ggscatterstats: Scatterplot with marginal distributions and statistical...

In ggstatsplot: 'ggplot2' Based Plots with Statistical Details

Scatterplot with marginal distributions and statistical results

Description

Scatterplots from {ggplot2} combined with marginal distributions plots with statistical details.

Usage

ggscatterstats(
  data,
  x,
  y,
  type = "parametric",
  conf.level = 0.95,
  bf.prior = 0.707,
  bf.message = TRUE,
  tr = 0.2,
  digits = 2L,
  results.subtitle = TRUE,
  label.var = NULL,
  label.expression = NULL,
  marginal = TRUE,
  point.args = list(size = 3, alpha = 0.4, stroke = 0),
  point.width.jitter = 0,
  point.height.jitter = 0,
  point.label.args = list(size = 3, max.overlaps = 1e+06),
  smooth.line.args = list(linewidth = 1.5, color = "blue", method = "lm", formula = y ~
    x),
  xsidehistogram.args = list(fill = "#009E73", color = "black", na.rm = TRUE),
  ysidehistogram.args = list(fill = "#D55E00", color = "black", na.rm = TRUE),
  xlab = NULL,
  ylab = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ggtheme = ggstatsplot::theme_ggstatsplot(),
  ggplot.component = NULL,
  ...
)

Arguments

data	A data frame (or a tibble) from which variables specified are to be taken. Other data types (e.g., matrix,table, array, etc.) will not be accepted. Additionally, grouped data frames from {dplyr} should be ungrouped before they are entered as data.
x	The column in data containing the explanatory variable to be plotted on the x-axis.
y	The column in data containing the response (outcome) variable to be plotted on the y-axis.
type	A character specifying the type of statistical approach: "parametric" "nonparametric" "robust" "bayes" You can specify just the initial letter.
conf.level	Scalar between 0 and 1 (default: ⁠95%⁠ confidence/credible intervals, 0.95). If NULL, no confidence intervals will be computed.
bf.prior	A number between 0.5 and 2 (default 0.707), the prior width to use in calculating Bayes factors and posterior estimates. In addition to numeric arguments, several named values are also recognized: "medium", "wide", and "ultrawide", corresponding to r scale values of 1/2, sqrt(2)/2, and 1, respectively. In case of an ANOVA, this value corresponds to scale for fixed effects.
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).
tr	Trim level for the mean when carrying out robust tests. In case of an error, try reducing the value of tr, which is by default set to 0.2. Lowering the value might help.
digits	Number of digits for rounding or significant figures. May also be "signif" to return significant figures or "scientific" to return scientific notation. Control the number of digits by adding the value as suffix, e.g. digits = "scientific4" to have scientific notation with 4 decimal places, or digits = "signif5" for 5 significant figures (see also signif()).
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.
label.var	Variable to use for points labels entered as a symbol (e.g. var1).
label.expression	An expression evaluating to a logical vector that determines the subset of data points to label (e.g. y < 4 & z < 20). While using this argument with purrr::pmap(), you will have to provide a quoted expression (e.g. quote(y < 4 & z < 20)).
marginal	Decides whether marginal distributions will be plotted on axes using ggside functions. The default is TRUE. The package ggside must already be installed by the user.
point.args	A list of additional aesthetic arguments to be passed to geom_point geom used to display the raw data points.
point.width.jitter, point.height.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.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 geom_smooth geom used to display the regression line.
xsidehistogram.args, ysidehistogram.args	A list of arguments passed to respective geom_s from the {ggside} package to change the marginal distribution histograms plots.
xlab	Label for x axis variable. If NULL (default), variable name for x will be used.
ylab	Labels for y axis variable. If NULL (default), variable name for y will be used.
title	The text for the plot title.
subtitle	The text for the plot subtitle. Will work only if results.subtitle = FALSE.
caption	The text for the plot caption. This argument is relevant only if bf.message = FALSE.
ggtheme	A {ggplot2} theme. Default value is ggstatsplot::theme_ggstatsplot(). Any of the {ggplot2} themes (e.g., theme_bw()), or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.). But note that sometimes these themes will remove some of the details that {ggstatsplot} plots typically contains. For example, if relevant, ggbetweenstats() shows details about multiple comparison test as a label on the secondary Y-axis. Some themes (e.g. ggthemes::theme_fivethirtyeight()) will remove the secondary Y-axis and thus the details as well.
ggplot.component	A ggplot component to be added to the plot prepared by {ggstatsplot}. This argument is primarily helpful for grouped_ variants of all primary functions. Default is NULL. The argument should be entered as a {ggplot2} function or a list of {ggplot2} functions.
...	Currently ignored.

Details

For details, see: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html

Summary of graphics

graphical element	geom used	argument for further modification
raw data	ggplot2::geom_point()	point.args
labels for raw data	ggrepel::geom_label_repel()	point.label.args
smooth line	ggplot2::geom_smooth()	smooth.line.args
marginal histograms	ggside::geom_xsidehistogram(), ggside::geom_ysidehistogram()	xsidehistogram.args, ysidehistogram.args

Correlation analyses

The table below provides summary about:

• statistical test carried out for inferential statistics

• type of effect size estimate and a measure of uncertainty for this estimate

• functions used internally to compute these details

Hypothesis testing and Effect size estimation

Type	Test	CI available?	Function used
Parametric	Pearson's correlation coefficient	Yes	correlation::correlation()
Non-parametric	Spearman's rank correlation coefficient	Yes	correlation::correlation()
Robust	Winsorized Pearson's correlation coefficient	Yes	correlation::correlation()
Bayesian	Bayesian Pearson's correlation coefficient	Yes	correlation::correlation()

Note

The plot uses ggrepel::geom_label_repel() to attempt to keep labels from over-lapping to the largest degree possible. As a consequence plot times will slow down massively (and the plot file will grow in size) if you have a lot of labels that overlap.

See Also

grouped_ggscatterstats, ggcorrmat, grouped_ggcorrmat

Examples

set.seed(123)

# creating a plot
p <- ggscatterstats(
  iris,
  x = Sepal.Width,
  y = Petal.Length,
  label.var = Species,
  label.expression = Sepal.Length > 7.6
) +
  ggplot2::geom_rug(sides = "b")

# looking at the plot
p

# extracting details from statistical tests
extract_stats(p)

ggstatsplot documentation built on Sept. 11, 2024, 7:48 p.m.