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
)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).
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html
# NOT RUN {
# to get reproducible results from bootstrapping
set.seed(123)
# creating dataframe with rownames converted to a new column
mtcars_new <- tibble::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,
axes.range.restrict = TRUE,
centrality.para = "median",
xfill = NULL
)
# }
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