R visualization: Beeswarm by ggplot2

Beeswarm with boxplot and point

Last updated on Jul 15, 2023 5 min read Visualization, ggplot2

Introduction

Beeswarm is useful to show the differences among groups.

Loading required packages

knitr::opts_chunk$set(message = FALSE, warning = FALSE)

library(tidyverse)
library(ggbeeswarm)
library(ggpubr)

rm(list = ls())
options(stringsAsFactors = F)

# group & color
group_names <- c("setosa", "versicolor", "virginica")
group_colors <- c("#0073C2FF", "#EFC000FF", "#CD534CFF")

Data preparation

Loading iris dataset
Factorizing Species

data("iris")

plotdata <- iris |>
  dplyr::select(Sepal.Length, Species) |>
  dplyr::mutate(Species = factor(Species, levels = group_names)) |>
  dplyr::rename(Group = Species,
                Index = Sepal.Length)

head(plotdata)

##   Index  Group
## 1   5.1 setosa
## 2   4.9 setosa
## 3   4.7 setosa
## 4   4.6 setosa
## 5   5.0 setosa
## 6   5.4 setosa

Plotting

apply stat_boxplot and geom_boxplot for boxplot
add beeswarm by geom_quasirandom

pl <- ggplot(data = plotdata, aes(x = Group, y = Index, color = Group, shape = Group)) +
  stat_boxplot(geom = "errorbar", width = 0.4) +
  geom_boxplot(width = .4, outlier.shape = NA, notch = TRUE) +
  geom_quasirandom(method = "smiley", size = 1.5) +
  stat_compare_means(comparisons = list(c("setosa", "versicolor"),
                                        c("setosa", "virginica")),
                     method = "t.test",
                     label = "p.signif") +
  labs(x = "") +
  scale_y_continuous(expand = expansion(mult = c(0.1, 0.1))) +
  scale_color_manual(values = group_colors) +
  scale_shape_manual(values = c(15, 16, 17)) +
  guides(color = "none", shape = "none") +
  theme_classic() +
  theme(axis.title = element_text(size = 12, color = "black", face = "bold"),
        axis.text = element_text(size = 10, color = "black"),
        text = element_text(size = 9, color = "black"))

pl

Conclusion

Compared to single boxplot, beeswarm not only shows differences among group, but also displays the distribution of each value, providing more information.

Systemic information

devtools::session_info()

## ─ Session info ───────────────────────────────────────────────────────────────
##  setting  value
##  version  R version 4.1.3 (2022-03-10)
##  os       macOS Big Sur/Monterey 10.16
##  system   x86_64, darwin17.0
##  ui       X11
##  language (EN)
##  collate  en_US.UTF-8
##  ctype    en_US.UTF-8
##  tz       Asia/Shanghai
##  date     2023-07-24
##  pandoc   3.1.3 @ /Users/zouhua/opt/anaconda3/bin/ (via rmarkdown)
## 
## ─ Packages ───────────────────────────────────────────────────────────────────
##  package     * version date (UTC) lib source
##  abind         1.4-5   2016-07-21 [2] CRAN (R 4.1.0)
##  backports     1.4.1   2021-12-13 [2] CRAN (R 4.1.0)
##  beeswarm      0.4.0   2021-06-01 [2] CRAN (R 4.1.0)
##  blogdown      1.18    2023-06-19 [2] CRAN (R 4.1.3)
##  bookdown      0.34    2023-05-09 [2] CRAN (R 4.1.2)
##  broom         1.0.5   2023-06-09 [2] CRAN (R 4.1.3)
##  bslib         0.5.0   2023-06-09 [2] CRAN (R 4.1.3)
##  cachem        1.0.8   2023-05-01 [2] CRAN (R 4.1.2)
##  callr         3.7.3   2022-11-02 [2] CRAN (R 4.1.2)
##  car           3.1-2   2023-03-30 [2] CRAN (R 4.1.2)
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##  colorspace    2.1-0   2023-01-23 [2] CRAN (R 4.1.2)
##  crayon        1.5.2   2022-09-29 [2] CRAN (R 4.1.2)
##  devtools      2.4.5   2022-10-11 [2] CRAN (R 4.1.2)
##  digest        0.6.33  2023-07-07 [1] CRAN (R 4.1.3)
##  dplyr       * 1.1.2   2023-04-20 [2] CRAN (R 4.1.2)
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##  fansi         1.0.4   2023-01-22 [2] CRAN (R 4.1.2)
##  farver        2.1.1   2022-07-06 [2] CRAN (R 4.1.2)
##  fastmap       1.1.1   2023-02-24 [2] CRAN (R 4.1.2)
##  forcats     * 1.0.0   2023-01-29 [2] CRAN (R 4.1.2)
##  fs            1.6.2   2023-04-25 [2] CRAN (R 4.1.2)
##  generics      0.1.3   2022-07-05 [2] CRAN (R 4.1.2)
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##  gtable        0.3.3   2023-03-21 [2] CRAN (R 4.1.2)
##  highr         0.10    2022-12-22 [2] CRAN (R 4.1.2)
##  hms           1.1.3   2023-03-21 [2] CRAN (R 4.1.2)
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##  [1] /Users/zouhua/Library/R/x86_64/4.1/library
##  [2] /Library/Frameworks/R.framework/Versions/4.1/Resources/library
## 
## ──────────────────────────────────────────────────────────────────────────────

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