Graphics with ggplot2

This lesson is a brief overview of the ggplot2 package, which is a R implementation of the “grammar of graphics”. In base R, there are different functions for different types of graphics (plot, boxplot, hist, etc.) and each may have their own specific parameters in addition to general plot options. In contrast, ggplot2 constructs plots one layer at a time; for example, the output of a linear regression could be plotted by defining the axes, then adding individual points, tracing the line of best fit, and finally specifying overall layout parameters such as font sizes and background color.

This layered approach allows for highly customizable graphics. Even when a plot requires several lines of code, that code is broken down in simple components that are easy to interpret.

Let’s start by loading a few packages along with a sample dataset, which is the surveys table from the Portal Project Teaching Database. We filter the data to remove rows that have missing values for the species_id, sex, or weight columns. (This is not strictly necessary, but it will prevent ggplot from returning missing values warnings.)

library(dplyr)
library(ggplot2)
surveys <- read.csv("data/surveys.csv", na.strings = "") %>%
    filter(!is.na(species_id), !is.na(sex), !is.na(weight))

Constructing layered graphics in ggplot

As a first example, this code plots the inviduals’ weights by species:

ggplot(data = surveys,
       aes(x = species_id, y = weight)) +
    geom_point()

plot of chunk plot_pt

In ggplot, we specified a data frame (surveys) and a number of aesthetic mappings (aes). The aes function associates variables from that data frame to visual elements in the plot: here, species_id on the x-axis and weight on the y-axis. The ggplot function by itself does not plot anything until we add a geom layer such as geom_point. In this particular case, individual points are hard to distinguish; what could we use instead? (Try geom_boxplot.)

Multiple geom layers can be combined in a single plot:

ggplot(data = surveys,
       aes(x = species_id, y = weight)) +
    geom_boxplot() +
    geom_point(stat = "summary",
               fun.y = "mean",
               color = "red")

plot of chunk plot_box

This geom_point layer definition illustrates a couple new features:

Quick plotting with qplot

The qplot function provides a shortcut to ggplot that looks more like the base R plot function, e.g. qplot(x = species_id, y = weight, data = surveys, geom = "boxplot"). This can be useful to quickly produce simple graphs, especially those with a single geom.

Exercise 1

Using dplyr and ggplot show how the mean weight of individuals of the species DM varies across years and between males and females.

View solution

Adding a regression line

The code below shows one graph answering the question in the exercise. I added a geom_smooth layer that displays a regression line with confidence intervals (95% CI by default). The method = "lm" parameter specifies that a linear model is used for smoothing.

surveys_dm <- filter(surveys, species_id == "DM")
ggplot(data = surveys_dm,
       aes(x = year, y = weight)) + 
    geom_point(aes(shape = sex),
               size = 3,
	       stat = "summary",
	       fun.y = "mean") +
    geom_smooth(method = "lm")

plot of chunk plot_lm

To get separate regression lines for females and males, we could add a group aesthetic mapping to geom_smooth:

ggplot(data = surveys_dm,
       aes(x = year, y = weight)) + 
    geom_point(aes(shape = sex),
               size = 3,
	       stat = "summary",
	       fun.y = "mean") +
    geom_smooth(aes(group = sex), method = "lm")

plot of chunk plot_lm_group

Even better would be to distinguish the two lines by color:

year_wgt <- ggplot(data = surveys_dm,
                   aes(x = year,
		       y = weight,
		       color = sex)) + 
    geom_point(aes(shape = sex),
               size = 3,
	       stat = "summary",
	       fun.y = "mean") +
    geom_smooth(method = "lm")
year_wgt

plot of chunk plot_lm_color

Notice that by adding the aesthetic mapping in the ggplot command, it is applied to all layers that recognize that aesthetic (color).

Storing and re-plotting

The output of ggplot can be assigned to a variable (here, it’s year_wgt). It is then possible to add new elements to it with the + operator. We will use this method to try different color scales for the previous plot

year_wgt + scale_color_manual(values = c("darkblue", "orange"),
                              labels = c("Female", "Male"))

plot of chunk plot_lm_scales

year_wgt + scale_color_manual(values = c("black", "red"),
                              labels = c("Female", "Male"))

plot of chunk plot_lm_scales_2

The labels parameter sets the names to display in the legend.

Exercise 2

Create a histogram, using a geom_histogram() layer, of the weights of individuals of species DM and divide the data by sex. Note that instead of using color in the aesthetic, you’ll use fill to distinguish the sexes. Also look at the documentation and determine how to explicitly set the bin width.

View solution

Axes, labels and themes

Let’s start from the histogram like the one generated in the exercise.

histo <- ggplot(data = surveys_dm,
                aes(x = weight, fill = sex)) +
    geom_histogram(binwidth = 3, color = "white")
histo

plot of chunk plot_hist

We change the title and axis labels with the labs function. We have various functions related to the scale of each axis, i.e. the range, breaks and any transformations of the values on the axis. Here, we use scale_x_continuous to modify a continuous (as opposed to discrete) x-axis.

histo <- histo + 
  labs(title = "Dipodomys merriami weight distribution",
       x = "Weight (g)",
       y = "Count") +
  scale_x_continuous(limits = c(20, 60),
                     breaks = c(20, 30, 40, 50, 60))
histo

plot of chunk plot_hist_axes

For information on how to add special symbols and formatting to plot labels, see ?plotmath.

Many plot-level options in ggplot, from background color to font sizes, are defined as part of themes. The next modification to histo changes the base theme of the plot to theme_bw (replacing the default theme_grey) and set a few options manually with the theme function. Try ?theme for a list of available theme options.

histo <- histo +
  theme_bw() +
  theme(legend.position = c(0.2, 0.5),
        plot.title = element_text(face = "bold", vjust = 2),
        axis.title.y = element_text(size = 13, vjust = 1), 
        axis.title.x = element_text(size = 13, vjust = 0))
histo

plot of chunk plot_hist_themes

Note that position is relative to plot size (i.e. between 0 and 1).

Facets

To conclude this overview of ggplot2, here are a few examples that show different subsets of the data in panels called facets. The facet_wrap function takes a formula argument that specifies the grouping on either side of a ‘~’. First, we specify that month is a factor, rather than an integer, so grouping works.

surveys_dm$month <- as.factor(surveys_dm$month)
levels(surveys_dm$month) <- c("January", "February", "March", "April", "May", "June",
                              "July", "August", "September", "October", "November", "December")
ggplot(data = surveys_dm,
       aes(x = weight)) +
  geom_histogram() +
  facet_wrap( ~ month) +
  labs(title = "DM weight distribution by month",
       x = "Count",
       y = "Weight (g)")

plot of chunk plot_facets

The un-grouped data may be added as a layer on each panel, but you have to drop the grouping variable (i.e. month).

ggplot(data = surveys_dm,
       aes(x = weight)) +
  geom_histogram(data = select(surveys_dm, -month),
                 alpha = 0.2) +
  geom_histogram() +
  facet_wrap( ~ month) +
  labs(title = "DM weight distribution by month",
       x = "Count",
       y = "Weight (g)")

plot of chunk plot_facets_2

Finally, let’s show off with some nice styling and the very unusual ..density.. argument in the aesthetic. The notation signifies the ggplot is to calculate the probability density, rather than plot frequency as before.

ggplot(data = surveys_dm,
       aes(x = weight, fill = month)) +
  geom_histogram(data = select(surveys_dm, -month),
                 aes(y = ..density..),
                 fill = "black") +
  geom_histogram(aes(y = ..density..),
                 alpha = 0.8) +
  facet_wrap( ~ month) +
  labs(title = "DM weight distribution by month",
       x = "Count",
       y = "Weight (g)") +
  guides(fill = FALSE)

plot of chunk plot_facets_3

Exercise 3

Here’s a take-home challenge for you to try later. For records with species_id “DM” and “PB”, create facets along two categorical variables, species_id and sex, using facet_grid instead of facet_wrap.

View solution

Additional information

Exercise solutions

Solution 1

filter(surveys, species_id == "DM") %>%
  ggplot(aes(x = year, y = weight, color = sex)) +
  geom_line(stat = "summary", fun.y = "mean")

plot of chunk sol1

Return

Solution 2

filter(surveys, species_id == "DM") %>%
  ggplot(aes(x = weight, fill = sex)) +         
  geom_histogram(binwidth = 1)

plot of chunk sol2

Return

Solution 3

filter(surveys, species_id %in% c("DM", "PB")) %>%
  ggplot(aes(x = weight)) +
  geom_histogram() +
  facet_grid(sex ~ species_id) +
  labs(title = "DM and RO weight distribution by sex",
       x = "Count",
       y = "Weight (g)")

plot of chunk sol3

Return