Package 'ggbeeswarm'

Points, jittered to reduce overplotting using the beeswarm package

Description

The beeswarm geom is a convenient means to offset points within categories to reduce overplotting. Uses the beeswarm package

Usage

geom_beeswarm(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  ...,
  method = "swarm",
  cex = 1,
  side = 0L,
  priority = "ascending",
  fast = TRUE,
  dodge.width = NULL,
  corral = "none",
  corral.width = 0.9,
  groupOnX = NULL,
  beeswarmArgs = list(),
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
stat	The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")
...	Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.
method	Method for arranging points (see Details below)
cex	Scaling for adjusting point spacing (see beeswarm::swarmx()). Values between 1 (default) and 3 tend to work best.
side	Direction to perform jittering: 0: both directions; 1: to the right or upwards; -1: to the left or downwards.
priority	Method used to perform point layout (see Details below)
fast	Use compiled version of swarm algorithm? This option is ignored for all methods expect "swarm" and "compactswarm".
dodge.width	Amount by which points from different aesthetic groups will be dodged. This requires that one of the aesthetics is a factor.
corral	string. Method used to adjust points that would be placed to wide horizontally, default is "none". See details below.
corral.width	numeric. Width of the corral, default is 0.9.
groupOnX	No longer needed.
beeswarmArgs	No longer used.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Aesthetics

@section Aesthetics: geom_point()understands the following aesthetics (required aesthetics are in bold):

• x

• y

• alpha

• colour

• fill

• group

• shape

• size

• stroke

Learn more about setting these aesthetics in vignette("ggplot2-specs").

See Also

geom_quasirandom() an alternative method, beeswarm::swarmx() how spacing is determined, ggplot2::geom_point() for regular, unjittered points, ggplot2::geom_jitter() for jittered points, ggplot2::geom_boxplot() for another way of looking at the conditional distribution of a variable

Examples

ggplot2::qplot(class, hwy, data = ggplot2::mpg, geom='beeswarm')
  # Generate fake data
  distro <- data.frame(
    'variable'=rep(c('runif','rnorm'),each=100),
    'value'=c(runif(100, min=-3, max=3), rnorm(100))
  )
  ggplot2::qplot(variable, value, data = distro, geom='beeswarm')
  ggplot2::ggplot(distro,aes(variable, value)) +
    geom_beeswarm(priority='density',size=2.5)

---

Points, jittered to reduce overplotting using the vipor package

Description

The quasirandom geom is a convenient means to offset points within categories to reduce overplotting. Uses the vipor package

Usage

geom_quasirandom(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  ...,
  method = "quasirandom",
  width = NULL,
  varwidth = FALSE,
  bandwidth = 0.5,
  nbins = NULL,
  dodge.width = NULL,
  groupOnX = NULL,
  orientation = NULL,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
stat	The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")
...	Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.
method	the method used for distributing points (quasirandom, pseudorandom, smiley, maxout, frowney, minout, tukey, tukeyDense). See vipor::offsetSingleGroup() for the details of each method.
width	the maximum amount of spread (default: 0.4)
varwidth	vary the width by the relative size of each group
bandwidth	the bandwidth adjustment to use when calculating density Smaller numbers (< 1) produce a tighter "fit". (default: 0.5)
nbins	the number of bins used when calculating density (has little effect with quasirandom/random distribution)
dodge.width	Amount by which points from different aesthetic groups will be dodged. This requires that one of the aesthetics is a factor. To disable dodging between groups, set this to NULL.
groupOnX	See orientation.
orientation	The orientation (i.e., which axis to group on) is inferred from the data. This can be overridden by setting orientation to either "x" or "y".
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Aesthetics

@section Aesthetics: geom_point()understands the following aesthetics (required aesthetics are in bold):

• x

• y

• alpha

• colour

• fill

• group

• shape

• size

• stroke

Learn more about setting these aesthetics in vignette("ggplot2-specs").

See Also

vipor::offsetSingleGroup() how spacing is determined, ggplot2::geom_point() for regular, unjittered points, ggplot2::geom_jitter() for jittered points, geom_boxplot() for another way of looking at the conditional distribution of a variable

Examples

ggplot2::qplot(class, hwy, data = ggplot2::mpg, geom='quasirandom')
  # Generate fake data
  distro <- data.frame(
    'variable'=rep(c('runif','rnorm'),each=100),
    'value'=c(runif(100, min=-3, max=3), rnorm(100))
  )
  ggplot2::qplot(variable, value, data = distro, geom = 'quasirandom')
  ggplot2::ggplot(distro,aes(variable, value)) + geom_quasirandom(width=0.1)

---

ggbeeswarm extends ggplot2 with violin point/beeswarm plots

Description

This package allows plotting of several groups of one dimensional data as a violin point/beeswarm plot in ggplot2 by arranging data points to resemble the underlying distribution. The development version of this package is on https://github.com/eclarke/ggbeeswarm.

Author(s)

Erik Clarke, [email protected]

See Also

position_quasirandom()

Examples

ggplot2::ggplot(ggplot2::mpg,aes(class, hwy)) + geom_quasirandom()
  # Generate fake data
  distro <- data.frame(
    'variable'=rep(c('runif','rnorm'),each=100),
    'value'=c(runif(100, min=-3, max=3), rnorm(100))
  )
  ggplot2::ggplot(distro,aes(variable, value)) + geom_quasirandom()
  ggplot2::ggplot(distro,aes(variable, value)) + geom_quasirandom(width=.1)

---

Arrange points using the ⁠\link[beeswarm]⁠ package.

Description

Arrange points using the ⁠\link[beeswarm]⁠ package.

Usage

position_beeswarm(
  method = "swarm",
  cex = 1,
  side = 0L,
  priority = "ascending",
  fast = TRUE,
  groupOnX = NULL,
  dodge.width = 0,
  corral = "none",
  corral.width = 0.2
)

Arguments

method	Method for arranging points (see Details below)
cex	Scaling for adjusting point spacing (see beeswarm::swarmx()). Values between 1 (default) and 3 tend to work best.
side	Direction to perform jittering: 0: both directions; 1: to the right or upwards; -1: to the left or downwards.
priority	Method used to perform point layout (see Details below)
fast	Use compiled version of swarm algorithm? This option is ignored for all methods expect "swarm" and "compactswarm".
groupOnX	No longer needed.
dodge.width	Amount by which points from different aesthetic groups will be dodged. This requires that one of the aesthetics is a factor.
corral	string. Method used to adjust points that would be placed to wide horizontally, default is "none". See details below.
corral.width	numeric. Width of the corral, default is 0.9.

Details

method: specifies the algorithm used to avoid overlapping points. The default "swarm" method places points in increasing order. If a point would overlap with an existing point, it is shifted sideways (along the group axis) by a minimal amount sufficient to avoid overlap.

While the "swarm" method places points in a predetermined order, the "compactswarm" method uses a greedy strategy to determine which point will be placed next. This often leads to a more tightly-packed layout. The strategy is very simple: on each iteration, a point that can be placed as close as possible to the non-data axis is chosen and placed. If there are two or more equally good points, priority is used to break ties.

The other 3 methods first discretise the values along the data axis, in order to create more efficient packing. The "square" method places points on a square grid, whereas "hex" uses a hexagonal grid. "centre"/"center" uses a square grid to produce a symmetric swarm. The number of break points for discretisation is determined by a combination of the available plotting area and the cex argument.

priority: controls the order in which points are placed, which generally has a noticeable effect on the plot appearance. "ascending" gives the 'traditional' beeswarm plot. "descending" is the opposite. "density" prioritizes points with higher local density. "random" places points in a random order. "none" places points in the order provided.

corral: By default, swarms from different groups are not prevented from overlapping, i.e. ⁠"corral = "none"⁠. Thus, datasets that are very large or unevenly distributed may produce ugly overlapping beeswarms. To control runaway points one can use the following methods. "gutter" collects runaway points along the boundary between groups. "wrap" implement periodic boundaries. "random" places runaway points randomly in the region. "omit" omits runaway points.

See Also

geom_beeswarm(), position_quasirandom(), beeswarm::swarmx()

Other position adjustments: offset_beeswarm(), position_quasirandom()

---

Arrange points using quasirandom noise to avoid overplotting

Description

Arrange points using quasirandom noise to avoid overplotting

Usage

position_quasirandom(
  method = "quasirandom",
  width = NULL,
  varwidth = FALSE,
  bandwidth = 0.5,
  nbins = NULL,
  dodge.width = 0,
  orientation = NULL,
  groupOnX = NULL,
  na.rm = FALSE
)

Arguments

method	the method used for distributing points (quasirandom, pseudorandom, smiley, maxout, frowney, minout, tukey, tukeyDense). See vipor::offsetSingleGroup() for the details of each method.
width	the maximum amount of spread (default: 0.4)
varwidth	vary the width by the relative size of each group
bandwidth	the bandwidth adjustment to use when calculating density Smaller numbers (< 1) produce a tighter "fit". (default: 0.5)
nbins	the number of bins used when calculating density (has little effect with quasirandom/random distribution)
dodge.width	Amount by which points from different aesthetic groups will be dodged. This requires that one of the aesthetics is a factor. To disable dodging between groups, set this to NULL.
orientation	The orientation (i.e., which axis to group on) is inferred from the data. This can be overridden by setting orientation to either "x" or "y".
groupOnX	See orientation.
na.rm	if FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

See Also

vipor::offsetSingleGroup(), geom_quasirandom()

Other position adjustments: offset_beeswarm(), position_beeswarm()

---