Ggplot2 Course1 ch1 Slides PDF

DATA VISUALIZATION WITH GGPLOT2
Introduction
Data Visualization with ggplot2
Your Instructor - Rick Scave!a

● rick.scave!a@science-cra".com
● @Rick_Scave!a
Data Visualization
Data Visualization & Data Science

Data Visualization & Data Science

Statistics Design
Graphical Communication
Data Analysis & Perception
Exploratory versus Explanatory
Explore Explain
Confirm Inform
and and
Analyse Persuade
MASS::mammals
> library(MASS)
> mammals
body brain
Arctic fox 3.385 44.50
Owl monkey 0.480 15.50
Mountain beaver 1.350 8.10
Cow 465.000 423.00
Grey wolf 36.330 119.50
Goat 27.660 115.00
Roe deer 14.830 98.20
...
Pig 192.000 180.00
Echidna 3.000 25.00
Brazilian tapir 160.000 169.00
Tenrec 0.900 2.60
Phalanger 1.620 11.40
Tree shrew 0.104 2.50
Red fox 4.235 50.40
Sca!er Plot ●
> library(ggplot2) 4000

> ggplot(mammals, aes(x = body, y = brain)) +
geom_point()
brain
2000
●
●● ●
● ●
●
●
●
●
● ●
●●
●
●
●
0 ●
0 2000 4000 6000

body
Explore - Statistics 6000

geom_point(alpha = 0.6) + 4000
stat_smooth(method = "lm", col = "red", se = FALSE)
brain
2000
0 2000 4000 6000

body
Explore - Fine-tuning 10000

geom_point(alpha = 0.6) +
100
coord_fixed() +
brain
scale_x_log10() +
scale_y_log10() +
stat_smooth(method = "lm", 1
col = "#C42126",  
se = FALSE, size = 1) 1e−01 1e+01 1e+03
body
Publication-ready plot
> library(scales) # functions trans_breaks and trans_format
annotation_logticks() +
geom_point(alpha = 0.6) +
coord_fixed(xlim = c(10^-3, 10^4), ylim = c(10^-1, 10^4)) +
scale_x_log10(expression("Body weight (log"["10"]*"(Kg))"),
breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
scale_y_log10(expression("Brain weight (log"["10"]*"(g))"),
breaks = trans_breaks("log10", function(x) 10^x),
labels = trans_format("log10", math_format(10^.x))) +
stat_smooth(method = "lm", col = "#C42126", se = FALSE, size = 1) +
theme_classic()
4
10
Brain weight (log10(g))
3
10
2
10
1
10
0
10
−1
10
−3 −2 −1 0 1 2 3 4
10 10 10 10 10 10 10 10
Body weight (log10(Kg))
Anscombe Plots
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15
10
0
0 5 10 15 20
15 15
10 10
5 5
0 0
0 5 10 15 20 0 5 10 15 20
15 15
10 10
5 5
0 0
0 5 10 15 20 0 5 10 15 20
Sepals
Species
Width (cm)
Setosa
Versicolor
3
Virginica
2
4 5 6 7 8
Length (cm)
Sepals
Species
Width (cm)
Setosa
Versicolor
3
Virginica
2
4 5 6 7 8
Length (cm)
4
Species, Flower Part
Virginica, Sepals
Width (cm)
3 Virginica, Petals
Versicolor, Sepals
Versicolor, Petals
2
Setosa, Sepals
Setosa, Petals
0
0 1 2 3 4 5 6 7 8
Length (cm)
Setosa Versicolor Virginica

5
4
Width (cm)
Flower Part
3
Sepal
2 Petal
1
0
0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8
Length (cm)
4
Species, Flower Part
Virginica, Sepals
Width (cm)
3 Virginica, Petals
Versicolor, Sepals
Versicolor, Petals
2
Setosa, Sepals
Setosa, Petals
0
0 1 2 3 4 5 6 7 8
Length (cm)

5
4
Width (cm)
Flower Part
3
Sepal
2 Petal
1
0
0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8 0 1 2 3 4 5 6 7 8
Length (cm)

8
5
Centimeters
Flower Part
4 Sepal
Petal
0
Length Width Length Width Length Width
Measure
10 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
Vocabulary test score
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
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● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
5 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
0 5 10 15 20
Education (years)
10
0
0 5 10 15 20
Education (years)
10
0
0 5 10 15 20
Education (years)
10 ● ● ● ● ● ● ● ● ● ● ●● ● ●●
● ●
● ● ● ● ● ●
●●
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● ● ● ● ● ● ● ● ● ● ●●●●● ● ● ● Proportion
● ● ● ● ● ● ● ● ● ● ● ●●● ● ● ● ● ● ● ● 0.1
5 ● ● ● ● ● ● ● ● ●● ●●● ● ● ● ● ● ● ● ●
● 0.2
●
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● ● ● ● ● ● ● ● ● ● ● ● ● ●
● ● ● ● ●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 0.3
● ●●● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
●● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
0 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
0 5 10 15 20
Education (years)
Case Study: CHIS
500
250
Under−weight
0
500
Number of Individuals
250
Healthy−weight
0
500
250
Over−weight
0
500
250
Obese
0
20 40 60 80
Age
Case Study: CHIS
1.00
0.75
BMI Category
Proportion
Obese
0.50 Over−weight
Healthy−weight
Under−weight
0.25
0.00
20 40 60 80
Age
Case Study: CHIS
1.00
0.75
BMI Category
Obese
Proportion
0.50 Over−weight
Healthy−weight
Under−weight
0.25
0.00
0 10000 20000 30000 40000
Individuals
Case Study: CHIS
1.00
0.75
residual
8
Proportion
4
0.50
0
−4
−8
0.25
0.00
0 10000 20000 30000 40000
Individuals
Outline
● Course 1
● Concepts, data, aesthetics, geometries
● Course 2
● Statistics, coordinates, facets, themes
● Best practices
● Case study
● Course 3
● Advanced plots and ggplot2 internals
Let’s practice!
Grammar of Graphics
The quick brown fox jumps over the lazy dog
Article The A The
Adjective quick brown rabid red
Noun fox fox Hunter
Verb jumps bit shot
Preposition over
Article the the the
Adjective lazy friendly rabid red
Noun dog. dog. fox.

Grammar of Graphics
● Plo!ing Framework
● Leland Wilkinson, Grammar of Graphics, 1999
● 2 principles
● Graphics = distinct layers of grammatical elements
● Meaningful plots through aesthetic mapping
Essential Grammatical Elements

Element Description
Data The dataset being plo!ed.
Aesthetics The scales onto which we map our data.
Geometries The visual elements used for our data.

All Grammatical Elements

Element Description
Data The dataset being plo!ed.
Aesthetics The scales onto which we map our data.
Geometries The visual elements used for our data.
Facets Plo!ing small multiples.
Statistics Representations of our data to aid understanding.
Coordinates The space on which the data will be plo!ed.
Themes All non-data ink.

Diagram
Data {variables of interest}
x-axis colour size alpha line width
Aesthetics y-axis fill labels shape line type
Geometries point line histogram bar boxplot
Facets columns rows
Statistics binning smoothing descriptive inferential
Coordinates cartesian fixed polar limits
Themes non-data ink

Grammar of Graphics
● Building blocks
● Solid, creative, meaningful visualizations
● Course 1: First 3 layers
● Course 2: Remaining 4 layers
Let’s practice!
ggplot2
ggplot2
● Hadley Wickham
● Layer grammatical elements
● Aesthetic Mappings
ggplot2 Layers - Data
Data
Iris dataset
● Edgar Anderson
● R.A. Fischer
setosa versicolor virginica
Source: Wikimedia
Iris dataset
> iris
Sepal.Length Sepal.Width Petal.Length Petal.Width 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
... 
50 5.0 3.3 1.4 0.2 setosa
51 7.0 3.2 4.7 1.4 versicolor
52 6.4 3.2 4.5 1.5 versicolor
53 6.9 3.1 4.9 1.5 versicolor
... 
100 5.7 2.8 4.1 1.3 versicolor
101 6.3 3.3 6.0 2.5 virginica
102 5.8 2.7 5.1 1.9 virginica
103 7.1 3.0 5.9 2.1 virginica
...
150 5.9 3.0 5.1 1.8 virginica
ggplot2 Layers - Aesthetics
Aesthetics
Data
ggplot2 Layers - Aesthetics
Species Sepal.Length Sepal.Width Petal.Length Petal.Width

X Y
ggplot2 Layers - Geometries
Geometries
Aesthetics
Data
ggplot2 Layers - Geometries

> ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width)) +
geom_jitter(alpha = 0.6)
4.5
4.0
Sepal.Width
3.5
3.0
2.5
2.0
5 6 7 8
Sepal.Length
ggplot2 Layers - Facets
Facets
Geometries
Aesthetics
Data
ggplot2 Layers - Facets

geom_jitter(alpha = 0.6) +
facet_grid(. ~ Species)
setosa versicolor virginica

4.5
4.0
Sepal.Width
3.5
3.0
2.5
2.0
5 6 7 8 5 6 7 8 5 6 7 8
Sepal.Length
ggplot2 Layers - Statistics
Statistics
Facets
Geometries
Aesthetics
Data
ggplot2 Layers - Statistics

facet_grid(. ~ Species) +
stat_smooth(method = "lm", se = F, col = "red")
4.5
4.0
Sepal.Width
3.5
3.0
2.5
2.0
5 6 7 8 5 6 7 8 5 6 7 8
Sepal.Length
ggplot2 Layers - Coordinates
Coordinates
Statistics
Facets
Geometries
Aesthetics
Data
ggplot2 Layers - Coordinates

> levels(iris$Species) <- c("Setosa", "Versicolor", "Virginica")
facet_grid(. ~ Species) +
stat_smooth(method = "lm", se = F, col = "red") +
scale_y_continuous("Sepal Width (cm)",  
limits = c(2,5),  
expand = c(0,0)) +
scale_x_continuous("Sepal Length (cm)",
limits = c(4,8),
expand = c(0,0)) +
coord_equal()
Sepal Width (cm)

5
4
3
2
4 5 6 7 84 5 6 7 84 5 6 7 8
Sepal Length (cm)
ggplot2 Layers - Themes

Theme
Coordinates
Statistics
Facets
Geometries
Aesthetics
Data

> levels(iris$Species) <- c("Setosa", "Versicolor", "Virginica") 
> library(grid)
... # previous code left out
coord_equal() +
theme(panel.background = element_blank(),
plot.background = element_blank(),
legend.background = element_blank(),
legend.key = element_blank(),
strip.background = element_blank(),
axis.text = element_text(colour = "black"),
axis.ticks = element_line(colour = "black"),
panel.grid.major = element_blank(),
panel.grid.minor = element_blank(),
axis.line = element_line(colour = "black"),
strip.text = element_blank(),
panel.margin = unit(1, "lines")
)

Sepal Width (cm)
5
4
3
2
4 5 6 7 8 4 5 6 7 8 4 5 6 7 8
Sepal Length (cm)
Let’s practice!

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DATA VISUALIZATION WITH GGPLOT2

Your Instructor - Rick Scave!a

Data Visualization & Data Science

Data Visualization & Data Science

Exploratory versus Explanatory

> library(ggplot2) 4000

0 2000 4000 6000

Explore - Statistics 6000

> ggplot(mammals, aes(x = body, y = brain)) +

0 2000 4000 6000

Explore - Fine-tuning 10000

> ggplot(mammals, aes(x = body, y = brain)) +

Setosa Versicolor Virginica

Setosa Versicolor Virginica

Setosa Versicolor Virginica

Case Study: CHIS

Case Study: CHIS

Case Study: CHIS

Case Study: CHIS

The quick brown fox jumps over the lazy dog

Article The A The

Adjective quick brown rabid red

Noun fox fox Hunter

Verb jumps bit shot

Article the the the

Adjective lazy friendly rabid red

Noun dog. dog. fox.

Essential Grammatical Elements

Data The dataset being plo!ed.

Aesthetics The scales onto which we map our data.

Geometries The visual elements used for our data.

All Grammatical Elements

Data The dataset being plo!ed.

Aesthetics The scales onto which we map our data.

Geometries The visual elements used for our data.

Facets Plo!ing small multiples.

Statistics Representations of our data to aid understanding.

Coordinates The space on which the data will be plo!ed.

Themes All non-data ink.

Facets columns rows

Statistics binning smoothing descriptive inferential

Coordinates cartesian fixed polar limits

Themes non-data ink

ggplot2 Layers - Data

setosa versicolor virginica

ggplot2 Layers - Aesthetics

ggplot2 Layers - Aesthetics

Species Sepal.Length Sepal.Width Petal.Length Petal.Width

ggplot2 Layers - Geometries

ggplot2 Layers - Geometries

ggplot2 Layers - Facets

ggplot2 Layers - Facets

setosa versicolor virginica

ggplot2 Layers - Statistics

ggplot2 Layers - Statistics

ggplot2 Layers - Coordinates

ggplot2 Layers - Coordinates

Setosa Versicolor Virginica

ggplot2 Layers - Themes

ggplot2 Layers - Themes

ggplot2 Layers - Themes

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