DATA VISUALIZATION WITH GGPLOT2

Sca!er Plots
 Data Visualization with ggplot2

37 Geometries
abline density2d line rect vline
area dotplot linerange ribbon
bar errorbar map rug
bin2d errorbarh path segment
blank freqpoly point smooth
boxplot hex pointrange step
contour histogram polygon text
crossbar hline quantile tile
density ji!er raster violin
 Data Visualization with ggplot2

Common plot types

● Sca!er plots
● points, ji!er, abline
● Bar plots
● histogram, bar, errorbar
● Line plots
● line
 Data Visualization with ggplot2

Sca!er Plot
4.5
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4.0 ●
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Each geom has specific aesthetic mappings

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Sepal.Width
3.5 ● ● ● ●
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3.0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●

● geom_point()
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2.5 ● ● ● ● ● ● ●
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● Essential: x, y 2.0 ●
● ●

5 6 7 8
Sepal.Length

> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width)) +

geom_point()
 Data Visualization with ggplot2

Sca!er Plot
4.5
●

●
●
4.0 ●
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● ● ● ●
● ●●

Each geom has specific aesthetic mappings

● ●● ●

Sepal.Width
3.5 ●●● ● Species
● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
Virginica
geom_point()
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●
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2.5 ● ● ●●● ● ●
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● Essential: x, y 2.0 ●
● ●

5 6 7 8
Sepal.Length
● Optional: alpha, colour, fill, shape, size

> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +

geom_point()
 Data Visualization with ggplot2

aes() inside geom_()

> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point()

> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width)) +

geom_point(aes(col = Species)) same plot results!

4.5
●
control aesthetic mappings 

of each layer independently
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●
4.0 ●
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Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
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● ●● ● ●
2.5 ● ● ●●● ● ●
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● ●

2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Summary Statistics
> head(iris)
Species Sepal.Length Sepal.Width Petal.Length Petal.Width
1 Setosa 5.1 3.5 1.4 0.2
2 Setosa 4.9 3.0 1.4 0.2
3 Setosa 4.7 3.2 1.3 0.2
4 Setosa 4.6 3.1 1.5 0.2
5 Setosa 5.0 3.6 1.4 0.2
6 Setosa 5.4 3.9 1.7 0.4

> iris.summary <- aggregate(iris[2:5], list(iris$Species), mean)

> names(iris.summary)[1] <- "Species"
> iris.summary
Species Sepal.Length Sepal.Width Petal.Length Petal.Width
1 Setosa 5.006 3.428 1.462 0.246
2 Versicolor 5.936 2.770 4.260 1.326
3 Virginica 6.588 2.974 5.552 2.026
 Data Visualization with ggplot2

Add Layers
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +

geom_point() + inherits data and aes from ggplot()

different data
geom_point(data = iris.summary, shape = 15, size = 5)
inherits aes

4.5
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●
4.0 ●
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Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
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2.5 ● ● ●●● ● ●
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2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

shape ~ pch
0 ● 1 2 3 4

5 6 7 8 9

● 10 11 12 ● 13 14

15 ● 16 17 18 ● 19

● 20 ● 21 22 23 24 25

both fill and color

 Data Visualization with ggplot2

Example
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point() +
geom_point(data = iris.summary, 

shape = 21, size = 5, fill = "#00000080")

4.5
●

●
●
4.0 ●
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Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
● ● ● ● ●●
● ●● ● ●
2.5 ● ● ●●● ● ●
● ●
● ● ● ●
● ●

2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Crosshairs
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point() +
geom_vline(data = iris.summary)

4.5
●

●
●
4.0 ●
●
● ● ●●
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Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ●●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
● ● ● ● ●●
● ●● ● ●
2.5 ● ● ●●● ● ●
● ●
● ● ● ●
●●

2.0 ●

0 2 4 6 8
Sepal.Length
 Data Visualization with ggplot2

Crosshairs
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point() +
geom_vline(data = iris.summary, aes(xintercept = Sepal.Length))

4.5
●

●
●
4.0 ●
●
● ● ● ●
● ●●
● ●● ●
Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
● ● ● ● ●●
● ●● ● ●
2.5 ● ● ●●● ● ●
● ●
● ● ● ●
● ●

2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Crosshairs
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point() +
geom_vline(data = iris.summary, aes(xintercept = Sepal.Length)) +
geom_hline(data = iris.summary, aes(yintercept = Sepal.Width))

4.5
●

●
●
4.0 ●
●
● ● ● ●
● ●●
● ●● ●
Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
● ● ● ● ●●
● ●● ● ●
2.5 ● ● ●●● ● ●
● ●
● ● ● ●
● ●

2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Crosshairs
ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point() +
geom_vline(data = iris.summary, linetype = 2,
aes(xintercept = Sepal.Length, col = Species)) +
geom_hline(data = iris.summary, linetype = 2),

aes(yintercept = Sepal.Width, col = Species),
4.5
●
0
●
●
4.0 ●
● 1
● ● ● ●
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● ●● ●
Sepal.Width

3.5 ●●● ● Species 2

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
● ● ● ● ●●
● ●● ● ● 4
2.5 ● ● ●●● ● ●
● ●
● ● ● ●
● ● 5

2.0 ●

5 6 7 8 6
Sepal.Length
 Course Title

Remarks
● ggplot2 can also calculate statistics
● mean only = no good
4.5
●

●
●
4.0 ●
●
● ● ● ●
● ●●
● ●● ●
Sepal.Width

3.5 ●●● ● Species

● ● ●●● ● ● ●●
●● ● ● ● Setosa
● ●● ● ● ●● ●●● ●
● ●● ● ● ●
● Versicolor
3.0 ●● ●●● ● ●● ●●● ●●●● ●● ●●
● ●● ●●●●● ● ●
● Virginica
●●● ●●●●● ● ● ●
● ● ● ● ●●
● ●● ● ●
2.5 ● ● ●●● ● ●
● ●
● ● ● ●
● ●

2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Ji!er
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_point(position = "jitter")

4.5
●

●
●
4.0 ●
●●
●
● ● ●
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●
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Sepal.Width

3.5 ●
● ●
●● ● Species
● ● ● ● ● ●
● ● ● ●
● ● ●
●● ● ●
●
● Setosa
● ● ●● ●
● ●●● ● ● ●
● ● ●
● ● ●●
● ●
●
● Versicolor
3.0 ●●
● ●
● ● ●●● ●● ● ● ●●
● ● ●
●● ● ● ●●● ● ●
● ●
● ● ●● ●
●●
● ● Virginica
●
● ● ● ● ●
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●
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2.5 ● ●● ●
●●
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●
● ●

2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Ji!er
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_jitter()

●
●
●
4.0 ●
●
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●●
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3.5 ●
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Sepal.Width

●
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● ● Species
● ● ●
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●●
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● ● Setosa
● ●● ● ●
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●
● ●
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●● ●●
●
● Versicolor
●
3.0 ●● ●● ● ● ●
● ● ● ● ● ●● ●
●
● ●● ● ●● ●
●
●
●
●
● ● ●● ● ● ● Virginica
● ● ● ● ● ●
●●●● ● ●
● ●
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2.5 ●
●●
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2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Ji!er
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_jitter(alpha = 0.6)

4.5

4.0
Sepal.Width

3.5 Species
Setosa
Versicolor
3.0
Virginica

2.5

2.0

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Ji!er
> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
geom_jitter(shape = 1)

4.5
●

●
●
4.0 ●
●
●● ● ● ●
● ● ●
● ● ● ●
Sepal.Width

3.5 ●
●●● ●
● Species
●● ● ●
● ●● ●● ● ●●
● ● ●
●
● ● Setosa
● ●
●●● ● ● ● ●● ●
● ● ●
● ●●● ● ● ●●
●
● ● Versicolor
● ● ●● ● ● ●●
3.0 ● ● ●● ● ● ● ● ●●● ●● ●● ● ●● ● Virginica
● ● ● ●● ● ● ● ●
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2.0 ●

5 6 7 8
Sepal.Length
 Data Visualization with ggplot2

Diamonds
> ggplot(diamonds, aes(carat, price)) +
geom_point()

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0
0 1 2 3 4 5
carat
 Data Visualization with ggplot2

Diamonds
> ggplot(diamonds, aes(carat, price)) +
geom_point(alpha = 0.1)

15000
price

10000

5000

0
0 1 2 3 4 5
carat
 Data Visualization with ggplot2

Diamonds
> ggplot(diamonds, aes(carat, price)) +
geom_point(alpha = 0.01, size = 4)

15000
price

10000

5000

0
0 1 2 3 4 5
carat
 Data Visualization with ggplot2

Diamonds
> ggplot(diamonds, aes(carat, price)) +
geom_point(alpha = 0.3, shape = ".")

15000
price

10000

5000

0
0 1 2 3 4 5
carat
DATA VISUALIZATION WITH GGPLOT2

Let’s practice!
DATA VISUALIZATION WITH GGPLOT2

Bar Plots
 Data Visualization with ggplot2

Common plot types

● Sca!er plots
● points, ji!er, abline
● Bar plots
● histogram, bar, errorbar
● Line plots
● line
 Data Visualization with ggplot2

Histogram
> ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram()
stat_bin: binwidth defaulted to range/30. Use 'binwidth = x' to
adjust this.

> diff(range(iris$Sepal.Width)) / 30
[1] 0.08
20

Plot of statistical function

count
Slightly different binning algorithm 10

2 3 4
Sepal.Width
 Data Visualization with ggplot2

Histogram
> ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram(binwidth = 0.1)

Many ways to do binning

20

No space between bars

count
x axis labels between the bars
10

Summary table in the background

2.0 2.5 3.0 3.5 4.0 4.5

Sepal.Width
 Data Visualization with ggplot2

Histogram
> ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram( aes(y = ..density..), binwidth = 0.1)
internal data frame

1.5

1.0
density

y axis re-labeled

0.5

0.0

2.0 2.5 3.0 3.5 4.0 4.5

Sepal.Width
 Data Visualization with ggplot2

Different Species
> ggplot(iris, aes(x = Sepal.Width , fill = Species)) +
geom_histogram(binwidth = 0.1)

20

Species
setosa
count

versicolor
10 virginica

2.0 2.5 3.0 3.5 4.0 4.5

Sepal.Width
 Data Visualization with ggplot2

Different Species
> ggplot(iris, aes(x = Sepal.Width, fill = Species)) +
geom_histogram(binwidth = 0.1, position = "stack")

20

Species
setosa
count

versicolor
10 virginica

2.0 2.5 3.0 3.5 4.0 4.5

Sepal.Width
 Data Visualization with ggplot2

dodge
> ggplot(iris, aes(x = Sepal.Width, fill = Species)) +
geom_histogram(binwidth = 0.1, position = "dodge")

12.5

10.0

7.5 Species
setosa
count

versicolor
5.0
virginica

2.5

0.0

2.0 2.5 3.0 3.5 4.0 4.5

Sepal.Width
 Data Visualization with ggplot2

fill
> ggplot(iris, aes(x = Sepal.Width, fill = Species)) +
geom_histogram(binwidth = 0.1, position = "fill")

1.00

0.75

Species
setosa
count

0.50
versicolor
virginica

0.25

0.00

2.0 2.5 3.0 3.5 4.0 4.5

Sepal.Width
 Data Visualization with ggplot2

Bar Plot
● geom_bar()
● All positions from before available
● Two types
● Absolute counts
● Distributions
 Data Visualization with ggplot2

Habits of Mammals 30

> # Cleaning up of sleep left out 20

count
> ggplot(sleep, aes(vore)) + geom_bar()
10
> str(sleep)
'data.frame': 76 obs. of 3 variables:
$ vore : Factor w/ 4 levels "Carnivore","Herbivore",..
$ total: num 12.1 17 14.4 14.9 4 14.4 8.7 10.1 3 5.3 ... 0
$ rem : num NA 1.8 2.4 2.3 0.7 2.2 1.4 2.9 NA 0.6 ... Carnivore Herbivore Insectivore Omnivore
vore
 Data Visualization with ggplot2

Habits of Mammals 30

> # Cleaning up of sleep left out 20

count
> ggplot(sleep, aes(vore)) + geom_bar(stat = "bin")
10
> str(sleep)
'data.frame': 76 obs. of 3 variables:
$ vore : Factor w/ 4 levels "Carnivore","Herbivore",..
$ total: num 12.1 17 14.4 14.9 4 14.4 8.7 10.1 3 5.3 ... 0
$ rem : num NA 1.8 2.4 2.3 0.7 2.2 1.4 2.9 NA 0.6 ... Carnivore Herbivore Insectivore Omnivore
vore
 Data Visualization with ggplot2

Distribution Bar Plots

> library(plyr)
> iris_melted <- melt(iris, value.name = "Value",

variable.name = "Measure")
> iris_summ <- ddply(iris_melted[iris_melted$Measure == "Sepal.Width",],
"Species", summarise, avg = mean(Value), 

stdev = sd(Value))

> str(iris_summ)
'data.frame': 3 obs. of 3 variables:
$ Species: Factor w/ 3 levels "setosa","versicolor",..: 1 2 3
$ avg : num 3.43 2.77 2.97
$ stdev : num 0.379 0.314 0.322
 Data Visualization with ggplot2

First try
> ggplot(iris_summ, aes(x = Species, y = avg)) +
geom_bar()
Error : Mapping a variable to y and also using stat="bin".
With stat="bin", it will attempt to set the y value to the count of cases in each group.
This can result in unexpected behavior and will not be allowed in a future version of ggplot2.
If you want y to represent counts of cases, use stat="bin" and don't map a variable to y.
If you want y to represent values in the data, use stat="identity".
See ?geom_bar for examples. (Defunct; last used in version 0.9.2)
avg

setosa versicolor virginica

Species
 Data Visualization with ggplot2

identity
> ggplot(iris_summ, aes(x = Species, y = avg)) +
geom_bar(stat = "identity")

2
avg

setosa versicolor virginica

Species
 Data Visualization with ggplot2

geom_errorbar
> ggplot(iris_summ, aes(x = Species, y = avg)) +
geom_bar(stat = "identity", fill = "grey50") +
geom_errorbar(aes(ymin = avg - stdev, ymax = avg + stdev),

width = 0.2)

3
Dynamite Plot
avg

setosa versicolor virginica

Species
DATA VISUALIZATION WITH GGPLOT2

Let’s practice!
DATA VISUALIZATION WITH GGPLOT2

Line Plots
Time Series
 Data Visualization with ggplot2

Common plot types

● Sca!er plots
● points, ji!er, abline
● Bar plots
● histogram, bar, errorbar
● Line plots
● line
 Data Visualization with ggplot2

Beaver
> str(beaver)
'data.frame': 101 obs. of 3 variables:
$ time : POSIXct, format: "2000-01-01 09:30:00" "2000-01-01 ...
$ temp : num 36.6 36.7 36.9 37.1 37.2 ...
$ active: Factor w/ 2 levels "0","1": 1 1 1 1 1 1 1 1 1 1 ...
 Data Visualization with ggplot2

Beaver
> ggplot(beaver, aes(x = time, y = temp)) +
geom_line()

38.0
temp

37.5

37.0

36.5
09:00 12:00 15:00 18:00 21:00 00:00
time
 Data Visualization with ggplot2

Beaver
> ggplot(beaver, aes(x = time, y = temp, col = factor(active))) +
geom_line()

38.0

factor(active)
temp

37.5 0
1

37.0

36.5
09:00 12:00 15:00 18:00 21:00 00:00
time
 Data Visualization with ggplot2

Aesthetics - categorical variables

Efficiency in Decoding Separate Groups
Low High
Filled Sequential Qualitative
Shapes Colours Colours

Shape
Hatching Outlines Labels

Line Width Line Type Line Colours

 Data Visualization with ggplot2

linetype
> ggplot(fish, aes(x = Year, y = Capture, linetype = Species)) +
geom_line()
> names(fish)
[1] "Species" "Year" "Capture"

6e+05

Species
Pink
4e+05
Chum
Capture

Sockeye
Coho
Rainbow
2e+05
Chinook
Atlantic

0e+00

1960 1980 2000

Year
 Data Visualization with ggplot2

size
> ggplot(fish, aes(x = Year, y = Capture, size = Species)) +
geom_line()

6e+05

Species
Pink
4e+05
Chum
Capture

Sockeye
Coho
Rainbow
2e+05
Chinook
Atlantic

0e+00

1960 1980 2000

Year
 Data Visualization with ggplot2

color
> ggplot(fish, aes(x = Year, y = Capture, color = Species)) +
geom_line()

6e+05

Species
Pink
4e+05
Chum
Capture

Sockeye
Coho
Rainbow
2e+05
Chinook
Atlantic

0e+00

1960 1980 2000

Year
 Data Visualization with ggplot2

fill
> ggplot(fish, aes(x = Year, y = Capture, fill = Species)) +
geom_area()

1200000

900000 Species
Pink
Chum
Capture

Sockeye
600000
Coho
Rainbow
Chinook
300000
Atlantic

1960 1980 2000

Year
 Data Visualization with ggplot2

fill (2)
> ggplot(fish, aes(x = Year, y = Capture, fill = Species)) +
geom_area(position = "fill")

1.00

Species
0.75
Pink
Chum
Capture

Sockeye
0.50
Coho
Rainbow
Chinook
0.25 Atlantic

0.00

1960 1980 2000

Year
 Data Visualization with ggplot2

geom_ribbon
> ggplot(fish, aes(x = Year, y = Capture, fill = Species)) +
geom_ribbon(aes(ymax = Capture, ymin = 0), alpha = 0.3)

6e+05

Species
Pink
4e+05
Chum
Capture

Sockeye
Coho
Rainbow
2e+05
Chinook
Atlantic

0e+00

1960 1980 2000

Year
DATA VISUALIZATION WITH GGPLOT2

Let’s practice!