1. R for Data Visualizaiton
and Graphics
Rob Kabacoff, Ph.D.
Vice President of Research
Source code for presentation: http://tinyurl.com/Kabacoff-CS20

2. R is a Statistical and Graphical
R Homepage - http://www.r-project.org/
Platform
CRAN Mirrors – http://cran.r-project.org/
•
•
•
•
•
•
•
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
2

3. Data Input
Statistical Packages
SAS
SPSS
Stata
Keyboard
ASCII
Text Files
Excel
netCDF
HDF5
R
XML
Webscraping
SQL
MySQL
Oracle
Other
Access
Database Management Systems
3

4. Statistical Methods
Descriptive Statistics
Experimental Design
Linear , Generalized, Nonlinear,
and Hierarchical Models
Analysis of Categorical Data
Nonparametric Analysis
Survival Analysis
Latent Variable Models
Bayesian Models
Missing Values Analysis
Cluster Analysis
Decision Trees
Data Mining
Classical Test Theory
Item Response Theory
Correspondence Analysis
Multidimensional Scaling
Meta Analysis
Structural Equation Modeling
Complex Survey Design
Time Series Analysis
Longitudinal Analysis
Social Network Analysis
Study of Mediation and
Moderation
Power Analysis
Clinical Trials
and …
4

5. Given : depth
Graphs!
200
300
400
500
10 Meter Contour Spacing
165 170 175 180 185
-35
-25
-15
lat
-35
-25
Meters West
-15
165 170 175 180 185
A Topographic Map of Maunga Whau
600
100 200 300 400 500 600
100
165 170 175 180 185
0
long
0
200
400
600
800
Meters North
Sinc(
8
6
4
2
0
-2
-10
10
r)
5
Y
0
-5
0
X
-5
5
10 -10
Survival on the Titanic
Child
University Salaries by Discipline
Age
Adult
Pearson
residuals:
14.3
Male
No
200000
Yes
Salary
Sex
Survived
discipline
4.0
2.0
0.0
-2.0
-4.0
150000
Theoretical
Applied
Yes No
Female
100000
-11.1
p-value =
<2e-16
50000
0
20
Years Since Ph.D.
40
5

6. 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)
6

7. 60
40
20
0
3 complete
graphics systems
Frequency
80
100
Base Graphics
50000
100000
150000
200000
Salary (dollars)
Lattice Graphics
ggplot2 Graphics
40
100
30
Frequency
Frequency
80
60
20
40
10
20
0
0
50000
50000
100000
150000
Salary (dollars)
200000
100000
150000
Salary (dollars)
200000

8. BASE GRAPHICS
8

9. histograms
Histogram with Rug plot
150000
8.0e-06
1.2e-05
100000
200000
50000
Salary (dollars)
100000
150000
200000
Salary (dollars)
0
20
40
60
80
100
Histogram with Normal Curve
Frequency
50000
0.0e+00 4.0e-06
Density
8.0e-06
0.0e+00 4.0e-06
Density
1.2e-05
Histogram of Kernal Density Curve
50000
100000
150000
Salary (dollars)
200000
9

10. bar charts
10

11. box plots
Singer Height by Voice Part
Soprano 1
Soprano 2
Alto 1
Alto 2
Tenor 1
Tenor 2
Bass 1
Bass 2
60
65
70
75
Heights in Inches
11

12. Monthly Airline Passengers
line charts
Passengers (K)
600
4000
UK Lung Cancer Deaths
3500
Total
Male
Female
500
400
300
200
3000
100
1950
1952
1954
1956
1958
1960
2500
Time
2000
Monthly Airline Passengers
500
1000
Passengers (K)
1500
600
1974
1975
1976
1977
year
1978
1979
1980
500
400
300
200
100
1950
1952
1954
1956
1958
1960
Time
12

13. time series
300
-60
Season Decomposition of a Time Series
300
Season Decomposition of a Time Series
0 20
remainder
60
200
trend
400
500
Season
Decomposition
-20 0 20
seasonal
60
100
data
500
Monthly Air Passengers
-40
Season Decomposition of a Time Series
1950
1952
1954
1956
1958
1960
time
Season Decomposition of a Time Series
13

14. scatterplots
10
15
High Density Scatterplot (n=10,000)
5
Iris Data
Y
7
0
5
-5
4
3
-10
Petal Length (cm)
6
2
-5
1
0
5
10
X
4.5
5.0
5.5
6.0
6.5
7.0
7.5
8.0
Sepal Length (cm)
14

15. scatterplot matrix
Anderson's Iris Data -- 3 species
3.0 3.5 4.0
0.5
1.0 1.5
2.0 2.5
6.5
7.5
2.0 2.5
4.0
4.5
5.5
Sepal.Length
5
6
7
2.0
3.0
Sepal.Width
1.5
2.5
1
2
3
4
Petal.Length
0.5
Petal.Width
4.5
5.5
6.5
7.5
1
2
3
4
5
6
7
15

16. dot plot
MPG by Automobile
Toyota Corolla
Fiat 128
Lotus Europa
Honda Civic
Fiat X1-9
Porsche 914-2
Merc 240D
Merc 230
Datsun 710
Toyota Corona
Volvo 142E
Hornet 4 Drive
Mazda RX4 Wag
Mazda RX4
Ferrari Dino
Pontiac Firebird
Merc 280
Hornet Sportabout
Valiant
Merc 280C
Merc 450SL
Merc 450SE
Ford Pantera L
Dodge Challenger
AMC Javelin
Merc 450SLC
Maserati Bora
Chrysler Imperial
Duster 360
Camaro Z28
Lincoln Continental
Cadillac Fleetwood
10
15
20
25
30
16

17. contour plots
A Topographic Map of Maunga Whau
600
10 Meter Contour Spacing
110
120
400
10
0
10
150
0
200
180
0
0
17
19
18
0
160
160
110
170
140
130
10
0
110
0
Meters West
110
0
200
400
Meters North
600
800
17

18. LATTICE GRAPHICS
18

19. 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

20. 3D graphs with faceting
20

21. lattice graph with faceting and a
customized panel function

22. GGPLOT2 GRAPHICS

23. 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!

24. kernel density plots with grouping
24

25. histogram with
faceting
Theoretical
Applied
20
AsstProf
15
10
5
0
AssocProf
count
20
15
10
5
0
20
15
Prof
10
5
0
50000
100000
150000
200000
50000
100000
150000
200000
salary
25

26. boxplots
Theoretical
Applied
200000
salary
sex
150000
Female
Male
100000
50000
AsstProf
AssocProf
Prof
AsstProf
AssocProf
Prof
rank
26

27. jittered plots
27

28. scatter plot with smooth line
28

29. scatterplot with fit lines, grouping,
and faceting
29

30. SPECIALIZED GRAPHS
30

31. Danger
Exp
Pred
Gest
Span
Sleep
Dream
NonD
BrainWgt
BodyWgt
Danger
Exp
Pred
Gest
Span
Sleep
Dream
NonD
BrainWgt
BodyWgt
0
2
4
8
Combinations
6
10
Number of missings
12
14
visualizing missing data
VIM
package
1
1
2
2
2
3
9
42
31

32. car
package
scatterplot matrices
10
20
30
40
50
60
10 20 30 40 50
0
50
0
Frequency
yrs.since.phd
yrs.service
0
10
20
30
40
50
salary
100000
Frequency
x
200000
0 10
30
Frequency
x
100000
150000
x
200000
32

33. cyl
corrplot
package
wt
78
89
hp
83
79
66
hp
carb
53
39
43
75
carb
qsec
-59
-43
-17
-71
-66
wt
90
disp
visualizing correlations
disp
qsec
variables reordered
to find clusters
-49
-56
-58
-13
27
-21
am
-52
-59
-69
-24
6
-23
79
am
drat
-70
-71
-71
-45
-9
9
70
71
drat
vs
-81
-71
-55
-72
-57
74
21
17
44
mpg
-85
-85
-87
-78
-55
42
48
60
68
-1
-0.8
-0.6
-0.4
-0.2
0
0.2
0.4
0.6
vs
gear
gear
non-significant (.05)
correlations indicated
with an X
66
0.8
1
33

34. Heatmap
Specification Variables
disp
hp
mpg
qsec
gear
drat
wt
carb
vs
am
cyl
Toyota Corona
Porsche 914-2
Datsun 710
Volvo 142E
Merc 230
Lotus Europa
Merc 280
Merc 280C
Mazda RX4 Wag
Mazda RX4
Merc 240D
Ferrari Dino
Fiat 128
Fiat X1-9
Toyota Corolla
Honda Civic
Merc 450SL
Merc 450SE
Merc 450SLC
Dodge Challenger
AMC Javelin
Hornet 4 Drive
Valiant
Duster 360
Camaro Z28
Ford Pantera L
Pontiac Firebird
Hornet Sportabout
Cadillac Fleetwood
Lincoln Continental
Chrysler Imperial
Maserati Bora
Car Models
stats
package
34

35. visualizing categorical data
2000
vcd
package
Sex
1500
1000
500
0
Male Female
Survived
1500
1000
500
0
No
Yes
1000
800
600
400
200
0
Class
1st 2nd 3rd
35

36. visualizing effects (linear models)
2 x 3 ANCOVA
36

37. rank by sex interaction (means)
adjusting for other variables
effects
package
rank*sex effect plot
AsstProf
sex : Female
AssocProf
Prof
sex : Male
130000
120000
salary
110000
100000
90000
80000
70000
AsstProf
AssocProf
Prof
rank
37

38. visualizing effects (generalized
linear models)
Logistic regression with 8 predictors
38

39. rating effects (prob) by gender adjusting
for other variables
effects
package
39

40. scatterplot3d
package
3D Scatterplot
Automobile Data
35
Toyota Corolla
Fiat 128
30
Honda Civic
Lotus Europa
Fiat X1-9
Merc 240D
Merc 230
Ferrari Dino
Merc 280C
Hornet 4 Drive
Pontiac Firebird
Valiant
Chrysler Imperial
Hornet Sportabout
Merc 450SL
Merc 450SE
20
Merc 450SLCChallenger
Dodge
Maserati Bora
AMC JavelinPantera L
Ford
Duster 360
Camaro Z28
6
Lincoln Continental
Cadillac Fleetwood
5
15
4
Weight (lb/1000)
25
Datsun 710
Volvo 142E
Mazda RX4 Wag
Toyota Corona
Mazda RX4 Merc 280
3
2
10
Miles/(US) Gallon
Porsche 914-2
1
0
100
200
300
400
500
Displacement (cu. in.)
40

41. INTERACTIVE GRAPHICS
41

42. iplots
hold [Ctrl] and mouse
over graph for info
42

43. rggobi
• GGobi is an open source visualization program for
exploring high-dimensional data
• rggobi provides R command line interface to
GGobi
Installation
1. install GGobi: download from www.ggobi.org
2. in R: install.packages("rggobi")
see:
http://www.ggobi.org/rggobi/introduction.pdf
43

44. Display to
open new
windows
Interaction
to select,
identity, or
brush
View to change
type of xy plot
right mouse
to select
44

45. 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
45

46. 46

47. 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)
pkgs <- c("Rcpp", "httpuv", "shiny")
– Rstudio hosted
install.packages(pkgs)
library(shiny)
– distribute as a package runExample("06_tabsets")
47

48. shiny example
48

49. RESOURCES

50. www.statmethods.net

51. Books
R in Action
Robert I. Kabacoff
R Graphics Cookbook
Winston Chang
Lattice
Deepayan Sarkar
ggplot2
Hadley Wickham
51

52. additional websites
• Cookbook for R
http://www.cookbook-r.com/
• ggplot2 documentation
http://docs.ggplot2.org/current/
• R-Bloggers
http://www.r-bloggers.com/
52