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

ggscatterstats(
data,
x,
y,
type = "pearson",
conf.level = 0.95,
bf.prior = 0.707,
bf.message = TRUE,
label.var = NULL,
label.expression = NULL,
xlab = NULL,
ylab = NULL,
method = "lm",
method.args = list(),
formula = y ~ x,
point.color = "black",
point.size = 3,
point.alpha = 0.4,
point.width.jitter = 0,
point.height.jitter = 0,
line.size = 1.5,
line.color = "blue",
marginal = TRUE,
marginal.type = "histogram",
marginal.size = 5,
margins = c("both", "x", "y"),
package = "wesanderson",
palette = "Royal1",
direction = 1,
xfill = "#009E73",
yfill = "#D55E00",
xalpha = 1,
yalpha = 1,
xsize = 0.7,
ysize = 0.7,
centrality.para = NULL,
results.subtitle = TRUE,
stat.title = NULL,
title = NULL,
subtitle = NULL,
caption = NULL,
nboot = 100,
beta = 0.1,
k = 2,
axes.range.restrict = FALSE,
ggtheme = ggplot2::theme_bw(),
ggstatsplot.layer = TRUE,
ggplot.component = NULL,
return = "plot",
messages = TRUE
)

## Arguments

data A dataframe (or a tibble) from which variables specified are to be taken. A matrix or tables will not be accepted. 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). 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. Scalar between 0 and 1. If unspecified, the defaults return 95% lower and upper confidence intervals (0.95). A numeric value between 0.5 and 2 (default 0.707), the prior width to use in calculating Bayes Factors. Logical that decides whether to display Bayes Factor in favor of the null hypothesis. This argument is relevant only for parametric test (Default: TRUE). 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). 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). Labels for x and y axis variables. If NULL (default), variable names for x and y will be used. Labels for x and y axis variables. If NULL (default), variable names for x and y will be used. Smoothing method (function) to use, accepts either a character vector, e.g. "auto", "lm", "glm", "gam", "loess" or a function, e.g. MASS::rlm or mgcv::gam, stats::lm, or stats::loess. For method = "auto" 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"). 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 = "auto" would use, then set method = "gam", formula = y ~ s(x, bs = "cs"). List of additional arguments passed on to the modelling function defined by method. Formula to use in smoothing function, eg. y ~ x, y ~ poly(x, 2), y ~ log(x) Aesthetics specifying geom point (defaults: point.color = "black", point.size = 3,point.alpha = 0.4). Degree of jitter in x and y direction, respectively. Defaults to 0 (0%) of the resolution of the data. Size for the regression line. color for the regression line. Decides whether ggExtra::ggMarginal() plots will be displayed; the default is TRUE. Type of marginal distribution to be plotted on the axes ("histogram", "boxplot", "density", "violin", "densigram"). 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. Character describing along which margins to show the plots. Any of the following arguments are accepted: "both", "x", "y". Name of package from which the palette is desired as string or symbol. Name of palette as string or symbol. Either 1 or -1. If -1 the palette will be reversed. Character describing color fill for x and y axes marginal distributions (default: "#009E73" (for x) and "#D55E00" (for y)). If set to NULL, manual specification of colors will be turned off and 2 colors from the specified palette from package will be selected. Numeric deciding transparency levels for the marginal distributions. Any numbers from 0 (transparent) to 1 (opaque). The default is 1 for both axes. Size for the marginal distribution boundaries (Default: 0.7). 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. 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. A character describing the test being run, which will be added as a prefix in the subtitle. The default is NULL. An example of a stat.title argument will be something like "Student's t-test: ". The text for the plot title. The text for the plot subtitle. Will work only if results.subtitle = FALSE. The text for the plot caption. Number of bootstrap samples for computing confidence interval for the effect size (Default: 100). bending constant (Default: 0.1). For more, see ?WRS2::pbcor. Number of digits after decimal point (should be an integer) (Default: k = 2). Logical that decides whether to restrict the axes values ranges to min and max values of the axes variables (Default: FALSE), only relevant for functions where axes variables are of numeric type. 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.). 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. 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. If the given function has an argument axes.range.restrict and if it has been set to TRUE, the added ggplot component might not work as expected. 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. Decides whether messages references, notes, and warnings are to be displayed (Default: TRUE).

## 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.

## References

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

grouped_ggscatterstats, ggcorrmat, grouped_ggcorrmat

## Examples

# \donttest{
# to get reproducible results from bootstrapping
set.seed(123)

# creating dataframe with rownames converted to a new column
mtcars_new <- mtcars %>%
tibble::rownames_to_column(., var = "car") %>%
tibble::as_tibble(x = .)

# simple function call with the defaults
ggstatsplot::ggscatterstats(
data = mtcars_new,
x = wt,
y = mpg,
type = "np",
label.var = car,
label.expression = wt < 4 & mpg < 20,
axes.range.restrict = TRUE,
centrality.para = "median",
xfill = NULL
)#> Coordinate system already present. Adding new coordinate system, which will replace the existing one.#> Warning: This plot can't be further modified with ggplot2 functions.
#> In case you want a ggplot object, set marginal = FALSE.#> # }