Creating Publication-Quality Graphics with ggplot2

Overview

Questions

• How can I create publication-quality graphics in R?

Objectives

• To be able to use ggplot2 to generate publication-quality graphics.
• To apply geometry, aesthetic, and statistics layers to a ggplot plot.
• To manipulate the aesthetics of a plot using different colors, shapes, and lines.
• To improve data visualization through transforming scales and paneling by group.
• To save a plot created with ggplot to disk.

Let’s make a new script for this episode, by choosing the menu options File, New File, R Script.

Although we loaded the tidyverse in the previous episode, we should make our scripts self-contained, so we should include library(tidyverse) in the new script.

R

library(tidyverse)

OUTPUT

── Attaching core tidyverse packages ──────────────────────── tidyverse 2.0.0 ──
✔ dplyr     1.1.4     ✔ readr     2.1.5
✔ forcats   1.0.0     ✔ stringr   1.5.1
✔ ggplot2   3.5.1     ✔ tibble    3.2.1
✔ lubridate 1.9.4     ✔ tidyr     1.3.1
✔ purrr     1.0.2
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

R

penguins <- read_csv("data/penguins_teaching.csv", col_types = cols(year = col_character()))

Plotting our data is one of the best ways to quickly explore it and the various relationships between variables.

There are three main plotting systems in R, the base plotting system, the lattice package, and the ggplot2 package.

Today we’ll be learning about the ggplot2 package, because it is the most effective for creating publication-quality graphics.

ggplot2 is built on the grammar of graphics, the idea that any plot can be built from the same set of components: a data set, mapping aesthetics, and graphical layers:

• Data sets are the data that you, the user, provide.

• Mapping aesthetics are what connect the data to the graphics. They tell ggplot2 how to use your data to affect how the graph looks, such as changing what is plotted on the X or Y axis, or the size or color of different data points.

• Layers are the actual graphical output from ggplot2. Layers determine what kinds of plot are shown (scatterplot, histogram, etc.), the coordinate system used (rectangular, polar, others), and other important aspects of the plot. The idea of layers of graphics may be familiar to you if you have used image editing programs like Photoshop, Illustrator, or Inkscape.

Let’s start off building an example using the penguins data from earlier. First let’s create a derived data set to plot! Let’s find out if the mean body mass of the Adelie penguins has changed over time.

R

penguins_bm <- penguins |>
  filter(species == c("Adelie")) |>
  group_by(year, island, species) |>
  summarize(mean_body_mass = mean(body_mass_g)) |>
  ungroup()

OUTPUT

`summarise()` has grouped output by 'year', 'island'. You can override using
the `.groups` argument.

The most basic function is ggplot, which lets R know that we’re creating a new plot. Any of the arguments we give the ggplot function are the global options for the plot: they apply to all layers on the plot.

R

library(ggplot2)
ggplot(data = penguins_bm)

Here we called ggplot and told it what data we want to show on our figure. This is not enough information for ggplot to actually draw anything. It only creates a blank slate for other elements to be added to.

Now we’re going to add in the mapping aesthetics using the aes function. aes tells ggplot how variables in the data map to aesthetic properties of the figure, such as which columns of the data should be used for the x and y locations.

R

ggplot(data = penguins_bm, mapping = aes(x = year, y = mean_body_mass))

Here we told ggplot we want to plot the “mean_body_mass” column of the our data frame on the x-axis, and the “year” column on the y-axis. Notice that we didn’t need to explicitly pass aes these columns (e.g. x = penguins[, "year"]), this is because ggplot is smart enough to know to look in the data for that column!

The final part of making our plot is to tell ggplot how we want to visually represent the data. We do this by adding a new layer to the plot using one of the geom functions.

R

ggplot(data = penguins_bm, mapping = aes(x = year, y = mean_body_mass)) +
  geom_point()

Here we used geom_point, which tells ggplot we want to visually represent the relationship between x and y as a scatterplot of points.

Notice that we use a “+” sign to add another layer to the plot, not a pipe “|>” which we’ve previously used to pass the output data from one data processing step to another step.

Challenge 1

Modify the example so that the figure shows how bill length (mm) varies with flipper length (mm) instead of body mass :

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = body_mass_g)) + geom_point()

Solution to challenge 1

Here is one possible solution:

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm)) + geom_point()

Scatter plot showing bill length (mm) versus flipper length (mm) for individual penguins, displaying each species as distinct points. All points are coloured on the plot are coloured black.

Challenge 2

In the previous examples and challenge we’ve used the aes function to tell the scatterplot geom about the x and y locations of each point. Another aesthetic property we can modify is the point color. Modify the code from the previous challenge to color the points by the “species” column. What trends do you see in the data? Are they what you expected?

Hint: Use ?aes or ?ggplot2 to get help on these functions if needed.

Solution to challenge 2

The solution presented below adds color=species to the call of the aes function. The general trend seems to indicate an increased bill length with flipper length. Visual inspection suggests that the strength of this relationship is similar across all three species.

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm, color=species)) +
  geom_point()

Scatter plot of body mass (g) vs flipper length (mm), with points color-coded by penguin species to show how body mass varies by species and flipper length, thus showing the value of ‘aes’ function

Layers

---

Using a scatterplot probably isn’t the best for visualizing change over time. Instead, let’s tell ggplot to visualize the data as a line plot:

R

ggplot(data = penguins_bm, mapping = aes(x=year, y=mean_body_mass)) +
  geom_line()

Instead of adding a geom_point layer, we’ve added a geom_line layer.

However, the result doesn’t look quite as we might have expected: it seems to be jumping around a lot within each year Let’s try to separate the data by island, plotting one line for each island:

R

ggplot(data = penguins_bm, mapping = aes(x=year, y=mean_body_mass, group=island)) +
  geom_line()

Let’s color the lines by island to make things clearer:

R

ggplot(data = penguins_bm, mapping = aes(x=year, y=mean_body_mass, group=island, color = island)) +
  geom_line()

We’ve added the group aesthetic, which tells ggplot to draw a line for each island.

But what if we want to visualize both lines and points on the plot? We can add another layer to the plot:

R

ggplot(data = penguins_bm, mapping = aes(x=year, y=mean_body_mass, group=island, color=island)) +
  geom_line() + 
  geom_point()

It’s important to note that each layer is drawn on top of the previous layer. In this example, the points have been drawn on top of the lines. Here’s a demonstration:

R

ggplot(data = penguins_bm, mapping = aes(x=year, y=mean_body_mass, group=island)) +
  geom_line(mapping = aes(color=island)) + geom_point()

In this example, the aesthetic mapping of color has been moved from the global plot options in ggplot to the geom_line layer so it no longer applies to the points. Now we can clearly see that the points are drawn on top of the lines.

Tip: Setting an aesthetic to a value instead of a mapping

So far, we’ve seen how to use an aesthetic (such as color) as a mapping to a variable in the data. For example, when we use geom_line(mapping = aes(color=island)), ggplot will give a different color to each island But what if we want to change the color of all lines to blue? You may think that geom_line(mapping = aes(color="blue")) should work, but it doesn’t. Since we don’t want to create a mapping to a specific variable, we can move the color specification outside of the aes() function, like this: geom_line(color="blue").

Challenge 3

Switch the order of the point and line layers from the previous example. What happened?

Solution to challenge 3

The lines now get drawn over the points!

R

ggplot(data = penguins_bm, mapping = aes(x=year, y=mean_body_mass, group=island)) +
  geom_point() +
  geom_line(mapping = aes(color=island)) 

Statistics

---

ggplot2 also makes it easy to overlay statistical models over the data. To demonstrate we’ll go back to our first challenge:

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm)) +
  geom_point()

We can modify the transparency of the points, using the alpha function, which is especially helpful when you have a large amount of data which is very clustered.

Tip Reminder: Setting an aesthetic to a value instead of a mapping

Notice that we used geom_point(alpha = 0.5). As the previous tip mentioned, using a setting outside of the aes() function will cause this value to be used for all points, which is what we want in this case. But just like any other aesthetic setting, alpha can also be mapped to a variable in the data. For example, we can give a different transparency to each island with geom_point(mapping = aes(alpha = island)).

We can fit a simple relationship to the data by adding another layer, geom_smooth:

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm)) +
  geom_point(alpha = 0.5) + 
  geom_smooth(method="lm")

OUTPUT

`geom_smooth()` using formula = 'y ~ x'

We can make the line thicker by setting the linewidth aesthetic in the geom_smooth layer:

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm)) +
  geom_point(alpha = 0.5) + 
  geom_smooth(method="lm", linewidth=1.5)

OUTPUT

`geom_smooth()` using formula = 'y ~ x'

There are two ways an aesthetic can be specified. Here we set the linewidth aesthetic by passing it as an argument to geom_smooth and it is applied the same to the whole geom. Previously in the lesson we’ve used the aes function to define a mapping between data variables and their visual representation.

Challenge 4a

Modify the color and size of the points on the point layer in the plot from Challenge 1 example.

Hint: do not use the aes function.

Hint: the equivalent of linewidth for points is size.

Solution to challenge 4a

Here a possible solution: Notice that the color argument is supplied outside of the aes() function. This means that it applies to all data points on the graph and is not related to a specific variable.

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm)) +
  geom_point(size = 2, color = "orange")

Challenge 4b

Modify your solution to Challenge 4a so that the points are now a different shape and are colored by species.

Hint: (1) The color argument can be used inside the aesthetic. (2) See this quick reference to find out more about available point shapes in R

Solution to challenge 4b

Here is a possible solution: Notice that supplying the color argument inside the aes() functions enables you to connect it to a certain variable. The shape argument, as you can see, modifies all data points the same way (it is outside the aes() call) while the color argument which is placed inside the aes() call modifies a point’s color based on its species value.

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm)) +
  geom_point(size = 2, shape = 17, aes(color=species)) 

Multi-panel figures

---

Earlier we visualized the relationship between bill length and flipper length across all species in one plot. Alternatively, we can split this out over multiple panels by adding a layer of facet panels.

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm, color = island)) +
  geom_point() +
  facet_wrap( ~ species) +
  theme(axis.text.x = element_text(angle = 45))

The facet_wrap layer took a “formula” as its argument, denoted by the tilde (~). This tells R to draw a panel for each unique value in the species column of the penguins dataset.

Note that we apply a “theme” definition to rotate the x-axis labels to maintain readability. Nearly everything in ggplot2 is customizable.

Modifying text

---

To clean this figure up for a publication we need to change some of the text elements. The x-axis is too cluttered, and the axis labels should read “Bill Length” and “Flipper Length, rather than the column names in the data frame.

We can do this by adding a couple of different layers. The theme layer controls the axis text, and overall text size. Labels for the axes, plot title and any legend can be set using the labs function. Legend titles are set using the same names we used in the aes specification. Thus below the color legend title is set using color = "Island", while the title of a fill legend would be set using fill = "MyTitle".

R

ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm, color = island)) +
  geom_point() +
  facet_wrap( ~ species) +
  labs(
    x = "Flipper Length (mm)",              # x axis title
    y = "Bill Length (mm)",   # y axis title
    title = "Figure 1",      # main title of figure
    color = "Island"      # title of legend
  ) +
  theme(axis.text.x = element_text(angle = 90, hjust = 1))

Exporting the plot

---

The ggsave() function allows you to export a plot created with ggplot. You can specify the dimension and resolution of your plot by adjusting the appropriate arguments (width, height and dpi) to create high quality graphics for publication. In order to save the plot from above, we first assign it to a variable bill_flipper_plot, then tell ggsave to save that plot in png format to a directory called results. (Make sure you have a results/ folder in your working directory.)

R

bill_flipper_plot <- ggplot(data = penguins, mapping = aes(x = flipper_length_mm, y = bill_length_mm, color = island)) +
  geom_point() +
  facet_wrap( ~ species) +
  labs(
    x = "Flipper Length (mm)",              # x axis title
    y = "Bill Length (mm)",   # y axis title
    title = "Figure 1",      # main title of figure
    color = "Island"      # title of legend
  ) +
  theme(axis.text.x = element_text(angle = 90, hjust = 1))

ggsave(filename = "results/bill_flipper_plot.png", plot = bill_flipper_plot, width = 12, height = 10, dpi = 300, units = "cm")

There are two nice things about ggsave. First, it defaults to the last plot, so if you omit the plot argument it will automatically save the last plot you created with ggplot. Secondly, it tries to determine the format you want to save your plot in from the file extension you provide for the filename (for example .png or .pdf). If you need to, you can specify the format explicitly in the device argument.

This is a taste of what you can do with ggplot2. RStudio provides a really useful cheat sheet of the different layers available, and more extensive documentation is available on the ggplot2 website. All RStudio cheat sheets are available from the RStudio website. Finally, if you have no idea how to change something, a quick Google search will usually send you to a relevant question and answer on Stack Overflow with reusable code to modify!

Challenge 5

Generate a boxplot to compare flipper length between species.

Advanced:

• Add axis labels
• Hide the legend

Solution to Challenge 5

Here a possible solution: xlab() and ylab() set labels for the x and y axes, respectively The axis title, text and ticks are attributes of the theme and must be modified within a theme() call.

R

ggplot(data = penguins, mapping = aes(x = species, y = flipper_length_mm, fill = species)) +
  geom_boxplot() +
  labs(
    x = "Species",              # x axis title
    y = "Flipper Length (mm)",   # y axis title
  ) +  
  theme(legend.position = "none")

Further reading

---

We recommend the following resources for some additional reading on the topic of this episode:

ggplot2

• ggplot2: Elegant Graphics for Data Analysis (3e)
• ggplot2
• cheat
• ggplot-doc

Other Plotting Systems

• basehttps://www.statmethods.net/graphs/index.html
• latticehttps://www.statmethods.net/advgraphs/trellis.html

Key Points

• Use ggplot2 to create plots.
• Think about graphics in layers: aesthetics, geometry, statistics, scale transformation, and grouping.