beeswarm

beeswarm is an add-on package for the R statistical environment. The bee swarm plot is a one-dimensional scatter plot like "stripchart", but with closely-packed, non-overlapping points.

As with most R packages, beeswarm can be obtained from CRAN, or can can be downloaded and installed automatically by entering the following line at the R prompt:

install.packages('beeswarm')

Please send questions or comments about beeswarm to Aron.

News

July 30, 2015: beeswarm is now on GitHub.

May 4, 2015: Version 0.2.0 is now available from CRAN. New features:

• The swarm layout algorithm is a bit more efficient.
• New argument "side" allows swarms to expand in only one direction rather than two.
• New argument "priority" controls the order in which points are added to the swarm and thus the appearance of the plot.
• See examples of these new arguments below (at the very bottom of this page).

Examples

library(beeswarm)

stripchart vs. beeswarm

stripchart(decrease ~ treatment, data = OrchardSprays, 
  vertical = TRUE, log = "y", method = 'jitter', jitter = 0.2, cex = 1,
  pch = 16, col = rainbow(8),
  main = 'stripchart')
beeswarm(decrease ~ treatment, data = OrchardSprays, 
  log = TRUE, pch = 16, col = rainbow(8),
  main = 'beeswarm')

The color of individual points can be specified

data(breast)
  beeswarm(time_survival ~ ER, data = breast,
    pch = 16, pwcol = 1 + as.numeric(event_survival),
    xlab = "", ylab = "Follow-up time (months)",
    labels = c("ER neg", "ER pos"))
  legend("topright", legend = c("Yes", "No"),
    title = "Censored", pch = 16, col = 1:2)

Compare the four methods for arranging points

## Generate some random data
set.seed(123)
distro <- list(runif = runif(100, min = -3, max = 3), 
               rnorm = rnorm(100))

for (m in c("swarm", "center", "hex", "square")) {
  beeswarm(distro, 
    col = 2:3, pch = 16,
    method = m, 
    main = paste('method = "', m, '"', sep = ''))
}

Compare the five "corral" methods

for (ii in c("none", "gutter", "wrap", "random", "omit")) {
  beeswarm(distributions, 
    pch = 21, col = 2:4, bg = "#00000050",
    corral = ii, 
    main = paste('corral = "', ii, '"', sep = ''))
}

Combining beeswarms with "boxplot" or "bxplot"

  boxplot(len ~ dose, data = ToothGrowth, 
    outline = FALSE,     ## avoid double-plotting outliers, if any
    main = 'boxplot + beeswarm')
  beeswarm(len ~ dose, data = ToothGrowth, 
    col = 4, pch = 16, add = TRUE)

  beeswarm(len ~ dose, data = ToothGrowth, 
    col = 4, pch = 16,
    main = 'beeswarm + bxplot')
  bxplot(len ~ dose, data = ToothGrowth, add = TRUE)

New arguments "side" and "priority"

  beeswarm(distributions, col = 2:4, 
    main = 'Default')
  beeswarm(distributions, col = 2:4, side = -1, 
    main = 'side = -1')
  beeswarm(distributions, col = 2:4, side = 1, 
    main = 'side = 1')
  beeswarm(distributions, col = 2:4, priority = "descending", 
    main = 'priority = "descending"')
  beeswarm(distributions, col = 2:4, priority = "random", 
    main = 'priority = "random"')  
  beeswarm(distributions, col = 2:4, priority = "density", 
    main = 'priority = "density"')