ggscatterstats

From ggstatsplot v0.0.11 by Indrajeet Patil

Scatterplot with marginal distributions

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

Usage

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.

x

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).

y

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

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.

conf.level

Scalar between 0 and 1. If unspecified, the defaults return 95% lower and upper confidence intervals (0.95).

bf.prior

A number between 0.5 and 2 (default 0.707), the prior width to use in calculating Bayes factors.

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).

label.var

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).

label.expression

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).

xlab

Labels for x and y axis variables. If NULL (default), variable names for x and y will be used.

ylab

Labels for x and y axis variables. If NULL (default), variable names for x and y will be used.

method

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). 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").

method.args

List of additional arguments passed on to the modelling function defined by method.

formula

Formula to use in smoothing function, eg. y ~ x, y ~ poly(x, 2), y ~ log(x)

point.color, point.size, point.alpha

Aesthetics specifying geom point (defaults: point.color = "black", point.size = 3,point.alpha = 0.4).

point.width.jitter, point.height.jitter

Degree of jitter in x and y direction, respectively. Defaults to 0 (0 data.

line.size

Size for the regression line.

line.color

color for the regression line.

marginal

Decides whether ggExtra::ggMarginal() plots will be displayed; the default is TRUE.

marginal.type

Type of marginal distribution to be plotted on the axes ("histogram", "boxplot", "density", "violin", "densigram").

marginal.size

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.

margins

Character describing along which margins to show the plots. Any of the following arguments are accepted: "both", "x", "y".

package

Name of package from which the palette is desired as string or symbol.

palette

Name of palette as string or symbol.

direction

Either 1 or -1. If -1 the palette will be reversed.

xfill, yfill

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.

xalpha, yalpha

Numeric deciding transparency levels for the marginal distributions. Any numbers from 0 (transparent) to 1 (opaque). The default is 1 for both axes.

xsize, ysize

Size for the marginal distribution boundaries (Default: 0.7).

centrality.para

Decides which measure of central tendency ("mean" or "median") is to be displayed as vertical (for x) and horizontal (for y) lines.

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.

stat.title

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: ".

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.

nboot

Number of bootstrap samples for computing confidence interval for the effect size (Default: 100).

beta

bending constant (Default: 0.1). For more, see ?WRS2::pbcor.

k

Number of digits after decimal point (should be an integer) (Default: k = 2).

axes.range.restrict

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.

ggtheme

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.).

ggstatsplot.layer

Logical that decides whether theme_ggstatsplot theme elements are to be displayed along with the selected ggtheme (Default: TRUE).

ggplot.component

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.

return

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, which will be a NULL if you set results.subtitle = FALSE. Setting this to "caption" will return the expression containing details about Bayes Factor analysis, but valid only when type = "p" and bf.message = TRUE, otherwise this will return a NULL.

messages

Decides whether messages references, notes, and warnings are to be displayed (Default: TRUE).

Note

marginal.type = "densigram" will work only with the development version of ggExtra that you can download from GitHub: remotes::install_github("daattali/ggExtra").
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

Examples

# NOT RUN {
# 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
)
# }

Documentation reproduced from package ggstatsplot, version 0.0.11, License: GPL-3 | file LICENSE

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