23. Introduction to Data Visualization with ggplot2

代写BA，DS和AF专业的R和python作业请私信

1. Introduction

1.1 Introduction

1.2 Explore and explain

In this video we made the distinction between plots for exploring and plots for explaining data. Which of the following are exploratory plots typically NOT?

Possible Answer
$\square$ Meant for a specialist audience.

$\square$ Data-heavy.

$■$ Pretty.

$\square$ Rough first drafts.

$\square$ Part of our data science toolkit as graphical data analysis.

1.3 Drawing your first plot

To get a first feel for ggplot2, let’s try to run some basic ggplot2 commands. The mtcars dataset contains information on 32 cars from a 1973 issue of Motor Trend magazine. This dataset is small, intuitive, and contains a variety of continuous and categorical variables.

Instruction

• Load the ggplot2 package using library().
• Use str() to explore the structure of the mtcars dataset.
• Hit Submit Answer. This will execute the example code on the right. See if you can understand what ggplot does with the data.

# Load the ggplot2 package
library(ggplot2)

# Explore the mtcars data frame with str()
str(mtcars)

# Execute the following command
ggplot(mtcars, aes(cyl, mpg)) +
  geom_point()

1.4 Data columns types affect plot types

The plot from the previous exercise wasn’t really satisfying. Although cyl (the number of cylinders) is categorical, you probably noticed that it is classified as numeric in mtcars. This is really misleading because the representation in the plot doesn’t match the actual data type. You’ll have to explicitly tell ggplot2 that cyl is a categorical variable.

Instruction

• Change the ggplot() command by wrapping factor() around cyl.

# Load the ggplot2 package
library(ggplot2)

# Change the command below so that cyl is treated as factor
ggplot(mtcars, aes(factor(cyl), mpg)) +
  geom_point()

1.5 The grammar of graphics

1.6 Mapping data columns to aesthetics

Let’s dive a little deeper into the three main topics in this course: The data, aesthetics, and geom layers. We’ll get to making pretty plots in the last chapter with the themes layer.

We’ll continue working on the 32 cars in the mtcars data frame.

Consider how the examples and concepts we discuss throughout these courses apply to your own data-sets!

Instruction 1

• Add a color aesthetic mapped to the displacement of the car engine: inside aes(), add a color argument equal to disp.

# Edit to add a color aesthetic mapped to disp
ggplot(mtcars, aes(wt, mpg, color = disp)) +
  geom_point()

Instruction 2

• This time, map disp to the size aesthetic.

# Change the color aesthetic to a size aesthetic
ggplot(mtcars, aes(wt, mpg, size = disp)) +
  geom_point()

1.7 Understanding variables

In the previous exercise you saw that disp can be mapped onto a color gradient or onto a continuous size scale.

Another argument of aes() is the shape of the points. There are a finite number of shapes which ggplot() can automatically assign to the points. However, if you try this command in the console to the right:

ggplot(mtcars, aes(wt, mpg, shape = disp)) +
  geom_point()

It gives an error. What does this mean?

Possible Answers
$\square$ shape is not a defined argument.

$■$ shape only makes sense with categorical data, and disp is continuous.

$\square$ shape only makes sense with continuous data, and disp is categorical.

$\square$ shape is not a variable in your dataset.

$\square$ shape has to be defined as a function.

1.8 ggplot2 layers

1.9 Adding geometries

The diamonds dataset contains details of 1,000 diamonds. Among the variables included are carat (a measurement of the diamond’s size) and price.

You’ll use two common geom layer functions:

• geom_point() adds points (as in a scatter plot).
• geom_smooth() adds a smooth trend curve.
  As you saw previously, these are added using the + operator.

ggplot(data, aes(x, y)) +
  geom_*()

Where * is the specific geometry needed.

Instruction 1
Explore the diamonds data frame with the str() function.

# Explore the diamonds data frame with str()
str(diamonds)

Instruction 2

• Edit the plot code to add a point geom. Use the + operator to add geom_point() to the ggplot() command.

# Add geom_point() with +
ggplot(diamonds, aes(carat, price)) +
  geom_point()

Instruction 3
Add a smooth geom to the plot. Use the + operator to add geom_smooth().

# Add geom_smooth() with +
ggplot(diamonds, aes(carat, price)) +
  geom_point() +
  geom_smooth()

1.10 Changing one geom or every geom

If you have multiple geoms, then mapping an aesthetic to data variable inside the call to ggplot() will change all the geoms. It is also possible to make changes to individual geoms by passing arguments to the geom_*() functions.

geom_point() has an alpha argument that controls the opacity of the points. A value of 1 (the default) means that the points are totally opaque; a value of 0 means the points are totally transparent (and therefore invisible). Values in between specify transparency.

The plot you drew last time is provided in the script.

Instruction 1

• Edit the plot code to map the color aesthetic to the clarity data variable.

# Make the points 40% opaque
ggplot(diamonds, aes(carat, price, color = clarity)) +
  geom_point() +
  geom_smooth()

Instruction 2

• Make the points translucent by setting the alpha argument to 0.4.

# Make the points 40% opaque
ggplot(diamonds, aes(carat, price, color = clarity)) +
  geom_point(alpha = 0.4) +
  geom_smooth()

1.11 Saving plots as variables

Plots can be saved as variables, which can be added two later on using the + operator. This is really useful if you want to make multiple related plots from a common base.

Instruction 1

• Using the diamonds dataset, plot the price (y-axis) versus the carat (x-axis), assigning to plt_price_vs_carat.
• Using geom_point(), add a point layer to plt_price_vs_carat.

# Draw a ggplot
plt_price_vs_carat <- ggplot(
  # Use the diamonds dataset
  diamonds,
  # For the aesthetics, map x to carat and y to price
  aes(carat, price)
)

# Add a point layer to plt_price_vs_carat
plt_price_vs_carat + geom_point()

Instruction 2

• Add an alpha argument to the point layer to make the points 20% opaque, assigning to plt_price_vs_carat_transparent.
• Type the plot’s variable name (plt_price_vs_carat_transparent) to display it.

# From previous step
plt_price_vs_carat <- ggplot(diamonds, aes(carat, price))

# Edit this to make points 20% opaque: plt_price_vs_carat_transparent
plt_price_vs_carat_transparent <- plt_price_vs_carat + geom_point(alpha = 0.2)

# See the plot
plt_price_vs_carat_transparent

Instruction 3

• Inside geom_point(), call aes() and map color to clarity, assigning to plt_price_vs_carat_by_clarity.
• Type the plot’s variable name (plt_price_vs_carat_by_clarity) to display it.

# From previous step
plt_price_vs_carat <- ggplot(diamonds, aes(carat, price))

# Edit this to map color to clarity
# Assign the updated plot to a new object
plt_price_vs_carat_by_clarity <- plt_price_vs_carat + geom_point(aes(color = clarity))

# See the plot
plt_price_vs_carat_by_clarity

2. Aesthetics

2.1 Visible aesthetics

2.2 All about aesthetics: color, shape and size

In the video you saw 9 visible aesthetics. Let’s apply them to a categorical variable — the cylinders in mtcars, cyl.

These are the aesthetics you can consider within aes() in this chapter: x, y, color, fill, size, alpha, labels and shape.

One common convention is that you don’t name the x and y arguments to aes(), since they almost always come first, but you do name other arguments.

In the following exercise the fcyl column is categorical. It is cyl transformed into a factor.

Instruction 1

• Map mpg onto the x aesthetic, and fcyl onto the y.

# Map x to mpg and y to fcyl
ggplot(mtcars, aes(mpg, fcyl)) +
  geom_point()

Instrution 2

• Swap the mappings of the first plot: fcyl onto the x aesthetic, and mpg onto the y.

# Swap mpg and fcyl
ggplot(mtcars, aes(fcyl, mpg)) +
  geom_point()

Instruction 3

• Map wt onto x, mpg onto y, and fcyl onto color.

# Map x to wt, y to mpg and color to fcyl
ggplot(mtcars, aes(wt, mpg, color = fcyl)) +
  geom_point()

Instruction 4

• Modify the point layer of the previous plot by changing the shape argument to 1 and increasing the size to 4.

ggplot(mtcars, aes(wt, mpg, color = fcyl)) +
  # Set the shape and size of the points
  geom_point(shape = 1, size = 4)

2.3 All about aesthetics: color vs. fill

Typically, the color aesthetic changes the outline of a geom and the fill aesthetic changes the inside. geom_point() is an exception: you use color (not fill) for the point color. However, some shapes have special behavior.

The default geom_point() uses shape = 19: a solid circle. An alternative is shape = 21: a circle that allow you to use both fill for the inside and color for the outline. This is lets you to map two aesthetics to each point.

All shape values are described on the points() help page.

fcyl and fam are the cyl and am columns converted to factors, respectively.

Instruction 1

• Change the aesthetics so that fcyl maps to fill rather than color.

ggplot(mtcars, aes(wt, mpg, fill = fcyl)) +
  # Change point shape; set alpha
  geom_point(shape = 1, size = 4)

Instruction 2
In geom_point() change the shape argument to 21 and add an alpha argument set to 0.6.

ggplot(mtcars, aes(wt, mpg, fill = fcyl)) +
  # Change point shape; set alpha
  geom_point(shape = 21, size = 4, alpha = 0.6)

Instruction 3

• In the ggplot() aesthetics, map fam to color.

# Map color to fam
ggplot(mtcars, aes(wt, mpg, fill = fcyl,color = fam)) +
  geom_point(shape = 21, size = 4, alpha = 0.6)

Shapely coding! Notice that mapping a categorical variable onto fill doesn’t change the colors, although a legend is generated! This is because the default shape for points only has a color attribute and not a fill attribute! Use fill when you have another shape (such as a bar), or when using a point that does have a fill and a color attribute, such as shape = 21, which is a circle with an outline. Any time you use a solid color, make sure to use alpha blending to account for over plotting.

2.4 All about aesthetics: comparomg aesthetics

Now that you’ve got some practice with using attributes, be careful of a major pitfall: these attributes can overwrite the aesthetics of your plot!

Instruction 1

• Using mtcars, create a plot base layer, plt_mpg_vs_wt. Map mpg onto y and wt onto x.
• Add a point layer, mapping the categorical no. of cylinders, fcyl, onto size.

# Establish the base layer
plt_mpg_vs_wt <- ggplot(mtcars, aes(wt, mpg))

# Map fcyl to size
plt_mpg_vs_wt +
  geom_point(aes(size = fcyl))

Instruction 2

• Change the mapping. This time fcyl should be mapped onto alpha.

# Base layer
plt_mpg_vs_wt <- ggplot(mtcars, aes(wt, mpg))

# Map fcyl to alpha, not size
plt_mpg_vs_wt +
  geom_point(aes(alpha = fcyl))

Instruction 3

• Change the mapping again. This time fycl should be mapped onto shape.

# Base layer
plt_mpg_vs_wt <- ggplot(mtcars, aes(wt, mpg))

# Map fcyl to shape, not alpha
plt_mpg_vs_wt +
  geom_point(aes(shape = fcyl))

Instruction 4

• Swap the geom layer: change points to text.
• Change the mapping again. This time fycl should be mapped onto label.

# Base layer
plt_mpg_vs_wt <- ggplot(mtcars, aes(wt, mpg))

# Use text layer and map fcyl to label
plt_mpg_vs_wt +
  geom_text(aes(label = fcyl))

2.5 Aesthetics for categorical & continuous variables

Many of the aesthetics can accept either continuous or categorical variables, but some are restricted to categorical data. Which aesthetics are only applicable to categorical data?

Possible Answers

KaTeX parse error: Undefined control sequence: \suqare at position 1: \̲s̲u̲q̲a̲r̲e̲ color & fill

KaTeX parse error: Undefined control sequence: \suqare at position 1: \̲s̲u̲q̲a̲r̲e̲ alpha & size

KaTeX parse error: Undefined control sequence: \blacksuqare at position 1: \̲b̲l̲a̲c̲k̲s̲u̲q̲a̲r̲e̲ label & shape

KaTeX parse error: Undefined control sequence: \suqare at position 1: \̲s̲u̲q̲a̲r̲e̲ alpha & label

KaTeX parse error: Undefined control sequence: \suqare at position 1: \̲s̲u̲q̲a̲r̲e̲ x & y

2.6 Using attributes

2.7 All about attributes: color, shape, size and alpha

This time you’ll use these arguments to set attributes of the plot, not map variables onto aesthetics.

You can specify colors in R using hex codes: a hash followed by two hexadecimal numbers each for red, green, and blue ("#RRGGBB"). Hexadecimal is base-16 counting. You have 0 to 9, and A representing 10 up to F representing 15. Pairs of hexadecimal numbers give you a range from 0 to 255. “#000000” is “black” (no color), "#FFFFFF" means “white”, and "#00FFFF" is cyan (mixed green and blue).

A hexadecimal color variable, my_blue has been defined for you.

Instruction 1
Set the point color to my_blue and the alpha to 0.6.

# A hexadecimal color
my_blue <- "#4ABEFF"

ggplot(mtcars, aes(wt, mpg)) +
  # Set the point color and alpha
  geom_point(color = my_blue, alpha = 0.6)

Instruction 2
Change the color mapping to a fill mapping. That is, fcyl should be mapped onto fill.
Set the color of the points to my_blue, point size to 10 and the point shape to 1.

# A hexadecimal color
my_blue <- "#4ABEFF"

# Change the color mapping to a fill mapping
ggplot(mtcars, aes(wt, mpg, fill = fcyl)) +
  # Set point size and shape
  geom_point(color = my_blue,size=10, shape = 1)

2.8 All about attributes: conflicts with aesthetics

In the videos you saw that you can use all the aesthetics as attributes. Let’s see how this works with the aesthetics you used in the previous exercises: x, y, color, fill, size, alpha, label and shape.

In this exercise you will set all kinds of attributes of the points!

You will continue to work with mtcars.

Instruction 1
Add a point layer, setting alpha, the transparency, to 0.5.

ggplot(mtcars, aes(wt, mpg, color = fcyl)) +
  # Add point layer with alpha 0.5
  geom_point(alpha = 0.5)

Instruction 2

• Add a text layer, setting the label to the rownames of the dataset mtcars, and the color to "red".

ggplot(mtcars, aes(wt, mpg, color = fcyl)) +
  # Add text layer with label rownames(mtcars) and color red
  geom_text(label = rownames(mtcars), color = 'red')

Instruction 3

• Add a point layer, setting the shape to 24 and the color to "yellow".

ggplot(mtcars, aes(wt, mpg, color = fcyl)) +
  # Add points layer with shape 24 and color yellow
  geom_point(shape = 24, color = 'yellow')

2.9 Going all out

In this exercise, you will gradually add more aesthetics layers to the plot. You’re still working with the mtcars dataset, but this time you’re using more features of the cars. Each of the columns is described on the mtcars help page. Columns fcyl and fam have been added (as before) as categorical versions of cyl and am respectively.

Notice that adding more aesthetic mappings to your plot is not always a good idea! You may just increase complexity and decrease readability.

Instruction 1

• Use mtcars to draw a plot of qsec vs. mpg, colored by fcyl.
• Add a point layer.

# 3 aesthetics: qsec vs. mpg, colored by fcyl
ggplot(mtcars, aes(x = mpg, y = qsec, color = fcyl)) +
  geom_point()

Instruction 2

• Add another aesthetic: map fam onto shape.

# 5 aesthetics: add a mapping of size to hp / wt
ggplot(mtcars, aes(mpg, qsec, 
                   color = fcyl, 
                   shape = fam)) +
  geom_point()

Instruction 3
Add another two aesthetics: map hp divided by wt onto size.

# 5 aesthetics: add a mapping of size to hp / wt
ggplot(mtcars, aes(mpg, qsec, 
                   color = fcyl, 
                   shape = fam, 
                   size = hp/wt)) +
  geom_point()

2.10 Modifying aesthetics

2.11 Updating aesthetic lables

In this exercise, you’ll modify some aesthetics to make a bar plot of the number of cylinders for cars with different types of transmission.

You’ll also make use of some functions for improving the appearance of the plot.

• labs() to set the x- and y-axis labels. It takes strings for each argument.
• scale_color_manual() defines properties of the color scale (i.e. axis). The first argument sets the legend title. values is a named vector of colors to use.

Instruction 1

• Set the x-axis label to "Number of Cylinders", and the y-axis label to "Count" using the x and y arguments of labs(), respectively.

ggplot(mtcars, aes(fcyl, fill = fam)) +
  geom_bar() +
  # Set the axis labels
  labs(x = "Number of Cylinders", 
       y = "Count")

*Instruction 2 *
Implement a custom fill color scale using scale_fill_manual(). Set the first argument to "Transmission", and values to palette.

palette <- c(automatic = "#377EB8", manual = "#E41A1C")

ggplot(mtcars, aes(fcyl, fill = fam)) +
  geom_bar() +
  labs(x = "Number of Cylinders", y = "Count") +
  # Set the fill color scale
  scale_fill_manual("Transmission", values = palette)

Instruction 3

• Modify the code to set the position to dodge so that the bars for transmissions are displayed side by side.

palette <- c(automatic = "#377EB8", manual = "#E41A1C")

# Set the position
ggplot(mtcars, aes(fcyl, fill = fam)) +
  geom_bar(position = 'dodge') +
  labs(x = "Number of Cylinders", y = "Count")
  scale_fill_manual("Transmission", values = palette)

2.12 Setting a dummy aethetics

In the last chapter you saw that all the visible aesthetics can serve as attributes and aesthetics, but I very conveniently left out x and y. That’s because although you can make univariate plots (such as histograms, which you’ll get to in the next chapter), a y-axis will always be provided, even if you didn’t ask for it.

You can make univariate plots in ggplot2, but you will need to add a fake y axis by mapping y to zero.

When using setting y-axis limits, you can specify the limits as separate arguments, or as a single numeric vector. That is, ylim(lo, hi) or ylim(c(lo, hi)).

Instruction 1

• Using mtcars, plot 0 vs. mpg.
• Make a scatter plot and add "jitter" to it.

# Plot 0 vs. mpg
ggplot(mtcars, aes(mpg, 0)) +
  # Add jitter
  geom_point(position="jitter")

Instruction 2

• Use ylim() to set the limits on the y-axis from -2 to 2.

ggplot(mtcars, aes(mpg, 0)) +
  geom_jitter() +
  # Set the y-axis limits
  ylim(-2, 2)

2.13 Aesthetics best practices

2.14 Appropriate mappings

Incorrect aesthetic mapping causes confusion or misleads the audience.

Typically, the dependent variable is mapped onto the the y-axis and the independent variable is mapped onto the x-axis.

In the ToothGrowth data set, we have three variables:

Variable	Description
len	Tooth length
supp	Supplement type (VC or OJ)
dose	Dose in milligrams/day

From the six possible ways to map three variables, one solution is shown in the viewer. Which of the remaining five would actually be a better solution?

Possible Answer

$■$ x = supp, y = len, color = dose

$\square$ x = dose, y = supp, color = len

$\square$ x = len, y = dose, color = supp

$\square$ x = len, y = supp, color = dose

$\square$ x = supp, y = dose, color = len

3. Geometries

3.1 Scatter plots

3.2 Overplotting 1: large datasets

Scatter plots (using geom_point()) are intuitive, easily understood, and very common, but we must always consider overplotting, particularly in the following four situations:

1. Large datasets
2. Aligned values on a single axis
3. Low-precision data
4. Integer data

Typically, alpha blending (i.e. adding transparency) is recommended when using solid shapes. Alternatively, you can use opaque, hollow shapes.

Small points are suitable for large datasets with regions of high density (lots of overlapping).

Let’s use the diamonds dataset to practice dealing with the large dataset case.

Instruction 1
Add a points layer to the base plot.

• Set the point transparency to 0.5.
• Set shape = ".", the point size of 1 pixel.

# Plot price vs. carat, colored by clarity
plt_price_vs_carat_by_clarity <- ggplot(diamonds, aes(carat, price, color = clarity))

# Set transparency to 0.5
plt_price_vs_carat_by_clarity + 
  geom_point(alpha = 0.5, shape = ".")

Instruction 2

• Update the point shape to remove the line outlines by setting shape to 16.

# Plot price vs. carat, colored by clarity
plt_price_vs_carat_by_clarity <- ggplot(diamonds, aes(carat, price, color = clarity))

# Set transparency to 0.5
plt_price_vs_carat_by_clarity + 
  geom_point(alpha = 0.5, shape = 16)

3.3 Overplotting 2: Aligned values

Let’s take a look at another case where we should be aware of overplotting: Aligning values on a single axis.

This occurs when one axis is continuous and the other is categorical, which can be overcome with some form of jittering.

In the mtcars data set, fam and fcyl are categorical variants of cyl and am.

Instruction 1

• Create a base plot plt_mpg_vs_fcyl_by_fam of fcyl by mpg, colored by fam.
• Add a points layer to the base plot.

# Plot base
plt_mpg_vs_fcyl_by_fam <- ggplot(mtcars, aes(fcyl, mpg, color = fam))

# Default points are shown for comparison
plt_mpg_vs_fcyl_by_fam + geom_point()

Instruction 2

• Add some jittering by using position_jitter(), setting the width to 0.3.

# Plot base
plt_mpg_vs_fcyl_by_fam <- ggplot(mtcars, aes(fcyl, mpg, color = fam))

# Default points are shown for comparison
plt_mpg_vs_fcyl_by_fam + 
  geom_point()

# Alter the point positions by jittering, width 0.3
plt_mpg_vs_fcyl_by_fam + 
  geom_point(position = position_jitter(width = 0.3))

Instruction 3
Alternatively, use position_jitterdodge(). Set jitter.width and dodge.width to 0.3 to separate subgroups further.

# Plot base
plt_mpg_vs_fcyl_by_fam <- ggplot(mtcars, aes(fcyl, mpg, color = fam))

# Default points are shown for comparison
plt_mpg_vs_fcyl_by_fam + geom_point()

# Now jitter and dodge the point positions
plt_mpg_vs_fcyl_by_fam + geom_point(position = position_jitterdodge(jitter.width = 0.3, dodge.width = 0.3))

3.4 Overplotting 3: Low-precision data

You already saw how to deal with overplotting when using geom_point() in two cases:

Large datasets
Aligned values on a single axis
We used position = 'jitter' inside geom_point() or geom_jitter().

Let’s take a look at another case:

1. Low-precision data

This results from low-resolution measurements like in the iris dataset, which is measured to 1mm precision (see viewer). It’s similar to case 2, but in this case we can jitter on both the x and y axis.

Instruction 1

• Change the points layer into a jitter layer.
• Reduce the jitter layer’s width by setting the width argument to 0.1.

ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
  # Swap for jitter layer with width 0.1
  geom_jitter(alpha = 0.5, width = 0.1)

Instruction 2
Let’s use a different approach:

• Within geom_point(), set position to “jitter”.

ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
  # Set the position to jitter
  geom_point(alpha = 0.5, position = "jitter")

Instruction 3
Provide an alternative specification:

• Have the position argument call position_jitter() with a width of 0.1.

ggplot(iris, aes(Sepal.Length, Sepal.Width, color = Species)) +
  # Use a jitter position function with width 0.1
  geom_point(alpha = 0.5, position = position_jitter(width = 0.1))

3.5 Overplotting 4: Integer data

Let’s take a look at the last case of dealing with overplotting:

1. Integer data

This can be type integer (i.e. 1 ,2, 3…) or categorical (i.e. class factor) variables. factor is just a special class of type integer.

You’ll typically have a small, defined number of intersections between two variables, which is similar to case 3, but you may miss it if you don’t realize that integer and factor data are the same as low precision data.

The Vocab dataset provided contains the years of education and vocabulary test scores from respondents to US General Social Surveys from 1972-2004.

Instruction 1

• Examine the Vocab dataset using str().
• Using Vocab, draw a plot of vocabulary vseducation.
• Add a point layer.

ggplot(Vocab, aes(education, vocabulary)) +
  # Change to a jitter layer
  geom_point()

Instruction 2

• Replace the point layer with a jitter layer.

ggplot(Vocab, aes(education, vocabulary)) +
  # Change to a jitter layer
  geom_jitter()

Instruction 3

• Set the jitter transparency to 0.2.

ggplot(Vocab, aes(education, vocabulary)) +
  # Set the transparency to 0.2
  geom_jitter(alpha = 0.2)

Instruction 4

• Set the shape of the jittered points to hollow circles, (shape 1).

ggplot(Vocab, aes(education, vocabulary)) +
  # Set the shape to 1
  geom_jitter(alpha = 0.2, shape = 1)

3.6 Histograms

3.7 Drawing histograms

Recall that histograms cut up a continuous variable into discrete bins and, by default, maps the internally calculated count variable (the number of observations in each bin) onto the y aesthetic. An internal variable called density can be accessed by using the .. notation, i.e. ..density...Plotting this variable will show the relative frequency, which is the height times the width of each bin.

Instruction 1
Using mtcars, map mpg onto the x aesthetic.
Add a histogram layer using geom_histogram().

# Plot mpg
ggplot(mtcars, aes(mpg)) +
  # Add a histogram layer
  geom_histogram()

Instruction 2

• Set the histogram binwidth to 1.

ggplot(mtcars, aes(mpg)) +
  # Set the binwidth to 1
  geom_histogram(binwidth = 1)

Instruction 3
Map y to the internal variable ..density.. to show frequency densities.

# Map y to ..density..
ggplot(mtcars, aes(mpg, ..density..)) +
  geom_histogram(binwidth = 1)

Instruction 4

• Set the fill color of the histogram bars to datacamp_light_blue.

datacamp_light_blue <- "#51A8C9"

ggplot(mtcars, aes(mpg, ..density..)) +
  # Set the fill color to datacamp_light_blue
  geom_histogram(binwidth = 1, fill = datacamp_light_blue)

3.8 Positions in histograms

Here, we’ll examine the various ways of applying positions to histograms. geom_histogram(), a special case of geom_bar(), has a position argument that can take on the following values:

• stack (the default): Bars for different groups are stacked on top of each other.
• dodge: Bars for different groups are placed side by side.
• fill: Bars for different groups are shown as proportions.
• identity: Plot the values as they appear in the dataset

Instruction 1
Update the aesthetics so that the fill color of the bars is determined by fam.

# Update the aesthetics so the fill color is by fam
ggplot(mtcars, aes(mpg, fill = fam)) +
  geom_histogram(binwidth = 1)

Instruction 2

• Update the histogram layer to position the bars side-by-side, that is, "dodge".

ggplot(mtcars, aes(mpg, fill = fam)) +
  # Change the position to dodge
  geom_histogram(binwidth = 1, position = 'dodge')

Instruction 3
Update the histogram layer so the bars’ positions "fill" the y-axis.

ggplot(mtcars, aes(mpg, fill = fam)) +
  # Change the position to fill
  geom_histogram(binwidth = 1, position = "fill")

Instruction 4

• Update the histogram layer so bars are top of each other, using the "identity" position. So each bar can be seen, set alpha to 0.4.

ggplot(mtcars, aes(mpg, fill = fam)) +
  # Change the position to identity, with transparency 0.4
  geom_histogram(binwidth = 1, position = "identity", alpha = 0.4)

3.9 Bar plots

3.10 Position in bar and col plots

Let’s see how the position argument changes geom_bar().

We have three position options:

• stack: The default
• dodge: Preferred
• fill: To show proportions

While we will be using geom_bar() here, note that the function geom_col() is just geom_bar() where both the position and stat arguments are set to "identity". It is used when we want the heights of the bars to represent the exact values in the data.

In this exercise, you’ll draw the total count of cars having a given number of cylinders (fcyl), according to manual or automatic transmission type (fam).

Instruction 1

• Using mtcars, plot fcyl, filled by fam.
• Add a bar layer using geom_bar().

# Plot fcyl, filled by fam
ggplot(mtcars, aes(fcyl, fill = fam)) +
  # Add a bar layer
  geom_bar()

Instruction 2

• Set the bar position argument to "fill".

ggplot(mtcars, aes(fcyl, fill = fam)) +
  # Change the position to "dodge"
  geom_bar(position = "fill")

Instruction 3

• Change the bar position argument to "dodge".

ggplot(mtcars, aes(fcyl, fill = fam)) +
  # Change the position to "dodge"
  geom_bar(position = "dodge")

3.11 Overlapping bar plots

You can customize bar plots further by adjusting the dodging so that your bars partially overlap each other. Instead of using position = "dodge", you’re going to use position_dodge(), like you did with position_jitter() in the the previous exercises. Here, you’ll save this as an object, posn_d, so that you can easily reuse it.

Remember, the reason you want to use position_dodge() (and position_jitter()) is to specify how much dodging (or jittering) you want.

For this example, you’ll use the mtcars dataset.

Instruction 1

• Use the functional form of the bar position: replace "dodge" with a call to position_dodge().
• Set its width to 0.2.

ggplot(mtcars, aes(cyl, fill = fam)) +
  # Change position to use the functional form, with width 0.2
  geom_bar(position = position_dodge(width = 0.2))

Instruction 2

• Set the bar transparency level of the bars to 0.6.

ggplot(mtcars, aes(cyl, fill = fam)) +
  # Set the transparency to 0.6
  geom_bar(position = position_dodge(width = 0.2), alpha = 0.6)

3.12 Bar plots: sequential color palette

In this bar plot, we’ll fill each segment according to an ordinal variable. The best way to do that is with a sequential color palette.

Here’s an example of using a sequential color palette with the mtcars dataset:

ggplot(mtcars, aes(fcyl, fill = fam)) +
  geom_bar() +
  scale_fill_brewer(palette = "Set1")

In the exercise, you’ll use similar code on the the Vocab dataset. Both datasets are ordinal.

Instruction 1

• Plot the Vocab dataset, mapping education onto x and vocabulary onto fill.

# Plot education, filled by vocabulary
ggplot(Vocab, aes(education, fill = vocabulary))+ geom_bar()

Instruction 2

• Add a bar layer, setting position to "fill".

# Plot education, filled by vocabulary
ggplot(Vocab, aes(education, fill = vocabulary)) +
  # Add a bar layer with position "fill"
  geom_bar(position = "fill")

Instruction 3
Add a brewer fill scale, using the default palette (don’t pass any arguments). Notice how this generates a warning message and an incomplete plot.

# Plot education, filled by vocabulary
ggplot(Vocab, aes(education, fill = vocabulary)) +
  # Add a bar layer with position "fill"
  geom_bar(position = "fill") +
  # Add a brewer fill scale with default palette
  scale_fill_brewer()

3.13 Line plots

3.14 Basic line plots

Here, we’ll use the economics dataset to make some line plots. The dataset contains a time series for unemployment and population statistics from the Federal Reserve Bank of St. Louis in the United States. The data is contained in the ggplot2 package.

To begin with, you can look at how the median unemployment time and the unemployment rate (the number of unemployed people as a proportion of the population) change over time.

Instruction 1

• Print the head of the economics dataset.
• Plot unemploy vs. date as a line plot.

# Print the head of economics
print(head(economics))

# Using economics, plot unemploy vs. date
ggplot(economics, aes(date, unemploy)) +
  # Make it a line plot
  geom_line()

Instruction 2

• Adjust the y-axis aesthetic of the plot so that it represents the proportion of the population that is unemployed.

# Change the y-axis to the proportion of the population that is unemployed
ggplot(economics, aes(date, unemploy/pop)) +
  geom_line()

3.15 Multiple time series

We already saw how the form of your data affects how you can plot it. Let’s explore that further with multiple time series. Here, it’s important that all lines are on the same scale, and if possible, on the same plot.

fish.species contains the global capture rates of seven salmon species from 1950–2010. Each variable (column) is a Salmon species and each observation (row) is one year. fish.tidy contains the same data, but in three columns: Species, Year, and Capture(i.e. one variable per column).

Instruction 1

• Use str() in the console to examine the structure of both fish.species and fish.tidy.
• Plot only the Rainbow salmon time series with geom_line().

# Plot the Rainbow Salmon time series
ggplot(fish.species, aes(x = Year, y = Rainbow)) +
  geom_line()

Instruction 2
Plot only the Pink salmon time series with geom_line().

# Plot the Pink Salmon time series
ggplot(fish.species, aes(x = Year, y = Pink)) +
  geom_line()

Instruction 3
Now try and plot all time series in a single plot.

• Plot the fish.tidy dataset, mapping Year to x and Capture to y.
• group by fish species within the aesthetics of geom_line().

# Plot multiple time-series by grouping by species
ggplot(fish.tidy, aes(Year, Capture)) +
  geom_line(aes(group= Species))

Instruction 4
Let’s add color to the previous plot to distinguish between the different time series.

• Plot the fish.tidy dataset again, this time making sure to color by Species.

# Plot multiple time-series by coloring by species
ggplot(fish.tidy, aes(Year, Capture, color = Species)) +
  geom_line()

4. Themes

4.1 Themes from scratch

4.2 Moving the legend

Let’s wrap up this course by making a publication-ready plot communicating a clear message.

To change stylistic elements of a plot, call theme() and set plot properties to a new value. For example, the following changes the legend position.

p + theme(legend.position = new_value)

Here, the new value can be

• "top", "bottom", "left", or "right'": place it at that side of the plot.
• "none": don’t draw it.
• c(x, y): c(0, 0) means the bottom-left and c(1, 1) means the top-right.
  Let’s revisit the recession period line plot (assigned to plt_prop_unemployed_over_time).

Instruction 1

• Update the plot to remove the legend.
• Look at the changes in the plot.

# View the default plot
plt_prop_unemployed_over_time

# Remove legend entirely
plt_prop_unemployed_over_time +
  theme(legend.position = "none")

Instruction 2

• Update the plot to position the legend at the bottom of the plot.
• Look at the changes in the plot.

# Position the legend at the bottom of the plot
plt_prop_unemployed_over_time +
  theme(legend.position = "bottom")

Instruction 3

• Position the legend inside the plot, with x-position 0.6 and y-position 0.1.
• Look at the changes in the plot.

# Position the legend inside the plot at (0.6, 0.1)
plt_prop_unemployed_over_time +
  theme(legend.position = c(0.6, 0.1))

4.3 Modifying theme elements

Many plot elements have multiple properties that can be set. For example, line elements in the plot such as axes and gridlines have a color, a thickness (size), and a line type (solid line, dashed, or dotted). To set the style of a line, you use element_line(). For example, to make the axis lines into red, dashed lines, you would use the following.

p + theme(axis.line = element_line(color = "red", linetype = "dashed"))

Similarly, element_rect() changes rectangles and element_text() changes text. You can remove a plot element using element_blank().

plt_prop_unemployed_over_time is available.

Instruction 1

• Give all rectangles in the plot, (the rect element) a fill color of "grey92" (very pale grey).
• Remove the legend.key’s outline by setting its color to be missing.
• Look at the changes in the plot.

plt_prop_unemployed_over_time +
  theme(
    # For all rectangles, set the fill color to grey92
    rect = element_rect(fill = "grey92"),
    # For the legend key, turn off the outline
    legend.key = element_rect(color = NA)
  )

Instruction 2

• Remove the axis ticks, axis.ticks by making them a blank element.
• Remove the panel gridlines, panel.grid in the same way.
• Look at the changes in the plot.

plt_prop_unemployed_over_time +
  theme(
    rect = element_rect(fill = "grey92"),
    legend.key = element_rect(color = NA),
    # Turn off axis ticks
    axis.ticks = element_blank() ,
    # Turn off the panel grid
    panel.grid = element_blank()
  )

Instruction 3

• Add the major horizontal grid lines back to the plot using panel.grid.major.y.
• Set the line color to "white", size to 0.5, and linetype to "dotted".
• Look at the changes in the plot.

plt_prop_unemployed_over_time +
  theme(
    rect = element_rect(fill = "grey92"),
    legend.key = element_rect(color = NA),
    axis.ticks = element_blank(),
    panel.grid = element_blank(),
    # Add major y-axis panel grid lines back
    panel.grid.major.y = element_line(
      # Set the color to white
      color = "white",
      # Set the size to 0.5
      size = 0.5,
      # Set the line type to dotted
      linetype = "dotted"
    )
  )

Instruction 4

• Make the axis tick labels’ text, axis.text, less prominent by changing the color to "grey25".
• Increase the plot.title’s, size to 16 and change its font face to "italic".
• Look at the changes in the plot.

plt_prop_unemployed_over_time +
  theme(
    rect = element_rect(fill = "grey92"),
    legend.key = element_rect(color = NA),
    axis.ticks = element_blank(),
    panel.grid = element_blank(),
    panel.grid.major.y = element_line(
      color = "white",
      size = 0.5,
      linetype = "dotted"),
    # Set the axis text color to grey25
    axis.text = element_text(color = "grey25"),
    # Set the plot title font face to italic and font size to 16
    plot.title = element_text(face = "italic", size = 16)
  )

4.4 Modifying whitespace

Whitespace means all the non-visible margins and spacing in the plot.

To set a single whitespace value, use unit(x, unit), where x is the amount and unit is the unit of measure.

Borders require you to set 4 positions, so use margin(top, right, bottom, left, unit). To remember the margin order, think TRouBLe.

The default unit is "pt" (points), which scales well with text. Other options include “cm”, “in” (inches) and “lines” (of text).

plt_mpg_vs_wt_by_cyl is available. The panel and legend are wrapped in blue boxes so you can see how they change.

Instruction 1

• Give the axis tick length, axis.ticks.length, a unit of 2 "lines".

# View the original plot
plt_mpg_vs_wt_by_cyl

plt_mpg_vs_wt_by_cyl +
  theme(
    # Set the axis tick length to 2 lines
    axis.ticks.length = unit(2, "lines")
  )

Instruction 2

• Give the legend key size, legend.key.size, a unit of 3 centimeters ("cm").

plt_mpg_vs_wt_by_cyl +
  theme(
    # Set the legend key size to 3 centimeters
    legend.key.size = unit(3, "cm")
  )

Instruction 3

• Set the legend.margin to 20 points ("pt") on the top, 30 pts on the right, 40 pts on the bottom, and 50 pts on the left.

plt_mpg_vs_wt_by_cyl +
  theme(
    # Set the legend margin to (20, 30, 40, 50) points
  legend.margin = margin(20,30,40,50,"pt")
  )

Instruction 4

• Set the plot margin, plot.margin, to 10, 30, 50, and 70 millimeters (“mm”).

plt_mpg_vs_wt_by_cyl +
  theme(
    # Set the plot margin to (10, 30, 50, 70) millimeters
    plot.margin = margin(10,30,50,70,"mm")
  )

4.5 Theme flexibility

4.6 Built-in themes

In addition to making your own themes, there are several out-of-the-box solutions that may save you lots of time.

• theme_gray() is the default.
• theme_bw() is useful when you use transparency.
• theme_classic() is more traditional.
• theme_void() removes everything but the data.
  plt_prop_unemployed_over_time is available.

Instruction 1

• Add a black and white theme, theme_bw(), to the plot.
• What changed in the plot?

# Add a black and white theme
plt_prop_unemployed_over_time +
  theme_bw()

Instruction 2

• Add a classic theme, theme_classic(), to the plot.
• What changed in the plot?

# Add a classic theme
plt_prop_unemployed_over_time +
  theme_classic()

Instruction 3

• Add a void theme, theme_void(), to the plot.
• What changed in the plot?

# Add a void theme
plt_prop_unemployed_over_time +
  theme_void()

4.7 Exploring ggthemes

Outside of ggplot2, another source of built-in themes is the ggthemes package. The workspace already contains the plt_prop_unemployed_over_time, the line plot from before. Let’s explore some of the ready-made ggthemes themes.

plt_prop_unemployed_over_time is available.

Instruction 1

• Add a fivethirtyeight.com theme, theme_fivethirtyeight(), to the plot.
• What changed in the plot?

# Use the fivethirtyeight theme
plt_prop_unemployed_over_time +
  theme_fivethirtyeight()

Instruction 2

• Add an Edward Tufte theme, theme_tufte(), to the plot.
• What changed in the plot?

# Use Tufte's theme
plt_prop_unemployed_over_time +
  theme_tufte()

Instruction 3

• Add a Wall Street Journal theme, theme_wsj(), to the plot.
• What changed in the plot?

# Use the Wall Street Journal theme
plt_prop_unemployed_over_time +
  theme_wsj()

4.8 Setting themes

Reusing a theme across many plots helps to provide a consistent style. You have several options for this.

1. Assign the theme to a variable, and add it to each plot.
2. Set your theme as the default using theme_set().
   A good strategy that you’ll use here is to begin with a built-in theme then modify it.

plt_prop_unemployed_over_time is available. The theme you made earlier is shown in the sample code.

Instruction 1

• Assign the theme to theme_recession.
• Add the Tufte theme and theme_recession together.
• Use the Tufte recession theme by adding it to the plot.

# Theme layer saved as an object, theme_recession
theme_recession <- theme(
  rect = element_rect(fill = "grey92"),
  legend.key = element_rect(color = NA),
  axis.ticks = element_blank(),
  panel.grid = element_blank(),
  panel.grid.major.y = element_line(color = "white", size = 0.5, linetype = "dotted"),
  axis.text = element_text(color = "grey25"),
  plot.title = element_text(face = "italic", size = 16),
  legend.position = c(0.6, 0.1)
)

# Combine the Tufte theme with theme_recession
theme_tufte_recession <- theme_tufte() + theme_recession

# Add the recession theme to the plot
plt_prop_unemployed_over_time + theme_tufte_recession

Instruction 2

• Use theme_set() to set theme_tufte_recession as the default theme.
• Draw the plot, plt_prop_unemployed_over_time, without explicitly adding a theme.
• Look at the plot. Was it styled with the default theme or the new theme?*

theme_recession <- theme(
  rect = element_rect(fill = "grey92"),
  legend.key = element_rect(color = NA),
  axis.ticks = element_blank(),
  panel.grid = element_blank(),
  panel.grid.major.y = element_line(color = "white", size = 0.5, linetype = "dotted"),
  axis.text = element_text(color = "grey25"),
  plot.title = element_text(face = "italic", size = 16),
  legend.position = c(0.6, 0.1)
)
theme_tufte_recession <- theme_tufte() + theme_recession

# Set theme_tufte_recession as the default theme
theme_set(theme_tufte_recession)

# Draw the plot (without explicitly adding a theme)
plt_prop_unemployed_over_time

4.9 Publication-quality plots

We’ve seen many examples of beautiful, publication-quality plots. Let’s take a final look and put all the pieces together.

plt_prop_unemployed_over_time is available.

Instruction 1
Add Tufte’s theme.

plt_prop_unemployed_over_time +
  # Add Tufte's theme
  theme_tufte()

Instruction 2
Call the function to add individual theme elements. Turn off the legend and the axis ticks.

plt_prop_unemployed_over_time +
  theme_tufte() +
  # Add individual theme elements
  theme(
    # Turn off the legend
    legend.position = "none",
    # Turn off the axis ticks
    axis.ticks = element_blank()
  )

Instruction 3
Set the axis title and axis text’s text color to grey60.

plt_prop_unemployed_over_time +
  theme_tufte() +
  theme(
    legend.position = "none",
    axis.ticks = element_blank(),
    # Set the axis title's text color to grey60
    axis.title = element_text(color = "grey60"),
    # Set the axis text's text color to grey60
    axis.text = element_text(color = "grey60")
  )

Instruction 4
Set the panel gridlines major y values. Set the color to grey60, the size to 0.25, and the line type to dotted.

plt_prop_unemployed_over_time +
  theme_tufte() +
  theme(
    legend.position = "none",
    axis.ticks = element_blank(),
    axis.title = element_text(color = "grey60"),
    axis.text = element_text(color = "grey60"),
    # Set the panel gridlines major y values
    panel.grid.major.y = element_line(
      # Set the color to grey60
      color = "grey60",
      # Set the size to 0.25
      size = 0.25,
      # Set the linetype to dotted
      linetype = "dotted"
    )
  )

4.10 Effective explanatory plots

4.11 Using geoms for explanatory plots

Let’s focus on producing beautiful and effective explanatory plots. In the next couple of exercises, you’ll create a plot that is similar to the one shown in the video using gm2007, a filtered subset of the gapminder dataset.

This type of plot will be in an info-viz style, meaning that it would be similar to something you’d see in a magazine or website for a mostly lay audience.

A scatterplot of lifeExp by country, colored by lifeExp, with points of size 4, is provided.

Instruction 1
geom_segment() adds line segments and requires two additional aesthetics: xend and yend. To draw a horizontal line for each point, map 30 onto xend and country onto yend.

# Add a geom_segment() layer
ggplot(gm2007, aes(x = lifeExp, y = country, color = lifeExp)) +
  geom_point(size = 4) +
  geom_segment(aes(xend = 30, yend = country), size = 2)

Instruction 2
geom_text also needs an additional aesthetic: label. Map lifeExp onto label, and set the attributes color to "white" and size to 1.5.

# Add a geom_text() layer
ggplot(gm2007, aes(x = lifeExp, y = country, color = lifeExp)) +
  geom_point(size = 4) +
  geom_segment(aes(xend = 30, yend = country), size = 2) +
  geom_text(aes(label = lifeExp), color = "white", size = 1.5)

Instruction 3

• The color scale has been set for you, but you need to clean up the scales. For the x scale:
• Set expand to c(0, 0) and limits to c(30, 90).
• Place the axis on the top of the plot with the position argument.

# Set the color scale
palette <- brewer.pal(5, "RdYlBu")[-(2:4)]

# Modify the scales
ggplot(gm2007, aes(x = lifeExp, y = country, color = lifeExp)) +
  geom_point(size = 4) +
  geom_segment(aes(xend = 30, yend = country), size = 2) +
  geom_text(aes(label = round(lifeExp,1)), color = "white", size = 1.5) +
  scale_x_continuous("", expand = c(0,0), limits = c(30,90), position = "top") +
  scale_color_gradientn(colors = palette)

Instruction 4
Make sure to label the plot appropriately using labs():

• Make the title “Highest and lowest life expectancies, 2007”.
• Add a reference by setting caption to “Source: gapminder”.

# Set the color scale
palette <- brewer.pal(5, "RdYlBu")[-(2:4)]

# Add a title and caption
ggplot(gm2007, aes(x = lifeExp, y = country, color = lifeExp)) +
  geom_point(size = 4) +
  geom_segment(aes(xend = 30, yend = country), size = 2) +
  geom_text(aes(label = round(lifeExp,1)), color = "white", size = 1.5) +
  scale_x_continuous("", expand = c(0,0), limits = c(30,90), position = "top") +
  scale_color_gradientn(colors = palette) +
  labs(title = "Highest and lowest life expectancies, 2007", caption = "Source: gapminder")

4.12 Using annotate() for embellishements

In the previous exercise, we completed our basic plot. Now let’s polish it by playing with the theme and adding annotations. In this exercise, you’ll use annotate() to add text and a curve to the plot.

The following values have been calculated for you to assist with adding embellishments to the plot:

global_mean <- mean(gm2007_full$lifeExp)
x_start <- global_mean + 4
y_start <- 5.5
x_end <- global_mean
y_end <- 7.5

Our previous plot has been assigned to plt_country_vs_lifeExp.

Instruction 1
Clean up the theme:

• Add a classic theme to the plot with theme_classic().
• Set axis.line.y, axis.ticks.y, and axis.title to element_blank().
• Set the axis.text color to "black".
• Remove the legend by setting legend.position to "none".

# Define the theme
plt_country_vs_lifeExp +
  theme_classic() +
  theme(axis.line.y = element_blank(),
        axis.ticks.y = element_blank(),
        axis.text = element_text(color = "black"),
        axis.title = element_blank(),
        legend.position = "none")

Instruction 2
Use geom_vline() to add a vertical line. Set xintercept to global_mean, specify the color to be "grey40", and set linetype to 3.

# Add a vertical line
plt_country_vs_lifeExp +
  step_1_themes +
  geom_vline(xintercept = global_mean, color = "grey40", linetype = 3)

Instruction 3
x_start and y_start will be used as positions to place text and have been calculated for you.

Add a "text" geom as an annotation.
For the annotation, set x to x_start, y to y_start, and label to "The\nglobal\naverage".

# Add text
plt_country_vs_lifeExp +
  step_1_themes +
  geom_vline(xintercept = global_mean, color = "grey40", linetype = 3) +
  annotate(
    "text",
    x = x_start, y = y_start,
    label = "The\nglobal\naverage",
    vjust = 1, size = 3, color = "grey40"
  )

Instruction 4
Annotate the plot with an arrow connecting your text to the line.

• Use a "curve" geom.
• Set the arrow ends xend to x_end and yend to y_end.
• Set the length of the arrowhead to 0.2 cm and the type to "closed".

# Add a curve
plt_country_vs_lifeExp +
  step_1_themes +
  geom_vline(xintercept = global_mean, color = "grey40", linetype = 3) +
  step_3_annotation +
  annotate(
    "curve",
    x = x_start, y = y_start,
    xend = x_end, yend = y_end,
    arrow = arrow(length = unit(0.2, "cm"), type = "closed"),
    color = "grey40"
  )