Data Visualization with R & ggplot2

Karthik Ram

September 2, 2013

Data Visualization with R & ggplot2 Karthik Ram

 Download this PDF

[Link]/karthikram/ggplot-lecture
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Some housekeeping

Install some packages (make sure you also have recent copies of
reshape2 and plyr)

[Link]("ggplot2", dependencies = TRUE)

Data Visualization with R & ggplot2 Karthik Ram

 Base graphics

Ugly, laborious, and verbose

There are better ways to describe statistical visualizations.

Data Visualization with R & ggplot2 Karthik Ram

 Why ggplot2?

Follows a grammar, just like any language.

It defines basic components that make up a sentence. In this
case, the grammar defines components in a plot.
Grammar of graphics originally coined by Lee Wilkinson

Data Visualization with R & ggplot2 Karthik Ram

 Why ggplot2?

Supports a continuum of expertise.

Get started right away but with practice you can effortless
build complex, publication quality figures.

Data Visualization with R & ggplot2 Karthik Ram

 Section 1

Basics

Data Visualization with R & ggplot2 Karthik Ram

 Some terminology

ggplot - The main function where you specify the dataset and
variables to plot
geoms - geometric objects
geom point(), geom bar(), geom density(), geom line(),
geom area()
aes - aesthetics
shape, transparency (alpha), color, fill, linetype.
scales Define how your data will be plotted
continuous, discrete, log

Data Visualization with R & ggplot2 Karthik Ram

 Section 2

Assembling your first ggplot

Data Visualization with R & ggplot2 Karthik Ram

 The iris dataset

head(iris)

## [Link] [Link] [Link] [Link] Species

## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa
## 3 4.7 3.2 1.3 0.2 setosa
## 4 4.6 3.1 1.5 0.2 setosa
## 5 5.0 3.6 1.4 0.2 setosa
## 6 5.4 3.9 1.7 0.4 setosa

Data Visualization with R & ggplot2 Karthik Ram

 Lets try an example

ggplot(data = iris, aes(x = [Link], y = [Link])) +

geom_point()

4.5

4.0




[Link]

3.5




3.0




2.5

2.0

5 6 7 8
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Basic structure

ggplot(data = iris, aes(x = [Link], y = [Link]))

+ geom_point()
myplot <- ggplot(data = iris, aes(x = [Link], y = [Link]))
myplot + geom_point()

Specify the data and variables inside the ggplot function.

Anything else that goes in here becomes a global setting.
Then add layers of geometric objects, statistical models, and
panels.

Data Visualization with R & ggplot2 Karthik Ram

 Quick note

Never use qplot - short for quick plot.

Youll end up unlearning and relearning a good bit.

Data Visualization with R & ggplot2 Karthik Ram

 Increase the size of points

ggplot(data = iris, aes(x = [Link], y = [Link])) +

geom_point(size = 3)

4.5

4.0




[Link]

3.5





3.0




2.5

2.0

5 6 7 8
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Add some color

ggplot(iris, aes([Link], [Link], color = Species)) +

geom_point(size = 3)

4.5

4.0




[Link]

3.5 Species

setosa

versicolor
3.0
virginica



2.5

2.0

5 6 7 8
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Differentiate points by shape

ggplot(iris, aes([Link], [Link], color = Species)) +

geom_point(aes(shape = Species), size = 3)

4.5

4.0




[Link]

3.5 Species

setosa

versicolor
3.0
virginica

2.5

2.0

5 6 7 8
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Exercise 1

# Make a small sample of the diamonds dataset

d2 <- diamonds[sample(1:dim(diamonds)[1], 1000), ]

Then generate this plot below.

color


15000



D




E




F
price

10000





G




















H













5000

































I











































































J

























































0
1 2 3
carat

Data Visualization with R & ggplot2 Karthik Ram

 Section 3

Box plots

Data Visualization with R & ggplot2 Karthik Ram

 See ?geom boxplot for list of options

library(MASS)
ggplot(birthwt, aes(factor(race), bwt)) + geom_boxplot()

5000

4000

3000
bwt

2000

1000

1 2 3
factor(race)

Data Visualization with R & ggplot2 Karthik Ram

 Section 4

Histograms

Data Visualization with R & ggplot2 Karthik Ram

 See ?geom histogram for list of options

h <- ggplot(faithful, aes(x = waiting))

h + geom_histogram(binwidth = 30, colour = "black")

150
count

100

50

0 50 100 150
waiting

Data Visualization with R & ggplot2 Karthik Ram

 h <- ggplot(faithful, aes(x = waiting))
h + geom_histogram(binwidth = 8, fill = "steelblue",
colour = "black")

60

40
count

20

30 50 70 90
waiting

Data Visualization with R & ggplot2 Karthik Ram

 Section 5

Line plots

Data Visualization with R & ggplot2 Karthik Ram

 climate <- [Link]("[Link]", header = T)
ggplot(climate, aes(Year, Anomaly10y)) +
geom_line()

0.5
Anomaly10y

0.0

1920 1950 1980

Year

climate <- [Link](text =

RCurl::getURL([Link]

Data Visualization with R & ggplot2 Karthik Ram

 We can also plot confidence regions
ggplot(climate, aes(Year, Anomaly10y)) +
geom_ribbon(aes(ymin = Anomaly10y - Unc10y,
ymax = Anomaly10y + Unc10y),
fill = "blue", alpha = .1) +
geom_line(color = "steelblue")

0.5
Anomaly10y

0.0

1920 1950 1980

Year

Data Visualization with R & ggplot2 Karthik Ram

 Exercise 2

Modify the previous plot and change it such that there are
three lines instead of one with a confidence band.

0.5
Anomaly10y

0.0

1920 1950 1980

Year

Data Visualization with R & ggplot2 Karthik Ram

 Section 6

Bar plots

Data Visualization with R & ggplot2 Karthik Ram

 ggplot(iris, aes(Species, [Link])) +
geom_bar(stat = "identity")

300
[Link]

200

100

setosa versicolor virginica

Species

Data Visualization with R & ggplot2 Karthik Ram

 df <- melt(iris, [Link] = "Species")
ggplot(df, aes(Species, value, fill = variable)) +
geom_bar(stat = "identity")

750

variable
500 [Link]
value

[Link]
[Link]
[Link]
250

setosa versicolor virginica

Species

Data Visualization with R & ggplot2 Karthik Ram

 Section 7

plyr and reshape are key for using R

Data Visualization with R & ggplot2 Karthik Ram

 plyr and reshape

These two packages are the swiss army knives of R.

plyr
1 ddply
2 llply
3 join
reshape.
1 melt
2 dcast
3 acast

Data Visualization with R & ggplot2 Karthik Ram

 iris[1:2, ]

## [Link] [Link] [Link] [Link] Species

## 1 5.1 3.5 1.4 0.2 setosa
## 2 4.9 3.0 1.4 0.2 setosa

df <- melt(iris, [Link] = "Species")

df[1:2, ]

## Species variable value

## 1 setosa [Link] 5.1
## 2 setosa [Link] 4.9

Data Visualization with R & ggplot2 Karthik Ram

 ggplot(df, aes(Species, value, fill = variable)) +
geom_bar(stat = "identity", position = "dodge")

6
variable
[Link]
value

4 [Link]
[Link]
[Link]

setosa versicolor virginica

Species

Data Visualization with R & ggplot2 Karthik Ram

 Exercise 3
Using the d2 dataset you created earlier, generate this plot below.
Take a quick look at the data first to see if it needs to be binned.

75

cut
Fair
Good
count

50
Very Good
Premium
Ideal
25

I1 SI2 SI1 VS2 VS1 VVS2 VVS1 IF

clarity

Data Visualization with R & ggplot2 Karthik Ram

 Exercise 4
Using the climate dataset, create a new variable called sign.
Make it logical (true/false) based on the sign of Anomaly10y.
Plot a bar plot and use sign variable as the fill.

0.5
Anomaly10y

sign
FALSE
TRUE

0.0

1920 1950 1980

Year

Data Visualization with R & ggplot2 Karthik Ram

 Section 8

Density Plots

Data Visualization with R & ggplot2 Karthik Ram

 Density plots

ggplot(faithful, aes(waiting)) + geom_density()

0.03
density

0.02

0.01

0.00

50 60 70 80 90
waiting

Data Visualization with R & ggplot2 Karthik Ram

 Density plots

ggplot(faithful, aes(waiting)) +
geom_density(fill = "blue", alpha = 0.1)

0.03
density

0.02

0.01

0.00

50 60 70 80 90
waiting

Data Visualization with R & ggplot2 Karthik Ram

 ggplot(faithful, aes(waiting)) +
geom_line(stat = "density")

0.03
density

0.02

0.01

50 60 70 80 90
waiting

Data Visualization with R & ggplot2 Karthik Ram

 Section 9

Mapping Variables to colors

Data Visualization with R & ggplot2 Karthik Ram

 Colors

aes(color = variable)
aes(color = "black")
# Or add it as a scale
scale_fill_manual(values = c("color1", "color2"))

Data Visualization with R & ggplot2 Karthik Ram

 The RColorBrewer package

library(RColorBrewer)
[Link]()

Data Visualization with R & ggplot2 Karthik Ram

 Using a color brewer palette
df <- melt(iris, [Link] = "Species")
ggplot(df, aes(Species, value, fill = variable)) +
geom_bar(stat = "identity", position = "dodge") +
scale_fill_brewer(palette = "Set1")

6
variable
[Link]
value

4 [Link]
[Link]
[Link]

setosa versicolor virginica

Species

Data Visualization with R & ggplot2 Karthik Ram

 Manual color scale
ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point() +
facet_grid(Species .) +
scale_color_manual(values = c("red", "green", "blue"))

4.5

4.0

setosa



3.5





3.0

2.5
2.0
[Link]

4.5 Species
versicolor
4.0 setosa
3.5

3.0




versicolor

2.5



2.0 virginica
4.5
4.0
virginica

3.5

3.0





2.5

2.0
5 6 7 8
Data Visualization with R & ggplot2 [Link] Karthik Ram
 Refer to a color chart for beautful visualizations

[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Section 10

Faceting

Data Visualization with R & ggplot2 Karthik Ram

 Faceting along columns
ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point() +
facet_grid(Species .)

4.5

4.0

setosa



3.5




3.0

2.5
2.0
[Link]

4.5 Species
versicolor
4.0 setosa
3.5

3.0




versicolor
2.5

2.0 virginica
4.5
4.0
virginica

3.5

3.0





2.5

2.0
5 6 7 8
[Link]
Data Visualization with R & ggplot2 Karthik Ram
 and along rows
ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point() +
facet_grid(. Species)

setosa versicolor virginica

4.5


4.0


[Link]

Species
3.5










setosa


versicolor
3.0




















virginica


2.5

2.0

5 6 7 8 5 6 7 8 5 6 7 8
[Link]
Data Visualization with R & ggplot2 Karthik Ram
 or just wrap your panels
ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point() +
facet_wrap( Species)

setosa versicolor virginica

4.5


4.0


[Link]

Species
3.5










setosa


versicolor
3.0




















virginica


2.5

2.0

5 6 7 8 5 6 7 8 5 6 7 8
[Link]
Data Visualization with R & ggplot2 Karthik Ram
 Section 11

Adding smoothers

Data Visualization with R & ggplot2 Karthik Ram

 ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point(aes(shape = Species), size = 3) +
geom_smooth(method = "lm")

4.5

[Link]

4.0 Species


3.5

setosa





3.0
versicolor
2.5 virginica

2.0
5 6 7 8
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point(aes(shape = Species), size = 3) +
geom_smooth(method = "lm") +
facet_grid(. Species)

setosa versicolor virginica

4.5



4.0



[Link]

Species
3.5
setosa


versicolor
3.0

virginica
2.5

2.0
5 6 7 8 5 6 7 8 5 6 7 8
[Link]

Data Visualization with R & ggplot2 Karthik Ram

 Section 12

Themes

Data Visualization with R & ggplot2 Karthik Ram

 Adding themes

Themes are a great way to define custom plots.

+theme()
# see ?theme() for more options

Data Visualization with R & ggplot2 Karthik Ram

 A themed plot

ggplot(iris, aes([Link], [Link], color = Species)) +

geom_point(size = 1.2, shape = 16) +
facet_wrap( Species) +
theme([Link] = element_rect(fill = NA),
[Link] = "bottom",
[Link] = element_rect(fill = NA),
[Link].y = element_text(angle = 0))

Data Visualization with R & ggplot2 Karthik Ram

 Adding themes

setosa versicolor virginica

4.5

4.0

3.5


[Link]





3.0








2.5

2.0

5 6 7 8 5 6 7 8 5 6 7 8
[Link]

Species
setosa
versicolor
virginica

Data Visualization with R & ggplot2 Karthik Ram

 ggthemes library

[Link]("ggthemes")
library(ggthemes)
# Then add one of these themes to your plot
+theme_stata()
+theme_excel()
+theme_wsj()
+theme_solarized()

Data Visualization with R & ggplot2 Karthik Ram

 Section 13

Create functions to automate your plotting

Data Visualization with R & ggplot2 Karthik Ram

 Write functions for day to day plots

my_custom_plot <- function(df, title = "", ...) {

ggplot(df, ...) +
ggtitle(title) +
whatever_geoms() +
theme(...)
}

Then just call your function to generate a plot. Its a lot easier to
fix one function that do it over and over for many plots

plot1 <- my_custom_plot(dataset1, title = "Figure 1")

Data Visualization with R & ggplot2 Karthik Ram

 Section 14

Scales

Data Visualization with R & ggplot2 Karthik Ram

 Commonly used scales

scale_fill_discrete(); scale_colour_discrete()
scale_fill_hue(); scale_color_hue()
scale_fill_manual(); scale_color_manual()
scale_fill_brewer(); scale_color_brewer()
scale_linetype(); scale_shape_manual()

Data Visualization with R & ggplot2 Karthik Ram

 Adding a continuous scale
library(MASS)
ggplot(birthwt, aes(factor(race), bwt)) +
geom_boxplot(width = .2) +
scale_y_continuous(labels = (paste0(1:4, " Kg")),
breaks = seq(1000, 4000, by = 1000))

4 Kg

3 Kg
bwt

2 Kg

1 Kg

1 2 3
factor(race)
Data Visualization with R & ggplot2 Karthik Ram
 Another continuous scale with custom labels

# Assign the plot to an object

dd <- ggplot(iris, aes([Link], [Link], color = Species)) +
geom_point(size = 4, shape = 16) +
facet_grid(. Species)
# Now add a scale
dd +
scale_y_continuous(breaks = seq(2, 8, by = 1),
labels = paste0(2:8, " cm"))

Data Visualization with R & ggplot2 Karthik Ram

 gradients

h + geom_histogram( aes(fill = ..count..), color="black") +

scale_fill_gradient(low="green", high="red")

20
count
25
20
count

15
10
10
5
0

40 60 80 100
waiting

Data Visualization with R & ggplot2 Karthik Ram

 Section 15

Publication quality figures

Data Visualization with R & ggplot2 Karthik Ram

 If the plot is on your screen
ggsave("/path/to/figure/[Link]")

If your plot is assigned to an object

ggsave(plot1, file = "/path/to/figure/[Link]")

Specify a size
ggsave(file = "/path/to/figure/[Link]", width = 6,
height =4)

or any format (pdf, png, eps, svg, jpg)

ggsave(file = "/path/to/figure/[Link]")
ggsave(file = "/path/to/figure/[Link]")
ggsave(file = "/path/to/figure/[Link]")

Data Visualization with R & ggplot2 Karthik Ram

 Further help
Youve just scratched the surface with ggplot2.
Practice
Read the docs (either locally in R or at
[Link]
Work together

Data Visualization with R & ggplot2 Karthik Ram