Create ggplot boxplot with compact letter display

Performs pairwise comparisons using TukeyHSD and produces boxplots with compact letter display showing significance pairwise differences. Letters are produced by multcompLetters. Plots are produced by ggplot2. Raw data can also be overlaid in various ways according to the value of raw.

Usage

boxplot_letters(
  data,
  x,
  y,
  fill,
  group,
  test = c("tukey", "kruskalmc"),
  type = c("two-way", "one-way"),
  where = c("box", "whisker", "mean", "median", "se", "sd", "cl_normal", "cl_boot"),
  raw = c("none", "points", "dots", "jitter"),
  pt_col = "slategray",
  ...,
  hjust = 0,
  vjust = -0.2,
  lab_size = 4,
  na.rm = TRUE,
  threshold = 0.05
)

Arguments

data: A data.frame in "long" format.
x: variable to plot on x axis.
y: variable to plot on y axis.
fill: column or color to fill boxplots
group: A grouping variable (to allow faceting).
test: Which test to run for pairwise comparisons. Either tukey (the default) or kruskalmc.
type: If a grouping variable is provided, determines whether to run separate tests for each facet (one-way) or a single (two-way) test (with an interaction term between x and group). Defaults to two-way. This argument only applies if the Tukey test is selected, since there is no two-way Kruskal-Wallis test.
where: Where to put the letters. Either above the box (box) or upper whisker (whisker) of a boxplot; at the mean or median; or at the top of the error bars calculated from the standard error (se), standard deviation sd, or 95% confidence intervals returned by smean.cl.normal, or smean.cl.boot.
raw: Whether to plot raw data and (if so), how. The current options are none, geom_point, geom_dotplot, or geom_jitter.
pt_col: Color of points, if raw data is plotted.
...: Additional arguments to geom_point, geom_dotplot, or geom_jitter, according to the value of raw.
hjust: Horizontal adjustment of label. Argument to geom_text.
vjust: Vertical adjustment of label. Argument to geom_text.
lab_size: Label size. Argument to geom_text.
na.rm: Logical. Whether to remove observations with NAs for the provided factors (i.e. x and group) before plotting.
threshold: Statistical threshold for significance. Defaults to 0.05.

Value

Returns the specified plot as a ggplot object.

Details

Allows group variable for faceting

Note

Adapted from a helpful blog post by Justin Mathias.

Author

Ethan Bass

Examples

set.seed(1)
data <- data.frame("Category" = c(rep("Low", 10), rep("Medium", 10), rep("High", 10)),
                   "Value" = c(rnorm(10, 5), rnorm(10, 5.5), rnorm(10, 10)),
                   "Size" = c("Big","Small"))
boxplot_letters(data, Category, Value)

boxplot_letters(data, x=Category, y=Value, group=Size)