geom_beeswarm: Beeswarm points

In csdaw/ggbeeswarm2: Categorical Scatter (Violin Point) Plots

Beeswarm points

Description

The beeswarm geom is a convenient shortcut for geom_point(position = "beeswarm"). It shifts points to avoid overplotting using the swarmx function from the beeswarm package.

Usage

geom_beeswarm(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  ...,
  method = "swarm",
  spacing = 1,
  side = 0L,
  priority = "ascending",
  fast = TRUE,
  dodge.width = NULL,
  corral = "none",
  corral.width = 0.2,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping	Set of aesthetic mappings created by aes() or 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, as a string.
...	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	string. Method for arranging points, default is "swarm". See details below.
spacing	numeric. Relative spacing between points, default is 1. You should adjust this if you change the size of the points. Generally the spacing should be 2/3 of the point size i.e. if size = 3, then spacing = 2, but this is ultimately up to personal preference.
side	integer. Direction to perform jittering: use 0L for both directions; 1L for right/upwards; -1L for left/downwards.
priority	string. Method used to perform point layout when method is "swarm", "swarm2", or "compactswarm", default is "ascending"; ignored otherwise. See details below.
fast	Use compiled version of algorithm? This option is ignored for all methods except "swarm", "swarm2", and "compactswarm".
dodge.width	numeric. Amount to dodge points from different aesthetic groups, default is NULL for no dodging.
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 0.2.
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().

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. The "swarm2" method is very similar to "swarm" but more closely follows the method used in the beeswarm package.

While the "swarm" and "swarm2" 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 spacing 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.

Aesthetics

geom_beeswarm() 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

position_beeswarm() for the underlying function to this geom. geom_quasirandom() for another method of shifting points to avoid overplotting.

Examples

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csdaw/ggbeeswarm2 documentation built on Sept. 10, 2022, 9:23 a.m.