ggforce: geom_sina – R documentation

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geom_sina

Sina plot

Description

The sina plot is a data visualization chart suitable for plotting any single variable in a multiclass dataset. It is an enhanced jitter strip chart, where the width of the jitter is controlled by the density distribution of the data within each class.

Usage

stat_sina(
  mapping = NULL,
  data = NULL,
  geom = "sina",
  position = "dodge",
  scale = "area",
  method = "density",
  bw = "nrd0",
  kernel = "gaussian",
  maxwidth = NULL,
  adjust = 1,
  bin_limit = 1,
  binwidth = NULL,
  bins = NULL,
  seed = NA,
  ...,
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

geom_sina(
  mapping = NULL,
  data = NULL,
  stat = "sina",
  position = "dodge",
  ...,
  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)`).
`geom`	The geometric object to use display the data
`position`	Position adjustment, either as a string, or the result of a call to a position adjustment function.
`scale`	How should each sina be scaled. Corresponds to the `scale` parameter in `ggplot2::geom_violin()`? Available are: `'area'` for scaling by the largest density/bin among the different sinas `'count'` as above, but in addition scales by the maximum number of points in the different sinas. `'width'` Only scale according to the `maxwidth` parameter For backwards compatibility it can also be a logical with `TRUE` meaning `area` and `FALSE` meaning `width`
`method`	Choose the method to spread the samples within the same bin along the x-axis. Available methods: "density", "counts" (can be abbreviated, e.g. "d"). See `Details`.
`bw`	The smoothing bandwidth to be used. If numeric, the standard deviation of the smoothing kernel. If character, a rule to choose the bandwidth, as listed in `stats::bw.nrd()`.
`kernel`	Kernel. See list of available kernels in `density()`.
`maxwidth`	Control the maximum width the points can spread into. Values between 0 and 1.
`adjust`	A multiplicate bandwidth adjustment. This makes it possible to adjust the bandwidth while still using the a bandwidth estimator. For example, `adjust = 1/2` means use half of the default bandwidth.
`bin_limit`	If the samples within the same y-axis bin are more than `bin_limit`, the samples's X coordinates will be adjusted.
`binwidth`	The width of the bins. The default is to use `bins` bins that cover the range of the data. You should always override this value, exploring multiple widths to find the best to illustrate the stories in your data.
`bins`	Number of bins. Overridden by binwidth. Defaults to 50.
`seed`	A seed to set for the jitter to ensure a reproducible plot
`...`	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.
`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()`.
`stat`	The statistical transformation to use on the data for this layer, as a string.

Details

There are two available ways to define the x-axis borders for the samples to spread within:

method == "density"

A density kernel is estimated along the y-axis for every sample group, and the samples are spread within that curve. In effect this means that points will be positioned randomly within a violin plot with the same parameters.
method == "counts":

The borders are defined by the number of samples that occupy the same bin.

Aesthetics

geom_sina understand the following aesthetics (required aesthetics are in bold):

x
y
color
group
size
alpha

Computed variables

density: The density or sample counts per bin for each point
scaled: density scaled by the maximum density in each group
n: The number of points in the group the point belong to

Author(s)

Nikos Sidiropoulos, Claus Wilke, and Thomas Lin Pedersen

Examples

ggplot(midwest, aes(state, area)) + geom_point()

# Boxplot and Violin plots convey information on the distribution but not the
# number of samples, while Jitter does the opposite.
ggplot(midwest, aes(state, area)) +
  geom_violin()

ggplot(midwest, aes(state, area)) +
  geom_jitter()

# Sina does both!
ggplot(midwest, aes(state, area)) +
  geom_violin() +
  geom_sina()

p <- ggplot(midwest, aes(state, popdensity)) +
  scale_y_log10()

p + geom_sina()

# Colour the points based on the data set's columns
p + geom_sina(aes(colour = inmetro))

# Or any other way
cols <- midwest$popdensity > 10000
p + geom_sina(colour = cols + 1L)

# Sina plots with continuous x:
ggplot(midwest, aes(cut_width(area, 0.02), popdensity)) +
  geom_sina() +
  scale_y_log10()


### Sample gaussian distributions
# Unimodal
a <- rnorm(500, 6, 1)
b <- rnorm(400, 5, 1.5)

# Bimodal
c <- c(rnorm(200, 3, .7), rnorm(50, 7, 0.4))

# Trimodal
d <- c(rnorm(200, 2, 0.7), rnorm(300, 5.5, 0.4), rnorm(100, 8, 0.4))

df <- data.frame(
  'Distribution' = c(
    rep('Unimodal 1', length(a)),
    rep('Unimodal 2', length(b)),
    rep('Bimodal', length(c)),
    rep('Trimodal', length(d))
  ),
  'Value' = c(a, b, c, d)
)

# Reorder levels
df$Distribution <- factor(
  df$Distribution,
  levels(df$Distribution)[c(3, 4, 1, 2)]
)

p <- ggplot(df, aes(Distribution, Value))
p + geom_boxplot()
p + geom_violin() +
  geom_sina()

# By default, Sina plot scales the width of the class according to the width
# of the class with the highest density. Turn group-wise scaling off with:
p +
  geom_violin() +
  geom_sina(scale = FALSE)

ggforce

Accelerating 'ggplot2'

v0.3.3

MIT + file LICENSE

Authors

Thomas Lin Pedersen [cre, aut] (<https://orcid.org/0000-0002-5147-4711>), RStudio [cph]

Initial release