Introduction to ggplot2

Introduction to ggplot2Elegant Graphics for Data Analysis

Maik Röder15.12.2011

RUGBCN and Barcelona Code Meetup

1vendredi 16 décembre 2011

Data Analysis Steps• Prepare data

• e.g. using the reshape framework for restructuring data

• Plot data

• e.g. using ggplot2 instead of base graphics and lattice

• Summarize the data and refine the plots

• Iterative process


ggplot2grammar of graphics


Grammar

• Oxford English Dictionary:

• The fundamental principles or rules of an art or science

• A book presenting these in methodical form. (Now rare; formerly common in the titles of books.)

• System of rules underlying a given language

• An abstraction which facilitates thinking, reasoning and communicating


The grammar of graphics

• Move beyond named graphics (e.g. “scatterplot”)

• gain insight into the deep structure that underlies statistical graphics

• Powerful and flexible system for

• constructing abstract graphs (set of points) mathematically

• Realizing physical representations as graphics by mapping aesthetic attributes (size, colour) to graphs

• Lacking openly available implementation


Specification

• DATA - data operations that create variables from datasets. Reshaping using an Algebra with operations

• TRANS - variable transformations

• SCALE - scale transformations

• ELEMENT - graphs and their aesthetic attributes

• COORD - a coordinate system

• GUIDE - one or more guides

Concise description of components of a graphic


Birth/Death Rate

Source: http://www.scalloway.org.uk/popu6.htm


http://www.scalloway.org.uk/popu6.htm

http://www.scalloway.org.uk/popu6.htm

Excess birth (vs. death) rates in selected countries

Source: The grammar of Graphics, p.138vendredi 16 décembre 2011

Grammar of Graphics

DATA: source("demographics")DATA: longitude, latitude = map(source("World"))TRANS: bd = max(birth - death, 0)COORD: project.mercator()ELEMENT: point(position(lon * lat), size(bd), color(color.red))ELEMENT: polygon(position(longitude * latitude))

Source: The grammar of Graphics, p.13

Specification can be run in GPL implemented in SPSS


Grammar of Graphics

DataTrans

Element

ScaleGuide

Coord

Layered Grammar of Graphics Defaults

DataMapping

LayerDataMappingGeomStatPosition

ScaleCoordFacet

Rearrangement of Components


Layered Grammar of Graphics

w <- worldd <- demographicsd <- transform(d, bd = pmax(birth - death, 0))p <- ggplot(d, aes(lon, lat)) p <- p + geom_polygon(data = w)p <- p + geom_point(aes(size = bd), colour = "red")p <- p + coord_map(projection = "mercator")p

Implementation embedded in R using ggplot2


ggplot2

• Author: Hadley Wickham

• Open Source implementation of the layered grammar of graphics

• High-level R package for creating publication-quality statistical graphics

• Carefully chosen defaults following basic graphical design rules

• Flexible set of components for creating any type of graphics


ggplot2 installation

• In R console:

install.packages("ggplot2")library(ggplot2)


qplot

• Quickly plot something with qplot

• for exploring ideas interactively

• Same options as plot converted to ggplot2

qplot(carat, price, data=diamonds, main = "Diamonds", asp = 1)



Exploring with qplot

qplot(log(carat), log(price), data=diamonds)

qplot(carat, price, data=diamonds)

First try:

Log transform using functions on the variables:



from qplot to ggplot

qplot(carat, price, data=diamonds, main = "Diamonds", asp = 1)

p <- ggplot(diamonds, aes(carat, price)) p <- p + geom_point()p <- p + opts(title = "Diamonds", aspect.ratio = 1)p


Data and mapping

• If you need to flexibly restructure and aggregate data beforehand, use Reshape

• data is considered an independent concern

• Need a mapping of what variables are mapped to what aesthetic

• weight => x, height => y, age => size

• Mappings are defined in scales


Statistical Transformations

• a stat transforms data

• can add new variables to a dataset

• that can be used in aesthetic mappings


stat_smooth

• Fits a smoother to the data

• Displays a smooth and its standard error

ggplot(diamonds, aes(carat, price)) + geom_point() + geom_smooth()



Geometric Object

• Control the type of plot

• A geom can only display certain aesthetics


geom_histogram

ggplot(diamonds, aes(carat)) + geom_histogram()

• Distribution of carats shown in a histogram



Position adjustments

• Tweak positioning of geometric objects

• Avoid overlaps


position_jitter

x <- c(0, 0, 0, 0, 0)y <- c(0, 0, 0, 0, 0)overplotted <- data.frame(x, y)ggplot(overplotted, aes(x,y)) + geom_point(position=position_jitter(w=0.1, h=0.1))

• Avoid overplotting by jittering points



Scales

• Control mapping from data to aesthetic attributes

• One scale per aesthetic


scale_x_continuousscale_y_continuous

x <- c(0, 0, 0, 0, 0)y <- c(0, 0, 0, 0, 0)overplotted <- data.frame(x, y)ggplot(overplotted, aes(x,y)) + geom_point(position=position_jitter(w=0.1, h=0.1)) + scale_x_continuous(limits=c(-1,1)) + scale_y_continuous(limits=c(-1,1))



Coordinate System

• Maps the position of objects into the plane

• Affect all position variables simultaneously

• Change appearance of geoms (unlike scales)


coord_maplibrary("maps")

map <- map("nz", plot=FALSE)[c("x","y")]

m <- data.frame(map)

n <- qplot(x, y, data=m, geom="path")

n

d <- data.frame(c(0), c(0))

n + geom_point(data = d, colour = "red")



Faceting• lay out multiple plots on a page

• split data into subsets

• plot subsets into different panels


Facet Types2D grid of panels: 1D ribbon of panels

wrapped into 2D:


Faceting

aesthetics <- aes(carat, ..density..)p <- ggplot(diamonds, aesthetics)p <- p + geom_histogram(binwidth = 0.2) p + facet_grid(clarity ~ cut)



Faceting Formula

no faceting . ~ .

single row multiple columns . ~ a

single column, multiple rows b ~ .

multiple rows and columns a ~ b

multiple variables in rows and/or columns

. ~ a + ba + b ~.

a + b ~ c + d


Scales in Facets

scales value free

fixed -

free x, y

free_x x

free_y y

facet_grid(. ~ cyl, scales="free_x")


Layers

• Iterativey update a plot

• change a single feature at a time

• Think about the high level aspects of the plot in isolation

• Instead of choosing a static type of plot, create new types of plots on the fly

• Cure against immobility

• Developers can easily develop new layers without affecting other layers


Hierarchy of defaults

Omitted layer Default chosen by layer

Stat Geom

Geom Stat

Mapping Plot default

Coord Cartesian coordinates

Scale Chosen depending on aesthetic and type of variable

PositionLinear scaling for continuous variables

Integers for categorical variables


Thanks!

• Visit the ggplot2 homepage:

• http://had.co.nz/ggplot2/

• Get the ggplot2 book:

• http://amzn.com/0387981403

• Get the Grammar of Graphics book from Leland Wilkinson:

• http://amzn.com/0387245448


http://had.co.nz/ggplot2/

http://had.co.nz/ggplot2/

http://amzn.com/0387981403

http://amzn.com/0387981403

Design

Introduction to ggplot2