Graph info

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This graph requires:

✅ a categorical variable

✅ a numeric (continuous) variable

Description

The beeswarm plot uses points to display the distribution of a continuous variable across the levels of a categorical variable.

The points are grouped by level, and the shape (or swarm) of the distribution is mirrored above and below the quantitative axis (similar to a violin plot).

We can create beeswarm plot using geom_jitter() or the ggbeeswarm package.

Getting set up

PACKAGES:

Install packages.

Code 
devtools::install_github("eclarke/ggbeeswarm")
library(ggbeeswarm)
install.packages("palmerpenguins")
library(palmerpenguins) 
library(ggplot2)

DATA:

Artwork by @allison_horst

Create peng_beeswarm by grouping penguins by species, then calculating the bill_ratio (bill_length_mm / bill_depth_mm), and then removing any missing values from bill_ratio

Code 
peng_beeswarm <- palmerpenguins::penguins |> 
    dplyr::group_by(species) |> 
    dplyr::mutate(bill_ratio = bill_length_mm / bill_depth_mm) |>  
    dplyr::filter(!is.na(bill_ratio)) |> 
    dplyr::ungroup()
glimpse(peng_beeswarm)
Rows: 342
Columns: 9
$ species           <fct> Adelie, Adelie, Adelie, Adelie, Adelie, Adelie, Adel…
$ island            <fct> Torgersen, Torgersen, Torgersen, Torgersen, Torgerse…
$ bill_length_mm    <dbl> 39.1, 39.5, 40.3, 36.7, 39.3, 38.9, 39.2, 34.1, 42.0…
$ bill_depth_mm     <dbl> 18.7, 17.4, 18.0, 19.3, 20.6, 17.8, 19.6, 18.1, 20.2…
$ flipper_length_mm <int> 181, 186, 195, 193, 190, 181, 195, 193, 190, 186, 18…
$ body_mass_g       <int> 3750, 3800, 3250, 3450, 3650, 3625, 4675, 3475, 4250…
$ sex               <fct> male, female, female, female, male, female, male, NA…
$ year              <int> 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007, 2007…
$ bill_ratio        <dbl> 2.090909, 2.270115, 2.238889, 1.901554, 1.907767, 2.…

The grammar

CODE:

Create labels with labs()

Initialize the graph with ggplot() and provide data

Map species to the x axis and color

Map bill_ratio to the y axis

Add the ggbeeswarm::geom_beeswarm() layer (with alpha)

Remove the legend with show.legend = FALSE

Code 
labs_beeswarm <- labs(
    title = "Adult Foraging Penguins",
    subtitle = "Bill Length (mm) / Bill Depth (mm) = Bill Ratio",
    x = "Species",
    y = "Bill Ratio")
ggp2_beeswarm <- ggplot(data = peng_beeswarm,
    aes(x = species,
        y = bill_ratio,
        color = species)) +
    ggbeeswarm::geom_beeswarm(alpha = 2 / 3,
        show.legend = FALSE)
ggp2_beeswarm +
    labs_beeswarm

GRAPH:

Adjust the size/shape of the swarm using method = or the geom_quasirandom() function

More info

Below we cover some additional arguments and methods for beeswarm plots.

METHOD:

Use method to adjust the shape of the beeswarm (swarm, compactswarm, hex, square, center, or centre)

Set the point shape to 21 to control the fill and color

Code 
ggp2_compact_swarm <- ggplot(data = peng_beeswarm,
    mapping = aes(x = species,
                  y = bill_ratio,
                color = species)) +
    ggbeeswarm::geom_beeswarm(
      aes(fill = species),
        method = 'compactswarm', 
        dodge.width = 0.5,
        shape = 21,
        color = "#ffffff",
        alpha = 2/3, size = 1.7,
        show.legend = FALSE) 
ggp2_compact_swarm + 
    # add labels
    labs_beeswarm

SIDE:

For a beeswarm that falls across the vertical axis, use the side argument.

Code 
ggp2_rside_swarm <- ggplot(data = peng_beeswarm,
    mapping = aes(x = species,
                  y = bill_ratio,
                color = species)) +
    ggbeeswarm::geom_beeswarm(
      aes(fill = species),
        side = 1, # right/upwards
        shape = 21,
        color = "#ffffff",
        alpha = 2/3, 
        size = 1.7,
        show.legend = FALSE) 
ggp2_rside_swarm + 
    # add labels
    labs_beeswarm

CEX:

The cex argument controls the “scaling for adjusting point spacing”

Code 
ggp2_beeswarm_cex <- ggplot(data = peng_beeswarm,
    mapping = aes(x = species,
                  y = bill_ratio,
                color = species)) +
    ggbeeswarm::geom_beeswarm(
      aes(fill = species),
        cex = 1.6,
        shape = 21,
        color = "#ffffff",
        alpha = 2/3, 
        size = 1.7,
        show.legend = FALSE) 
ggp2_beeswarm_cex + 
    # add labels
    labs_beeswarm

JITTER:

We can also create a beeswarm using the geom_jitter() and setting the height and width.

Code 
ggp2_jitter_swarm <- ggplot(data = peng_beeswarm,
    mapping = aes(x = species,
        y = bill_ratio,
        color = species)) +
    geom_jitter(
        aes(fill = species),
        height = 0.05,
        width = 0.11,
        shape = 21,
        color = "#ffffff",
        alpha = 2 / 3,
        size = 1.7,
        show.legend = FALSE)
ggp2_jitter_swarm + 
    # add labels
    labs_beeswarm