Grouped scatterplots from ggplot2
combined with marginal
histograms/boxplots/density plots with statistical details added as a
subtitle.
grouped_ggscatterstats(
data,
x,
y,
grouping.var,
type = "pearson",
conf.level = 0.95,
bf.prior = 0.707,
bf.message = TRUE,
label.var = NULL,
label.expression = NULL,
title.prefix = NULL,
xlab = NULL,
ylab = NULL,
method = "lm",
method.args = list(),
formula = y ~ x,
point.color = "black",
point.size = 3,
point.alpha = 0.4,
line.size = 1.5,
point.width.jitter = 0,
point.height.jitter = 0,
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,
caption = NULL,
subtitle = 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
).
A single grouping variable (can be entered either as a
bare name x
or as a string "x"
).
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
).
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.
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
).
Aesthetics specifying geom point
(defaults: point.color = "black"
, point.size = 3
,point.alpha = 0.4
).
Aesthetics specifying geom point
(defaults: point.color = "black"
, point.size = 3
,point.alpha = 0.4
).
Size for the regression line.
Degree of jitter in x
and y
direction, respectively. Defaults to 0
(0%) of the resolution of the
data.
Degree of jitter in x
and y
direction, respectively. Defaults to 0
(0%) of the resolution of the
data.
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.
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.
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
).
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 caption.
The text for the plot subtitle. Will work only if
results.subtitle = FALSE
.
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
).
Arguments passed on to combine_plots
title.text
String or plotmath expression to be drawn as title for the combined plot.
title.color
Text color for title.
title.size
Point size of title text.
title.vjust
Vertical justification for title. Default = 0.5
(centered on y
). 0
= baseline at y
, 1
= ascender at y
.
title.hjust
Horizontal justification for title. Default = 0.5
(centered on x
). 0
= flush-left at x, 1
= flush-right.
title.fontface
The font face ("plain"
, "bold"
(default),
"italic"
, "bold.italic"
) for title.
caption.text
String or plotmath expression to be drawn as the caption for the combined plot.
caption.color
Text color for caption.
caption.size
Point size of title text.
caption.vjust
Vertical justification for caption. Default = 0.5
(centered on y). 0
= baseline at y, 1
= ascender at y.
caption.hjust
Horizontal justification for caption. Default = 0.5
(centered on x). 0
= flush-left at x, 1
= flush-right.
caption.fontface
The font face ("plain"
(default), "bold"
,
"italic"
, "bold.italic"
) for caption.
sub.text
The label with which the combined plot should be annotated. Can be a plotmath expression.
sub.color
Text color for annotation label (Default: "black"
).
sub.size
Point size of annotation text (Default: 12
).
sub.x
The x position of annotation label (Default: 0.5
).
sub.y
The y position of annotation label (Default: 0.5
).
sub.hjust
Horizontal justification for annotation label (Default:
0.5
).
sub.vjust
Vertical justification for annotation label (Default:
0.5
).
sub.vpadding
Vertical padding. The total vertical space added to the
label, given in grid units. By default, this is added equally above and
below the label. However, by changing the y and vjust parameters, this can
be changed (Default: ggplot2::unit(1, "lines")
).
sub.fontface
The font face ("plain"
(default), "bold"
, "italic"
,
"bold.italic"
) for the annotation label.
sub.angle
Angle at which annotation label is to be drawn (Default:
0
).
sub.lineheight
Line height of annotation label.
title.caption.rel.heights
Numerical vector of relative columns heights while combining (title, plot, caption).
title.rel.heights
Numerical vector of relative columns heights while combining (title, plot).
caption.rel.heights
Numerical vector of relative columns heights while combining (plot, caption).
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html
# NOT RUN {
# to ensure reproducibility
set.seed(123)
# basic function call
ggstatsplot::grouped_ggscatterstats(
data = dplyr::filter(
ggstatsplot::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)
ggstatsplot::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,
xfill = NULL,
ggplot.component = ggplot2::scale_y_continuous(sec.axis = ggplot2::dup_axis()),
package = "yarrr",
palette = "appletv",
messages = FALSE
)
# labeling without expression
ggstatsplot::grouped_ggscatterstats(
data = dplyr::filter(
.data = ggstatsplot::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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