identity, orbrush

View to changetype of xy plot

right mouseto select

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googleVis

• Provides access to Google Chart Tools– motion charts– annotated time lines– maps– other (e.g. line, bar, bubble, column, area, scatter,

candlestick, pie, org charts)– https://developers.google.com/chart/

• output is html code containing data and references to JavaScript functions hosted by Google

• an internet connection required to view the graphs

demo(WorldBank)

Hans Rosling in his TED talks

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Shiny

• Package for building interative web applications with R– homepage- http://www.rstudio.com/shiny/ – examples- http://www.rstudio.com/shiny/showcase/

• Distribution– self hosted (requires free Shiny Server on Linux

server)– Rstudio hosted– distribute as a package

pkgs <- c("Rcpp", "httpuv", "shiny")install.packages(pkgs)library(shiny)runExample("06_tabsets")

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shiny example

RESOURCES

www.statmethods.net

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Books

R in ActionRobert I. Kabacoff

R Graphics CookbookWinston Chang

LatticeDeepayan Sarkar

ggplot2Hadley Wickham

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additional websites

• Cookbook for R http://www.cookbook-r.com/

• ggplot2 documentationhttp://docs.ggplot2.org/current/

• R-Bloggershttp://www.r-bloggers.com/