grouped_ggscatterstats: Scatterplot with marginal distributions for all levels of a grouping variable

Description

Grouped scatterplots from ggplot2 combined with marginal histograms/boxplots/density plots with statistical details added as a subtitle.

Usage

grouped_ggscatterstats(
  data,
  x,
  y,
  grouping.var,
  label.var = NULL,
  label.expression = NULL,
  title.prefix = NULL,
  output = "plot",
  ...,
  plotgrid.args = list(),
  title.text = NULL,
  title.args = list(size = 16, fontface = "bold"),
  caption.text = NULL,
  caption.args = list(size = 10),
  sub.text = NULL,
  sub.args = list(size = 12)
)

Arguments

data

for use with formula, a data frame containing all the data

The column in data containing the explanatory variable to be plotted on the x-axis. Can be entered either as a character string (e.g., "x") or as a bare expression (e.g, x).

The column in data containing the response (outcome) variable to be plotted on the y-axis. Can be entered either as a character string (e.g., "y") or as a bare expression (e.g, y).

grouping.var

A single grouping variable (can be entered either as a bare name x or as a string "x").

label.var

Variable to use for points labels. Can be entered either as a character string (e.g., "var1") or as a bare expression (e.g, var1).

label.expression

An expression evaluating to a logical vector that determines the subset of data points to label. This argument can be entered either as a character string (e.g., "y < 4 & z < 20") or as a bare expression (e.g., y < 4 & z < 20).

title.prefix

Character string specifying the prefix text for the fixed plot title (name of each factor level) (Default: NULL). If NULL, the variable name entered for grouping.var will be used.

output

Character that describes what is to be returned: can be "plot" (default) or "subtitle" or "caption". Setting this to "subtitle" will return the expression containing statistical results. If you have set results.subtitle = FALSE, then this will return a NULL. Setting this to "caption" will return the expression containing details about Bayes Factor analysis, but valid only when type = "parametric" and bf.message = TRUE, otherwise this will return a NULL. For functions ggpiestats and ggbarstats, setting output = "proptest" will return a dataframe containing results from proportion tests.

...

Arguments passed on to ggscatterstats

point.label.args

A list of additional aesthetic arguments to be passed to ggrepel::geom_label_repel geom used to display the labels.

smooth.line.args

A list of additional aesthetic arguments to be passed to ggplot2::geom_smooth geom used to display the regression line.

point.args

A list of additional aesthetic arguments to be passed to ggplot2::geom_point geom used to display the raw data points.

marginal

Decides whether ggExtra::ggMarginal() plots will be displayed; the default is TRUE.

point.width.jitter

Degree of jitter in x and y direction, respectively. Defaults to 0 (0%) of the resolution of the data. Note that the jitter should not be specified in the point.args because this information will be passed to two different geoms: one displaying the points and the other displaying the labels for these points.

point.height.jitter

marginal.type

Type of marginal distribution to be plotted on the axes ("histogram", "boxplot", "density", "violin", "densigram").

marginal.size

Integer describing the relative size of the marginal plots compared to the main plot. A size of 5 means that the main plot is 5x wider and 5x taller than the marginal plots.

xfill

Character describing color fill for x and y axes marginal distributions (default: "#009E73" (for x) and "#D55E00" (for y)). The same colors will also be used for the lines denoting centrality parameters if centrality.parameter argument is set to TRUE. Note that the defaults are colorblind-friendly.

yfill

centrality.parameter

Decides which measure of central tendency ("mean" or "median") is to be displayed as vertical (for x) and horizontal (for y) lines. Note that mean values corresponds to arithmetic mean and not geometric mean.

vline.args

A list of additional aesthetic arguments to be passed to ggplot2::geom_vline and ggplot2::geom_hline geoms used to display the centrality parameter labels on vertical and horizontal lines.

hline.args

A list of additional aesthetic arguments to be passed to ggplot2::geom_vline and ggplot2::geom_hline geoms used to display the centrality parameter labels on vertical and horizontal lines.

type

Type of association between paired samples required (""parametric": Pearson's product moment correlation coefficient" or ""nonparametric": Spearman's rho" or ""robust": percentage bend correlation coefficient" or ""bayes": Bayes Factor for Pearson's r"). Corresponding abbreviations are also accepted: "p" (for parametric/pearson's), "np" (nonparametric/spearman), "r" (robust), "bf" (for bayes factor), resp.

conf.level

Scalar between 0 and 1. If unspecified, the defaults return 95% lower and upper confidence intervals (0.95).

bf.prior

A number between 0.5 and 2 (default 0.707), the prior width to use in calculating Bayes factors.

nboot

Number of bootstrap samples for computing confidence interval for the effect size (Default: 100).

beta

bending constant (Default: 0.1). For more, see ?WRS2::pbcor.

k

Number of digits after decimal point (should be an integer) (Default: k = 2).

formula

Formula to use in smoothing function, eg. y ~ x, y ~ poly(x, 2), y ~ log(x). NULL by default, in which case method = NULL implies formula = y ~ x when there are fewer than 1,000 observations and formula = y ~ s(x, bs = "cs") otherwise.

method

Smoothing method (function) to use, accepts either NULL or a character vector, e.g. "lm", "glm", "gam", "loess" or a function, e.g. MASS::rlm or mgcv::gam, stats::lm, or stats::loess. "auto" is also accepted for backwards compatibility. It is equivalent to NULL.

For method = NULL the smoothing method is chosen based on the size of the largest group (across all panels). stats::loess() is used for less than 1,000 observations; otherwise mgcv::gam() is used with formula = y ~ s(x, bs = "cs") with method = "REML". Somewhat anecdotally, loess gives a better appearance, but is \(O(N^{2})\) in memory, so does not work for larger datasets.

If you have fewer than 1,000 observations but want to use the same gam() model that method = NULL would use, then set method = "gam", formula = y ~ s(x, bs = "cs").

method.args

List of additional arguments passed on to the modelling function defined by method.

ggtheme

A function, ggplot2 theme name. Default value is ggplot2::theme_bw(). Any of the ggplot2 themes, or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.).

ggstatsplot.layer

Logical that decides whether theme_ggstatsplot theme elements are to be displayed along with the selected ggtheme (Default: TRUE). theme_ggstatsplot is an opinionated theme layer that override some aspects of the selected ggtheme.

bf.message

Logical that decides whether to display Bayes Factor in favor of the null hypothesis. This argument is relevant only for parametric test (Default: TRUE).

results.subtitle

Decides whether the results of statistical tests are to be displayed as a subtitle (Default: TRUE). If set to FALSE, only the plot will be returned.

xlab

Labels for x and y axis variables. If NULL (default), variable names for x and y will be used.

ylab

Labels for x and y axis variables. If NULL (default), variable names for x and y will be used.

subtitle

The text for the plot subtitle. Will work only if results.subtitle = FALSE.

caption

The text for the plot caption.

ggplot.component

A ggplot component to be added to the plot prepared by ggstatsplot. This argument is primarily helpful for grouped_ variant of the current function. Default is NULL. The argument should be entered as a function.

messages

Decides whether messages references, notes, and warnings are to be displayed (Default: TRUE).

margins

Along which margins to show the plots. One of: [both, x, y].

xparams

List of extra parameters to use only for the marginal plot along the x axis.

yparams

List of extra parameters to use only for the marginal plot along the y axis.

centrality.label.args

A list of additional aesthetic arguments to be passed to the geom_label used to display the label corresponding to the centrality parameter and test value.

plotgrid.args

A list of additional arguments to cowplot::plot_grid.

title.text

String or plotmath expression to be drawn as title for the combined plot.

title.args

A list of additional arguments provided to title, caption and sub, resp.

caption.text

String or plotmath expression to be drawn as the caption for the combined plot.

caption.args

A list of additional arguments provided to title, caption and sub, resp.

sub.text

The label with which the combined plot should be annotated. Can be a plotmath expression.

sub.args

A list of additional arguments provided to title, caption and sub, resp.

References

https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html

Examples

Run this code

# NOT RUN {
# to ensure reproducibility
set.seed(123)
library(ggstatsplot)

# basic function call
ggstatsplot::grouped_ggscatterstats(
  data = dplyr::filter(movies_long, genre == "Comedy" | genre == "Drama"),
  x = length,
  y = rating,
  method = "lm",
  formula = y ~ x + I(x^3),
  grouping.var = genre
)

# using labeling
# (also show how to modify basic plot from within function call)
grouped_ggscatterstats(
  data = dplyr::filter(ggplot2::mpg, cyl != 5),
  x = displ,
  y = hwy,
  grouping.var = cyl,
  title.prefix = "Cylinder count",
  type = "robust",
  label.var = manufacturer,
  label.expression = hwy > 25 & displ > 2.5,
  ggplot.component = ggplot2::scale_y_continuous(sec.axis = ggplot2::dup_axis()),
  messages = FALSE
)

# labeling without expression

ggstatsplot::grouped_ggscatterstats(
  data = dplyr::filter(
    .data = movies_long,
    rating == 7,
    genre %in% c("Drama", "Comedy")
  ),
  x = budget,
  y = length,
  grouping.var = genre,
  bf.message = FALSE,
  label.var = "title",
  marginal = FALSE,
  title.prefix = "Genre",
  caption.text = "All movies have IMDB rating equal to 7."
)
# }

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Description

Usage

Arguments

References

See Also

Examples