Help for package ggrain

Title:

A Rainclouds Geom for 'ggplot2'

Version:

0.1.0

Description:

The 'geom_rain()' function adds different geoms together using 'ggplot2' to create raincloud plots.

License:

MIT + file LICENSE

Encoding:

UTF-8

Depends:

ggplot2 (≥ 4.0.0), R (≥ 3.4.0)

Imports:

grid, ggpp (≥ 0.5.6), rlang, vctrs (≥ 0.5.0), cli

RoxygenNote:

7.3.3

URL:

https://github.com/njudd/ggrain

BugReports:

https://github.com/njudd/ggrain/issues

Suggests:

knitr, rmarkdown

VignetteBuilder:

knitr

NeedsCompilation:

Packaged:

2025-11-24 17:14:57 UTC; niju9118

Author:

Nicholas Judd

[aut, cre], Jordy van Langen

[aut], Micah Allen

[ctb], Rogier Kievit

[aut]

Maintainer:

Nicholas Judd <nickkjudd@gmail.com>

Repository:

CRAN

Date/Publication:

2025-11-24 17:30:02 UTC

Half Violin plot This is taken from gghalves great R package I am trying to remove the dependency

Description

A violin plot is a compact display of a continuous distribution. It is a blend of ggplot2::geom_boxplot() and ggplot2::geom_density(): a violin plot is a mirrored density plot displayed in the same way as a boxplot.

Usage

geom_half_violin(
  mapping = NULL,
  data = NULL,
  stat = "half_ydensity",
  position = "dodge",
  ...,
  side = "l",
  nudge = 0,
  quantiles = NULL,
  trim = TRUE,
  scale = "area",
  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)).

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".
For more information and other ways to specify the position, see the layer position documentation.

...

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.
When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.
Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

side

The side on which to draw the half violin plot. "l" for left, "r" for right, defaults to "l".

nudge

Add space between the violinplot and the middle of the space allotted to a given factor on the x-axis.

quantiles

If not NULL (default), compute the quantile variable and draw horizontal lines at the given quantiles in geom_violin().

trim

If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don't trim the tails.

scale

if "area" (default), all violins have the same area (before trimming the tails). If "count", areas are scaled proportionally to the number of observations. If "width", all violins have the same maximum width.

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. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

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. annotation_borders().

Details

The half-violin plot accepts an optional split aesthethic to compare data separated by a binary variable side-by-side.

References

Hintze, J. L., Nelson, R. D. (1998) Violin Plots: A Box Plot-Density Trace Synergism. The American Statistician 52, 181-184.

Paired raincloud plot

Description

Taking from https://raw.githubusercontent.com/yjunechoe/geom_paired_raincloud/master/geom_paired_raincloud.R on 30-10-22 attribution to https://yjunechoe.github.io/

Usage

geom_paired_raincloud(
  mapping = NULL,
  data = NULL,
  stat = "ydensity",
  position = "dodge",
  trim = TRUE,
  scale = "area",
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)

Arguments

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.

stat

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used to override the default coupling between geoms and stats. The stat argument accepts the following:

A Stat ggproto subclass, for example StatCount.
A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".
For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".
For more information and other ways to specify the position, see the layer position documentation.

trim

If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don't trim the tails.

scale

show.legend

inherit.aes

...

Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.
When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.
Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

Details

Create a paired raincloud plot (useful for visualizing difference between experimental conditions tested on the same subjects or items).

Adopted from the see::geom_violinhalf() source code from the see package

Examples

library(ggplot2)

Raincloud Plots

Description

This function displays individual data points, a boxplot and half a violin plot. It also has the option to connect data points with lines across groups by specifying an id to connect by. Lastly, if desired one can color the dots based of another variable.

Usage

geom_rain(
  mapping = NULL,
  data = NULL,
  inherit.aes = TRUE,
  id.long.var = NULL,
  cov = NULL,
  rain.side = NULL,
  likert = FALSE,
  seed = 42,
  ...,
  point.args = rlang::list2(...),
  point.args.pos = rlang::list2(position = position_jitter(width = 0.04, height = 0, seed
    = seed)),
  line.args = rlang::list2(alpha = 0.2, ...),
  line.args.pos = rlang::list2(position = position_jitter(width = 0.04, height = 0, seed
    = seed), ),
  boxplot.args = rlang::list2(outlier.shape = NA, ...),
  boxplot.args.pos = rlang::list2(width = 0.05, position = position_nudge(x = 0.1), ),
  violin.args = rlang::list2(...),
  violin.args.pos = rlang::list2(side = "r", width = 0.7, quantiles = NULL, position =
    position_nudge(x = 0.15), )
)

Arguments

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.

inherit.aes

id.long.var

A group to connect the lines by - must be a string (e.g., "id").

cov

A covariate to color the dots by - must be as a string (e.g., "cov")

rain.side

How you want the rainclouds displayed, right ("r"), left ("l") or flanking ("f"), for a 1-by-1 flanking raincloud use ("f1x1") and for a 2-by-2 use ("f2x2").

likert

Currently developing, right now just addes y-jitter.

seed

For the jittering in point & line to match.

...

Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.
When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.
Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

point.args

A list of args for the dots

point.args.pos

A list of positional args for the points

line.args

A list of args for the lines, you need to specify a group to connect them with id.long.var

line.args.pos

A list of positional args for the lines

boxplot.args

A list of args for the boxplot

boxplot.args.pos

A list of positional args for the boxplot

violin.args

A list of args for the violin

violin.args.pos

A list of positional args for the violin

Value

Returns a list of three environments to be used with the 'ggplot()' function in the 'ggplot2' package.

If the id.long.var argument is used the output will be a list of 4 environments.

These 4 environments have a similar structure to 'ggplot2::geom_boxplot()', 'ggplot2::geom_violin()', 'ggplot2::geom_point()' and 'ggplot2::geom_line()' from 'ggplot2'. need library(rlang) need library(ggplot2) depends = ggplot2

References

Allen, M., Poggiali, D., Whitaker, K., Marshall, T. R., van Langen, J., & Kievit, R. A. Raincloud plots: a multi-platform tool for robust data visualization Wellcome Open Research 2021, 4:63. https://doi.org/10.12688/wellcomeopenres.15191.2

Examples

e1 <- ggplot(iris, aes(Species, Sepal.Width, fill = Species))
e1 + geom_rain()

# x must be the discrete variable
# orinetation can be changed with coord_flip()
e1 + geom_rain(alpha = .5) + coord_flip()

# we can color the dots by a covariate
e1 + geom_rain(cov = "Sepal.Length")

# we can edit elements individually
e1 + geom_rain(violin.args = list(alpha = .3, color = NA))

# we can flip them
e1 + geom_rain(rain.side = 'l')
# and move them
e1 +
geom_rain(boxplot.args.pos = list(width = .1, position = position_nudge(x = -.2)))

# they also work longitudinally
e2 <- ggplot(sleep, aes(group, extra, fill = group))
e2 + geom_rain(id.long.var = "ID")

# we can add groups
sleep_dat <- cbind(sleep, data.frame(sex = c(rep("male", 5),
rep("female", 5), rep("male", 5), rep("female", 5))))
e3 <- ggplot(sleep_dat, aes(group, extra, fill = sex))
e3 + geom_rain(alpha = .6)

# add likert example
e4 <- ggplot(mpg, aes(1, hwy, fill = manufacturer))
e4 + geom_rain(likert= TRUE)

# lets make it look nicer
e4 + geom_rain(likert= TRUE,
 boxplot.args.pos = list(position = ggpp::position_dodgenudge(x = .095), width = .1),
 violin.args = list(color = NA, alpha = .5))

Points

Description

The point geom is used to create scatterplots. The scatterplot is most useful for displaying the relationship between two continuous variables. It can be used to compare one continuous and one categorical variable, or two categorical variables, but a variation like ggplot2::geom_jitter(), ggplot2::geom_count(), or ggplot2::geom_bin2d() is usually more appropriate. A bubblechart is a scatterplot with a third variable mapped to the size of points.

Arguments

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

...

Other arguments passed on to ggplot2::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.

Overplotting

The biggest potential problem with a scatterplot is overplotting: whenever you have more than a few points, points may be plotted on top of one another. This can severely distort the visual appearance of the plot. There is no one solution to this problem, but there are some techniques that can help. You can add additional information with ggplot2::geom_smooth(), ggplot2::geom_quantile() or ggplot2::geom_density_2d(). If you have few unique x values, ggplot2::geom_boxplot() may also be useful.

Alternatively, you can summarise the number of points at each location and display that in some way, using ggplot2::geom_count(), ggplot2::geom_hex(), or ggplot2::geom_density2d().

Another technique is to make the points transparent (e.g. ⁠[ggplot2::geom_point(alpha = 0.05)]⁠) or very small (e.g. ⁠[ggplot2::geom_point(shape = ".")]⁠).

Examples

p <- ggplot(mtcars, aes(wt, mpg))
p + ggplot2::geom_point()

# Add aesthetic mappings
p + ggplot2::geom_point(aes(colour = factor(cyl)))
p + ggplot2::geom_point(aes(shape = factor(cyl)))
# A "bubblechart":
p + ggplot2::geom_point(aes(size = qsec))

# Set aesthetics to fixed value
ggplot(mtcars, aes(wt, mpg)) + geom_point(colour = "red", size = 3)


# Varying alpha is useful for large datasets
d <- ggplot(diamonds, aes(carat, price))
d + ggplot2::geom_point(alpha = 1/10)
d + ggplot2::geom_point(alpha = 1/20)
d + ggplot2::geom_point(alpha = 1/100)


# For shapes that have a border (like 21), you can colour the inside and
# outside separately. Use the stroke aesthetic to modify the width of the
# border
ggplot(mtcars, aes(wt, mpg)) +
  geom_point(shape = 21, colour = "black", fill = "white", size = 5, stroke = 5)


# You can create interesting shapes by layering multiple points of
# different sizes
p <- ggplot(mtcars, aes(mpg, wt, shape = factor(cyl)))
p +
  ggplot2::geom_point(aes(colour = factor(cyl)), size = 4) +
  ggplot2::geom_point(colour = "grey90", size = 1.5)
p +
  ggplot2::geom_point(colour = "black", size = 4.5) +
  ggplot2::geom_point(colour = "pink", size = 4) +
  ggplot2::geom_point(aes(shape = factor(cyl)))

# ggplot2::geom_point warns when missing values have been dropped from the data set
# and not plotted, you can turn this off by setting na.rm = TRUE
set.seed(1)
mtcars2 <- transform(mtcars, mpg = ifelse(runif(32) < 0.2, NA, mpg))
ggplot(mtcars2, aes(wt, mpg)) +
  geom_point()
ggplot(mtcars2, aes(wt, mpg)) +
  geom_point(na.rm = TRUE)

This is taken from gghalves great R package I am trying to remove the dependency

Description

This is taken from gghalves great R package I am trying to remove the dependency

Usage

stat_half_ydensity(
  mapping = NULL,
  data = NULL,
  geom = "half_violin",
  position = "dodge",
  ...,
  bw = "nrd0",
  adjust = 1,
  kernel = "gaussian",
  trim = TRUE,
  scale = "area",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

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.

geom

This is only half_voilin

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".
For more information and other ways to specify the position, see the layer position documentation.

...

Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.
When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.
Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.
The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

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(). Note that automatic calculation of the bandwidth does not take weights into account.

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.

kernel

Kernel. See list of available kernels in density().

trim

If TRUE (default), trim the tails of the violins to the range of the data. If FALSE, don't trim the tails.

scale

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

inherit.aes

Half Violin plot This is taken from gghalves great R package I am trying to remove the dependency

Description

Usage

Arguments

Details

References

Paired raincloud plot

Description

Usage

Arguments

Details

See Also

Examples

Raincloud Plots

Description

Usage

Arguments

Value

References

Examples

Points

Description

Arguments

Overplotting

Examples

This is taken from gghalves great R package I am trying to remove the dependency

Description

Usage

Arguments

See Also