A Grammar of Graphics

A grammar of graphics:
past, present, and future

Hadley Wickham
Iowa State University
http://had.co.nz/
Past
If any number of
magnitudes are each
the same multiple of
the same number of
other magnitudes,
then the sum is that
multiple of the sum.
Euclid, ~300 BC
If any number of
magnitudes are each
the same multiple of
the same number of
other magnitudes,
then the sum is that
multiple of the sum.
Euclid, ~300 BC
m(x) = (mx)
The grammar of graphics

An abstraction which makes thinking,
reasoning and communicating graphics

easier
Developed by Leland Wilkinson, particularly

in The Grammar of Graphics 1999/2005
One of the cornerstones of my research

(Ill talk about the others later)
Present
ggplot
High-level package for creating statistical graphics.

A rich set of components + user friendly wrappers
Inspired by The Grammar of Graphics
Leland Wilkinson 1999
John Chambers award in 2006
Philosophy of ggplot
Examples from a recent paper
New methods facilitated by ggplot
Philosophy
Make graphics easier

Use the grammar to facilitate research into
new types of display
Continuum of expertise:
start simple by using the results of the theory

grow in power by understanding the theory
begin to contribute new components
Orthogonal components and minimal special

cases should make learning easy(er?)
Examples
J.Hobbs, H.Wickham, H.Hofmann, and D.Cook.

Glaciers melt as mountains warm: A graphical
case study. Computational Statistics. Special issue for
ASA Statistical Computing and Graphics Data Expo 2006.
Exploratory graphics created with GGobi,

Mondrian, Manet, Gauguin and R, but needed
consistent high-quality graphics that work in
black and white for publication
So... used ggplot to recreate the graphics
qplot(long, lat, data = expo, geom="tile", fill = ozone,

facets = year ~ month) +
scale_fill_gradient(low="white", high="black") + map
ggplot(df, aes(x = long + res * x, y = lat + res * y)) + map +

geom_polygon(aes(group = interaction(long, lat)), fill=NA, colour="black")
30
h
t
i
w
d
e
t
a
e
r
c
y
l
r
l
u
a
i
o
t
i
t
n
I
n
o
i
t
a
l
corre
20
10
10
20
ggplot(rexpo, aes(x = long + res * rtime, y = lat + res * rpressure))

+ map + geom_line(aes(group
= id))
110
85
60
library(maps)
outlines <- as.data.frame(map("world",xlim=-c(113.8, 56.2),ylim=c(-21.2, 36.2)))
map <- c(
geom_path(aes(x = x, y = y), data = outlines, colour = alpha("grey20", 0.2)),
scale_x_continuous("", limits = c(-113.8, -56.2), breaks = c(-110, -85, -60)),
scale_y_continuous("", limits = c(-21.2, 36.2))
)
310
temperature
300
290
280
270
1995
1996
1997
1998
1999
2000
date
qplot(date, temperature, data=clustered, group=id, geom="line")

+ pacific + elnino(clustered$temperature)
pacific <- brush(cluster %in% c(5,6))

brush <- function(condition, background = "grey60", brush = "red") {
cond_string <- deparse(substitute(condition), width=500)
colour <- paste(
"ifelse(", cond_string, ", '", brush, "', '", background, "')", sep=""
)
order <- paste(
"ifelse(", cond_string, ", 2, 1)", sep=""
)
size <- paste(
"ifelse(", cond_string, ", 2, 1)", sep=""
)
list(
aes_string(colour = colour, order = order, size=size),
scale_colour_identity(),
scale_size_identity()
)
}
ggplot(clustered, aes(x = long, y = lat))

+ geom_tile(aes(width = 2.5, height = 2.5,
fill = factor(cluster)))
+ facet_grid(cluster ~ .)
+ map
+ scale_fill_brewer(palette="Spectral")
qplot(date, value, data = clusterm, group = id,

geom = "line", facets = cluster ~ variable,
colour = factor(cluster))
+ scale_y_continuous("", breaks=NA)
+ scale_colour_brewer(palette="Spectral")
New methods
Supplemental statistical summaries
Iterating between graphics and models
Tables of plots
Inspired by ideas of Tukey (and others)
Exploratory graphics, not as pretty
Intro to data
Response of trees to gypsy moth attack
5 genotypes of tree: Dan-2, Sau-2, Sau-3,
Wau-1, Wau-2
2 treatments: NGM / GM
2 nutrient levels: low / high
5 reps
Measured: weight, N, tannin, salicylates
qplot(genotype, weight, data=b)

70
60
weight
50
30
20
40
10
Dan2
Sau2
Sau3
genotype
Wau1
Wau2
70
qplot(genotype, weight, data=b,

colour=nutr)
60
weight
50
30
High
20
10
Dan2
Sau2
nutr
Low
40
Sau3
genotype
Wau1
Wau2
70
60
weight
50
30
20
40
Low
10
Sau3
Dan2
Sau2
genotype
nutr
Wau2
Wau1
High
Comparing means
For inference, interested in comparing the
means of the groups
But hard to do visually - eyes naturally

compare ranges
What can we do? - Visual ANOVA
Supplemental summaries
Fro
m
smry <- stat_summary(

Hm
isc
fun="mean_cl_boot", conf.int=0.68,
geom="crossbar", width=0.3
)
Adds another layer with summary statistics:

mean + bootstrap estimate of standard error
Motivation: still exploratory, so minimise

distributional assumptions, will model explicitly
later
70

colour=nutr)
60
weight
50
30
20
40
Low
10
Sau3
Dan2
Sau2
genotype
nutr
Wau2
Wau1
High
70

colour=nutr) + smry
60
weight
50
30
20
40
Low
10
Sau3
Dan2
Sau2
genotype
nutr
Wau2
Wau1
High
Iterating graphics
and modelling
Clearly strong genotype effect. Is there a
nutr effect? Is there a nutr-genotype
interaction?
Hard to see from this plot - what if we
remove the genotype main effect? What if

we remove the nutr main effect?
How does this compare an ANOVA?
70

colour=nutr) + smry
60
weight
50
30
20
40
Low
10
Sau3
Dan2
Sau2
genotype
nutr
Wau2
Wau1
High
20
10
nutr
weight2
10
20
Low
b$weight2 <- resid(lm(weight ~ genotype, data=b))

qplot(genotype, weight2, data=b, colour=nutr) + smry
Sau3
Dan2
Sau2
genotype
Wau2
Wau1
High
10
weight3
nutr
Low
High
10
20
b$weight3 <- resid(lm(weight ~ genotype + nutr, data=b))

qplot(genotype, weight3, data=b, colour=nutr) + smry
Sau3
Dan2
Sau2
genotype
Wau2
Wau1
Df Sum Sq Mean Sq F value Pr(>F)

genotype
4 13331
3333
36.22 8.4e-13 ***
nutr
1
1053
1053
11.44 0.0016 **
genotype:nutr 4
144
36
0.39 0.8141
Residuals
40
3681
92
anova(lm(weight ~ genotype * nutr, data=b))
Graphics Model
In the previous example, we used graphics
to iteratively build up a model - a la
stepwise regression!
But: here interested in gestalt, not accurate

prediction, and must remember that this is
just one possible model
What about model graphics?
Model Graphics
If we model first, we need graphical tools to

summarise model results, e.g. post-hoc
comparison of levels
We can do better than SAS! But its hard

work: effects, multComp and multCompView
Rich research area
60
weight
20
40
bc
Sau3
Dan2
Sau2
Wau2
Wau1
genotype
Low
High
nutr
60
weight
nutr
Low
High
40
ggplot(b, aes(x=genotype, y=weight))

20
+ geom_hline(intercept = mean(b$weight))
+ geom_crossbar(aes(y=fit, min=lower,max=upper),
data=geffect)
+ 0geom_point(aes(colour
a
a
b = nutr))
bc
c
+ geom_text(aes(label
= group),
Sau3
Dan2
Sau2
Wau2 data=geffect)
Wau1
genotype
Tables of plots
Often interested in marginal, as well as
conditional, relationships
Or comparing one subset to the whole,

rather than to other subsets
Like in contingency table, we often want to

see margins as well
Dan2
Sau2
Sau3
Wau1
Wau2
4.5
4.0
3.0
2.5
High
3.5
trt
2.0
NGM
GM
4.5
4.0
3.0
2.5
2.0
Low
3.5
GM
NGM
GM
NGM
GM
NGM
trt
GM
NGM
GM
NGM
Dan2
Sau2
Sau3
Wau1
Wau2
(all)
4.5
4.0
3.0
2.5
2.0
High
3.5
4.5
trt
3.5
3.0
2.5
2.0
4.5
3.0
2.5
2.0
GM
NGM
GM
NGM
GM
NGM
GM
NGM
GM
NGM
GM
trt
NGM
(all)
3.5
4.0
Low
4.0
NGM
GM
Arranging plots
Facilitate comparisons of interest
Small differences need to be closer
together (big differences can be far apart)
Connections to model?
Summary
Need to move beyond canned statistical
graphics to experimenting with new

graphical methods
Strong links between graphics and models,
how can we best use them?
Static graphics often aren't enough
Future
GGobi
ggplot2
rggobi
classifly
meifly
clusterfly
faceoff
geozoo
Bio- and bibliographic tools for statistics
reshape
fda
hints
localmds
lvboxplot
scagnostics
DescribeDisplay
GGobi
ggplot2
fda
hints
localmds
lvboxplot
scagnostics
DescribeDisplay
rggobi
classifly
meifly
clusterfly
faceoff
geozoo
New methods
reshape
Foundations of
statistical graphics
Dissemination
and outreach
??
??
GGobi
rggobi
classifly
meifly
clusterfly
faceoff
geozoo
New methods
ggplot2
A grammar of
interactive
graphics
A grammar of
graphics for
categorical data
Foundations of
statistical graphics
reshape2
fda
hints
localmds
lvboxplot
scagnostics
DescribeDisplay
Dissemination
and outreach
Questions?

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What is the grammar of graphics?

What is the grammar of graphics?

What is ggplot?

What is ggplot?

A grammar of graphics:

past, present, and future

The grammar of graphics

reasoning and communicating graphics

Developed by Leland Wilkinson, particularly

One of the cornerstones of my research

High-level package for creating statistical graphics.

Make graphics easier

start simple by using the results of the theory

Orthogonal components and minimal special

J.Hobbs, H.Wickham, H.Hofmann, and D.Cook.

Exploratory graphics created with GGobi,

qplot(long, lat, data = expo, geom="tile", fill = ozone,

ggplot(df, aes(x = long + res * x, y = lat + res * y)) + map +

ggplot(rexpo, aes(x = long + res * rtime, y = lat + res * rpressure))

qplot(date, temperature, data=clustered, group=id, geom="line")

pacific <- brush(cluster %in% c(5,6))

ggplot(clustered, aes(x = long, y = lat))

qplot(date, value, data = clusterm, group = id,

qplot(genotype, weight, data=b)

qplot(genotype, weight, data=b,

But hard to do visually - eyes naturally

What can we do? - Visual ANOVA

smry <- stat_summary(

Adds another layer with summary statistics:

Motivation: still exploratory, so minimise

qplot(genotype, weight, data=b,

qplot(genotype, weight, data=b,

Hard to see from this plot - what if we

remove the genotype main effect? What if

How does this compare an ANOVA?

qplot(genotype, weight, data=b,

b$weight2 <- resid(lm(weight ~ genotype, data=b))

b$weight3 <- resid(lm(weight ~ genotype + nutr, data=b))

Df Sum Sq Mean Sq F value Pr(>F)

anova(lm(weight ~ genotype * nutr, data=b))

But: here interested in gestalt, not accurate

What about model graphics?

If we model first, we need graphical tools to

We can do better than SAS! But its hard

Rich research area

ggplot(b, aes(x=genotype, y=weight))

Or comparing one subset to the whole,

Like in contingency table, we often want to

together (big differences can be far apart)

graphics to experimenting with new

Bio- and bibliographic tools for statistics

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