On the current theme of writing papers, I’ve been preparing figures in R using ggplot2 for a manuscript. I need to put subscripts, greek letters and other non-standard bits of text into facet labels and axis labels, mostly to denote the units of a variable. I found that there are multiple ways to achieve this and unfortunately it seems like different ways are necessary in different contexts, however, a lot of what I needed to do could be covered by expression(), which constructs mathematical expressions in R using “plotmath” syntax.

I wrote notes on how to accomplish different tasks requiring plotmath and I thought I would put those notes here. See below:

Non-standard notation in ggplot2

expression() notation:

• Basic arithmetic - expression(x + y - z %*% a %/% b %+-% e %~~% q != p)
  • (x plus y minus z times a divided-by b plus-or-minus e approximately q does-not-equal p)
• Juxtaposition - expression(paste(x, y, z))
• Subscript - expression("cm"^2), expression("cm"^{x + y-2})
  • {} is used to group items together without adding brackets
• Superscript - expression("CO"[2])
  • To put a sub and superscript together: R[m]^2
• Degree symbol - expression(32 * degree)
  • The * signifies the start of a special character but without a space before it
• Greek letters - expression(alpha - omega)
• Brackets -
• Fractions - expression(frac('Top', 'Bottom'))
• Roots - expression(sqrt(x, y))
  • The y root of x
• Typeface - expression(plain(x) italic(y) bold(z) bolditalic(a) underline(b)
• Deliberate space - expression(x + phantom(0) + y)
• Normal space - expression("leaf" ~ "area" ~ (cm^2))

Notes:

• expression() can’t take spaces in quoted text, expression("leaf area" ~ (cm^2)) wouldn’t parse well, but expression("leaf" ~ "area" ~ (cm^2)) would be fine.

Example workflow for ggplot2 axis titles:

library(ggplot2)
library(dplyr)
library(tidyr)

area <- rnorm(n = 50, mean = 10, sd = 1)
leaf_chloro <- rnorm(n = 50, mean = 100, sd = 2)
groups <- rep(c("A", "B", "C", "D", "E"), times = 10)

df <- data.frame(area, leaf_chloro, groups)

ggplot(df, aes(x = groups, y = area)) + 
  geom_bar(stat = "identity", aes(fill = groups)) + 
  labs(x = "Group", y = expression("Leaf" ~ "area" ~ (cm^2)))

Facet labels:

df_long <- gather(df, key = var, value = value, -groups)

df_label <- df_long %>%
  mutate(var_exp = factor(var, 
    levels = c("area", "leaf_chloro"),
    labels = c(
      expression("Leaf" ~ "area" ~ (cm^2)),
      expression("Chlorophyll-" ~ alpha)
    )))

ggplot(df_label, aes(x = groups, y = value)) + 
  geom_bar(stat = "identity", aes(fill = groups)) +
  facet_wrap(~var_exp, labeller = label_parsed)

Axis labels:

ggplot(df, aes(x = groups, y = area)) + 
  geom_bar(stat = "identity", aes(fill = groups)) +
  scale_x_discrete(labels = c(
    "A" = expression(alpha),
    "B" = expression(beta), 
    "C" = expression(gamma),
    "D" = expression(epsilon), 
    "E" = expression(omega)))

Custom annotations and labels:

ggplot(df, aes(x = groups, y = area)) + 
  geom_bar(stat = "identity", aes(fill = groups)) +
  geom_label(aes(x = 1, y = 25, label = "(alpha != Alpha)"), 
    parse = T)