Scatterplots from ggplot2 combined with marginal
histograms/boxplots/density plots with statistical details added as a
subtitle.
ggscatterstats(
data,
x,
y,
type = "parametric",
conf.level = 0.95,
bf.prior = 0.707,
bf.message = TRUE,
label.var = NULL,
label.expression = NULL,
point.label.args = list(size = 3),
formula = y ~ x,
smooth.line.args = list(size = 1.5, color = "blue"),
method = "lm",
method.args = list(),
point.args = list(size = 3, alpha = 0.4),
point.width.jitter = 0,
point.height.jitter = 0,
marginal = TRUE,
marginal.type = "histogram",
margins = "both",
marginal.size = 5,
xfill = "#009E73",
yfill = "#D55E00",
xparams = list(fill = xfill),
yparams = list(fill = yfill),
centrality.parameter = "none",
centrality.label.args = list(size = 3),
vline.args = list(color = xfill, size = 1, linetype = "dashed"),
hline.args = list(color = yfill, size = 1, linetype = "dashed"),
results.subtitle = TRUE,
xlab = NULL,
ylab = NULL,
title = NULL,
subtitle = NULL,
caption = NULL,
nboot = 100,
beta = 0.1,
k = 2,
ggtheme = ggplot2::theme_bw(),
ggstatsplot.layer = TRUE,
ggplot.component = NULL,
output = "plot",
messages = TRUE,
...
)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).
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 number 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).
A list of additional aesthetic arguments to be passed
to ggrepel::geom_label_repel geom used to display the labels.
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.
A list of additional aesthetic arguments to be passed
to ggplot2::geom_smooth geom used to display the regression line.
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").
List of additional arguments passed on to the modelling
function defined by method.
A list of additional aesthetic arguments to be passed
to ggplot2::geom_point geom used to display the raw data points.
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.
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").
Along which margins to show the plots. One of: [both, x, y].
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 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.
List of extra parameters to use only for the marginal plot along the x axis.
List of extra parameters to use only for the marginal plot along the y axis.
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.
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.
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.
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.
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.
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).
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.
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.
Decides whether messages references, notes, and warnings are
to be displayed (Default: TRUE).
Currently ignored.
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html
# NOT RUN {
# to get reproducible results from bootstrapping
set.seed(123)
library(ggstatsplot)
# creating dataframe with rownames converted to a new column
mtcars_new <- as_tibble(mtcars, rownames = "car")
# 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,
centrality.parameter = "median"
)
# }
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