Scatter plots

I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2

Rick Scave a
Founder, Scave a Academy
48 geometries
geom_*
abline contour dotplot ji er pointrange ribbon spoke
area count errorbar label polygon rug step
bar crossbar errorbarh line qq segment text
bin2d curve freqpoly linerange qq_line sf tile
blank density hex map quantile sf_label violin
boxplot density2d histogram path raster sf_text vline
col density_2d hline point rect smooth

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Common plot types
Plot type Possible Geoms
Sca er plots points, ji er, abline, smooth, count

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Scatter plots
Each geom can accept speci c aesthetic ggplot(iris, aes(x = Sepal.Length,
mappings, e.g. geom_point(): y = Sepal.Width)) +
geom_point()
Essential
x,y

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Scatter plots
Each geom can accept speci c aesthetic ggplot(iris, aes(x = Sepal.Length,
mappings, e.g. geom_point(): y = Sepal.Width,
col = Species)) +
Essential Optional
geom_point()
alpha, color, ll, shape, size,
x,y
stroke

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Geom-specific aesthetic mappings
# These result in the same plot!
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))

Control aesthetic mappings of each layer independently:

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

head(iris, 3) # Raw data

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

iris %>%
group_by(Species) %>%
summarise_all(mean) -> iris.summary

iris.summary # Summary statistics

# A tibble: 3 x 5
Species Sepal.Length Sepal.Width Petal.Length Petal.Width
<fct> <dbl> <dbl> <dbl> <dbl>
1 setosa 5.01 3.43 1.46 0.246
2 versicolor 5.94 2.77 4.26 1.33
3 virginica 6.59 2.97 5.55 2.03

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

ggplot(iris, aes(x = Sepal.Length, y = Sepal.Width, col = Species)) +
# Inherits both data and aes from ggplot()
geom_point() +
# Different data, but inherited aes
geom_point(data = iris.summary, shape = 15, size = 5)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Shape attribute values

INTRODUCTION TO 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 = "black", stroke = 2)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

On-the-fly stats by ggplot2
See the second course for the stats layer.

Note: Avoid plo ing only the mean without a measure of spread, e.g. the standard
deviation.

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

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

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

geom_jitter()
A short-cut to geom_point(position = "jitter")

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

geom_jitter()

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Don't forget to adjust alpha
Combine ji ering with alpha-blending if necessary

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

geom_jitter(alpha = 0.6)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Hollow circles also help
shape = 1 is a. hollow circle.

Not necessary to also use alpha-blending.

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

geom_jitter(shape = 1)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

 Let's practice!
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2
 Histograms
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2

Rick Scave a
Founder, Scave a Academy
Common plot types
Plot type Possible Geoms
Sca er plots points, ji er, abline, smooth, count
Bar plots histogram, bar, col, errorbar
Line plots line, path

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Histograms
ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram()

A plot of binned values

i.e. a statistical function

`stat_bin()` using `bins = 30`.

Pick better value with `binwidth`.

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Default of 30 even bins
ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram()

A plot of binned values

i.e. a statistical function

# Default bin width:

diff(range(iris$Sepal.Width))/30

[1] 0.08

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Intuitive and meaningful bin widths
ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram(binwidth = 0.1)

Always set a meaningful bin widths for your

data.

No spaces between bars.

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Re-position tick marks
ggplot(iris, aes(x = Sepal.Width)) +
geom_histogram(binwidth = 0.1,
center = 0.05)

Always set a meaningful bin widths for your

data.

No spaces between bars.

X axis labels are between bars.

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Different Species
ggplot(iris, aes(x = Sepal.Width,
fill = Species)) +
geom_histogram(binwidth = .1,
center = 0.05)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Default position is "stack"
ggplot(iris, aes(x = Sepal.Width,
fill = Species)) +
geom_histogram(binwidth = .1,
center = 0.05,
position = "stack")

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

position = "dodge"
ggplot(iris, aes(x = Sepal.Width,
fill = Species)) +
geom_histogram(binwidth = .1,
center = 0.05,
position = "dodge")

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

position = "fill"
ggplot(iris, aes(x = Sepal.Width,
fill = Species)) +
geom_histogram(binwidth = .1,
center = 0.05,
position = "fill")

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

 Final Slide
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2
 Bar plots
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2

Rick Scave a
Founder, Scave a Academy
Bar Plots, with a categorical X-axis
Use geom_bar() or geom_col()

Geom Stat Action

geom_bar() "count" Counts the number of cases at each x position

geom_col() "identity" Plot actual values

All positions from before are available

Two types
Absolute counts

Distributions

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Bar Plots, with a categorical X-axis
Use geom_bar() or geom_col()

Geom Stat Action

geom_bar() "count" Counts the number of cases at each x position

geom_col() "identity" Plot actual values

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Bar Plots, with a categorical X-axis
Use geom_bar() or geom_col()

Geom Stat Action

geom_bar() "count" Counts the number of cases at each x position

geom_col() "identity" Plot actual values

All positions from before are available

Two types
Absolute counts

Distributions

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Habits of mammals
str(sleep)

'data.frame': 76 obs. of 3 variables:

$ vore : Factor w/ 4 levels "carni","herbi",..: 1 4 2 4 2 2 1 1 2 2 ...
$ total: num 12.1 17 14.4 14.9 4 14.4 8.7 10.1 3 5.3 ...
$ rem : num NA 1.8 2.4 2.3 0.7 2.2 1.4 2.9 NA 0.6 ...

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Bar plot
ggplot(sleep, aes(vore)) +
geom_bar()

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Plotting distributions instead of absolute counts
# Calculate Descriptive Statistics: iris_summ_long
iris %>%
select(Species, Sepal.Width) %>% Species avg stdev
gather(key, value, -Species) %>% setosa 3.43 0.38
group_by(Species) %>%
versicolor 2.77 0.31
summarise(avg = mean(value),
virginica 2.97 0.32
stdev = sd(value))
-> iris_summ_long

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Plotting distributions
ggplot(iris_summ_long, aes(x = Species,
y = avg)) +
geom_col() +
geom_errorbar(aes(ymin = avg - stdev,
ymax = avg + stdev),
width = 0.1)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

 Let's practice!
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2
 Line plots
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2

Rick Scave a
Founder, Scave a Academy
Common plot types
Plot type Possible Geoms
Sca er plots points, ji er, abline, smooth, count
Bar plots histogram, bar, col, errorbar
Line plots line, path

INTRODUCTION TO 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 09:40:00" "2000-01-01 09:50:00" ...
$ 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 ...

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

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

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

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

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

The fish catch dataset
str(fish)

'data.frame': 427 obs. of 3 variables:

$ Species: Factor w/ 7 levels "Pink","Chum",..: 1 2 3 4 5 6 7 1 2 3 ...
$ Year : int 1950 1950 1950 1950 1950 1950 1950 1951 1951 1951 ...
$ Capture: int 100600 139300 64100 30500 0 23200 10800 259000 155900 51200 ...

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Linetype aesthetic
ggplot(fish, aes(x = Year,
y = Capture,
linetype = Species)) +
geom_line()

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

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

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

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

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Aesthetics for categorical variables

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

Fill aesthetic with geom_area()
ggplot(fish, aes(x = Year,
y = Capture,
fill = Species)) +
geom_area()

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

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

INTRODUCTION TO 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)

INTRODUCTION TO DATA VISUALIZATION WITH GGPLOT2

 Let's practice!
I N T R O D U C T I O N T O D ATA V I S U A L I Z AT I O N W I T H G G P L O T 2