ggplot2

a layer-based introduction
NYC R Meetup
December
October 3rd,
1st, 2009

Harlan D. Harris
harlan@[Link]
 ggplot's philosophy
● Graphics are (should be!) created by combining
a specification with data. (Wilkinson, 2005)
● The specification is not the name of the visual
form (bar graph, scatterplot, histogram).
● The specification is a collection of rules that
together describe how to build a graph, a

Grammar of Graphics

December 3, 2009 Harlan D. Harris 2

 graphics as grammar
12

data
10

12 8 Column
10 1
6
8 Colum Column
2
6
4
n1
Colum date ct sz z 4

2
Column
n2 3
2 Colum 0
0 n3
Row 2 Row 4
Row 2 Row 4 Row 1 Row 3
Row 1 Row 3

x=date
y=ct/sz
me bars
group by z

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 advantages
● Flexible
● can define new graph types by changing
specifications
● can combine many forms into single graphs
● Smart
● compact: rules have useful defaults
● graphs always have meaning
● Reusable
● can plug new data into old specification
● can explore many types of plots from a set of data

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 ggplot2
● Hadley Wickham (Rice Univ.)
● also: reshape, plyr, etc.
● Extends & implements
The Grammar of Graphics (Wilkinson, 1995, 2005)
● Focus on layers; based on grid
● Specification as R objects constructed by functions
● Large library of components with good defaults
● ggplot2: Elegant Graphics for Data Analysis
(Wickham, 2009)

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 my gripes
● Specification is hierarchical structure;
grammar is left-to-right R expression
● Can't see the structure (usefully)
● Abuses both notation and R semantics
● Deep Magic with lazy evaluation, proto objects
● Existing tutorials lead to conceptual confusion,
requires relearning of fundamentals
● Start with the structure, not with the shortcuts

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 goal

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 data to plot

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 ggplot likes “long” data

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 will plot model vs. empirical

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 simplest plot
aes=”aesthetics”=”create mapping”

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you don't need
to know this!
structure
ggplot(data=[Link], mapping=aes(x=Parameter, y=Errors,
color=Condition)) +
layer(geom="line")

ggplot
data layers mapping scales coords facets options
x=Param.
(copy) Ø y=Errs
color=Cond.

layer[1]
data mapping geom stat geom_ stat_
identity params params
line

● structure(p), str(p)
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 add empirical data and chance

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you don't need
to know this!
structure so far
ggplot
data layers mapping scales coords facets options
x=Param.
(copy) y=Errs
color=Cond.

layer[1]
data mapping geom stat geom_ stat_
layer[1] line identity params params
data mapping geom stat geom_ stat_
layer[1] params params
(U)
data mapping
point
geom
identity
stat
size=3
geom_ stat_
layer[1] params params
(K)
data yint=Errs
mapping hline
geom hline
stat size=2
geom_ stat_
color=”black”
params params
linetype=2
yint=[64] hline hline size=.5

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 scales

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 coordinates & scales
● coordinates affect display of axes
● cartesian, polar, map, etc.
● scales affect data mapping
● colors, shapes, lines
● source of confusion
● set axis ticks/breaks and labels with
scale_x_continuous() or scale_y_discrete(), but
● set axis AND DATA range with
coord_cartesian(xlim=c(1,10))

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 options

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 shortcuts
● All those layer() calls are tedious!
● geom_*() creates a layer with a specific geom
(and various defaults, including a stat)
● stat_*() creates a layer with a specific stat
(and various defaults, including a geom)
● qplot() creates a ggplot and a layer

December 3, 2009 Harlan D. Harris 18

 quick note on stats
● stat=”identity”
● stat=”lm”
● fit y=f(x) with lm(), generate new data to be plotted
by geom_line(), CIs with geom_ribbon()
● stat=”smooth”
● fit y=f(x) with loess()
● stat=”summary”
● y=f(x) with arbitrary f()
● stat=”bin”
● histograms
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 simplest faceted plot

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 everything else (+alpha)

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 other things I find useful
● scale_x_continuous(breaks=seq(1,9,2),
labels=c(“one”, “”, “five”, “”, “nine”))
● geom_text(aes(x=.., y=.., label=..))
● annotate(geom=”text”, x=14, y=19, “outlier!”)
● geom_density()
● stat_summary([Link]=”mean_cl_boot”,
geom=”crossbar”)
● geom_jitter(position=position_jitter(width=.5))

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 takehomes
● a ggplot graph is generated by a specification +
data
● ggplot specifications are a core object plus
layers
● mappings among data, x/y, scales, and other
attributes are fundamental
● geom and stat shortcuts allow smart/compact
construction of graphs
● ggplot encourages good graphs, with facets,
good use of color, no chartjunk
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 thanks!

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 resources
● Wickham, H. (2009) ggplot2: Elegant Graphics
for Data Analysis. Springer.
● [Link]
● [Link]
● [Link]

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