# Writing non-standard notation in ggplot2

## 2019-08-20

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")`
• 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)
``````