# ggstatsplot v0.0.8

Monthly downloads

## 'ggplot2' Based Plots with Statistical Details

Extension of 'ggplot2', 'ggstatsplot' creates graphics with details
from statistical tests included in the plots themselves. It is targeted primarily at
behavioral sciences community to provide a one-line code to generate information-rich plots for
statistical analysis. of continuous (violin plots, scatterplots, histograms) or
categorical (pie charts) data. Currently, it supports only the most common types
of statistical tests: parametric, nonparametric, robust, and bayesian
versions of t-test/anova, correlation analyses, contingency table analysis,
and regression analyses.

## Readme

# ggstatsplot: `ggplot2`

Based Plots with Statistical Details

Package | Status | Usage | GitHub | References |
---|---|---|---|---|

# Overview

`ggstatsplot`

is an
extension of `ggplot2`

package
for creating graphics with details from statistical tests included in
the plots themselves and targeted primarily at behavioral sciences
community to provide a one-line code to produce information-rich plots.
In a typical exploratory data analysis workflow, data visualization and
statistical modelling are two different phases: visualization informs
modelling, and modelling in its turn can suggest a different
visualization method, and so on and so forth. The central idea of
*ggstatsplot* is simple: combine these two phases into one in the form
of graphics with statistical details, which makes data exploration
simpler and faster.

Currently, it supports only the most common types of statistical tests:
**parametric**, **nonparametric**, **robust**, and **bayesian** versions
of **t-test**/**anova**, **correlation** analyses, **contingency table**
analysis, and **regression** analyses.

It, therefore, produces a limited kinds of plots for the supported analyses:

**violin plots**(for comparisons*between*groups or conditions),**pie charts**(for categorical data),**scatterplots**(for correlations between two variables),**correlation matrices**(for correlations between multiple variables),**histograms**and**dot plots/charts**(for hypothesis about distributions),**dot-and-whisker plots**(for regression models).

In addition to these basic plots, `ggstatsplot`

also provides
** grouped_** versions for most functions that makes it easy to repeat
the same analysis for any grouping variable.

Future versions will include other types of statistical analyses and plots as well.

# Installation

To get the latest, stable CRAN release (`0.0.8`

):

```
utils::install.packages(pkgs = "ggstatsplot")
```

*Note*: If you are on a linux machine, you will need to have OpenGL
libraries installed (specifically, `libx11`

, `mesa`

and Mesa OpenGL
Utility library - `glu`

) for the dependency package `rgl`

to work.

You can get the **development** version of the package from GitHub
(`0.0.8.9000`

). To see what new changes (and bug fixes) have been made
to the package since the last release on `CRAN`

, you can check the
detailed log of changes here:
https://indrajeetpatil.github.io/ggstatsplot/news/index.html

If you are in hurry and want to reduce the time of installation, prefer-

```
# needed package to download from GitHub repo
utils::install.packages(pkgs = "devtools")
# downloading the package from GitHub
devtools::install_github(
repo = "IndrajeetPatil/ggstatsplot", # package path on GitHub
dependencies = FALSE, # assumes that you already have all packages installed needed for this package to work
quick = TRUE # skips docs, demos, and vignettes
)
```

If time is not a constraint-

```
devtools::install_github(
repo = "IndrajeetPatil/ggstatsplot", # package path on GitHub
dependencies = TRUE, # installs packages which ggstatsplot depends on
upgrade_dependencies = TRUE # updates any out of date dependencies
)
```

If you are not using the RStudio IDE and you
get an error related to “pandoc” you will either need to remove the
argument `build_vignettes = TRUE`

(to avoid building the vignettes) or
install pandoc. If you have the `rmarkdown`

R
package installed then you can check if you have pandoc by running the
following in R:

```
rmarkdown::pandoc_available()
#> [1] TRUE
```

# Citation

If you want to cite this package in a scientific journal or in any other
context, run the following code in your `R`

console:

```
utils::citation(package = "ggstatsplot")
```

There is currently a publication in preparation corresponding this package and the citation will be updated once it’s published.

# Documentation and Examples

To see the detailed documentation for each function in the stable
**CRAN** version of the package, see:

- README: https://cran.r-project.org/web/packages/ggstatsplot/readme/README.html
- Vignettes: https://cran.r-project.org/web/packages/ggstatsplot/vignettes/

To see the documentation relevant for the **development** version of the
package, see the dedicated website for `ggstatplot`

, which is updated
after every new commit: https://indrajeetpatil.github.io/ggstatsplot/.

## Help

In `R`

, documentation for any function can be accessed with the standard
`help`

command (e.g., `?ggbetweenstats`

).

Another handy tool to see arguments to any of the functions is `args`

.
For example-

```
args(name = ggstatsplot::ggscatterstats)
#> function (data, x, y, type = "pearson", conf.level = 0.95, bf.prior = 0.707,
#> bf.message = FALSE, 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, 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, messages = TRUE)
#> NULL
```

In case you want to look at the function body for any of the functions, just type the name of the function without the parentheses:

```
ggstatsplot::theme_ggstatsplot
#> function(ggtheme = ggplot2::theme_bw(),
#> ggstatsplot.layer = TRUE) {
#> if (isTRUE(ggstatsplot.layer)) {
#> ggtheme +
#> ggplot2::theme(
#> axis.title.x = ggplot2::element_text(size = 11, face = "bold"),
#> strip.text.x = ggplot2::element_text(size = 11, face = "bold"),
#> strip.text.y = ggplot2::element_text(size = 11, face = "bold"),
#> strip.text = ggplot2::element_text(size = 11, face = "bold"),
#> axis.title.y = ggplot2::element_text(size = 11, face = "bold"),
#> axis.text.x = ggplot2::element_text(size = 11, face = "bold"),
#> axis.text.y = ggplot2::element_text(size = 11, face = "bold"),
#> axis.line = ggplot2::element_line(),
#> legend.text = ggplot2::element_text(size = 11),
#> legend.title = ggplot2::element_text(size = 11, face = "bold"),
#> legend.title.align = 0.5,
#> legend.text.align = 0.5,
#> legend.key.height = grid::unit(x = 1, units = "line"),
#> legend.key.width = grid::unit(x = 1, units = "line"),
#> plot.margin = grid::unit(x = c(1, 1, 1, 1), units = "lines"),
#> panel.border = ggplot2::element_rect(
#> color = "black",
#> fill = NA,
#> size = 1
#> ),
#> plot.title = ggplot2::element_text(
#> color = "black",
#> size = 13,
#> face = "bold",
#> hjust = 0.5
#> ),
#> plot.subtitle = ggplot2::element_text(
#> color = "black",
#> size = 11,
#> face = "plain",
#> hjust = 0.5
#> )
#> )
#> } else {
#> ggtheme
#> }
#> }
#> <bytecode: 0x000000002be7e9c0>
#> <environment: namespace:ggstatsplot>
```

If you are not familiar either with what the namespace `::`

does or how
to use pipe operator `%>%`

, something this package and its documentation
relies a lot on, you can check out these links-

## Usage

`ggstatsplot`

relies on non-standard evaluation (NSE), i.e., rather than
looking at the values of arguments (`x`

, `y`

), it instead looks at their
expressions. This means that you **shouldn’t** enter arguments with the
`$`

operator and setting `data = NULL`

: ```
data = NULL, x = data$x, y =
data$y
```

. You **must** always specify the `data`

argument for all
functions. On the plus side, you can enter arguments either as a string
(`x = "x", y = "y"`

) or as a bare expression (`x = x, y = y`

) and it
wouldn’t matter. To read more about NSE, see-
http://adv-r.had.co.nz/Computing-on-the-language.html

`ggstatsplot`

is a very chatty package and will by default print helpful
notes on assumptions about linear models, warnings, etc. If you don’t
want your console to be cluttered with such messages, they can be turned
off by setting argument `messages = FALSE`

in the function call.

Here are examples of the main functions currently supported in
`ggstatsplot`

.

**Note**: If you are reading this on GitHub repository, the
documentation below is for the **development** version of the package.
So you may see some features available here that are not currently
present in the stable version of this package on **CRAN**. For
documentation relevant for the CRAN version, see:

- vignettes: https://cran.r-project.org/web/packages/ggstatsplot/vignettes/
- README: https://cran.r-project.org/web/packages/ggstatsplot/readme/README.html

`ggbetweenstats`

This function creates either a violin plot, a box plot, or a mix of two
for **between**-group or **between**-condition comparisons with results
from statistical tests in the subtitle. The simplest function call looks
like this-

```
# loading needed libraries
library(ggstatsplot)
# for reproducibility
set.seed(123)
# plot
ggstatsplot::ggbetweenstats(
data = iris,
x = Species,
y = Sepal.Length,
messages = FALSE
) + # further modification outside of ggstatsplot
ggplot2::coord_cartesian(ylim = c(3, 8)) +
ggplot2::scale_y_continuous(breaks = seq(3, 8, by = 1))
```

Note that this function returns a `ggplot2`

object and thus any of the
graphics layers can be further modified.

The `type`

(of test) argument also accepts the following abbreviations:
`"p"`

(for *parametric*) or `"np"`

(for *nonparametric*) or `"r"`

(for
*robust*) or `"bf"`

(for *Bayes Factor*). Additionally, the type of plot
to be displayed can also be modified (`"box"`

, `"violin"`

, or
`"boxviolin"`

).

A number of other arguments can be specified to make this plot even more informative or change some of the default options.

```
library(ggplot2)
# for reproducibility
set.seed(123)
# let's leave out one of the factor levels and see if instead of anova, a t-test will be run
iris2 <- dplyr::filter(.data = iris, Species != "setosa")
# let's change the levels of our factors, a common routine in data analysis
# pipeline, to see if this function respects the new factor levels
iris2$Species <-
base::factor(x = iris2$Species,
levels = c("virginica" , "versicolor"))
# plot
ggstatsplot::ggbetweenstats(
data = iris2,
x = Species,
y = Sepal.Length,
notch = TRUE, # show notched box plot
mean.plotting = TRUE, # whether mean for each group is to be displayed
mean.ci = TRUE, # whether to display confidence interval for means
mean.label.size = 2.5, # size of the label for mean
type = "p", # which type of test is to be run
bf.message = TRUE, # add a message with bayes factor favoring null
k = 3, # number of decimal places for statistical results
outlier.tagging = TRUE, # whether outliers need to be tagged
outlier.label = Sepal.Width, # variable to be used for the outlier tag
outlier.label.color = "darkgreen", # changing the color for the text label
xlab = "Type of Species", # label for the x-axis variable
ylab = "Attribute: Sepal Length", # label for the y-axis variable
title = "Dataset: Iris flower data set", # title text for the plot
ggtheme = ggthemes::theme_fivethirtyeight(), # choosing a different theme
ggstatsplot.layer = FALSE, # turn off ggstatsplot theme layer
package = "wesanderson", # package from which color palette is to be taken
palette = "Darjeeling1", # choosing a different color palette
messages = FALSE
)
```

In case of a parametric t-test, setting `bf.message = TRUE`

will also
attach results from Bayesian Student’s *t*-test. That way, if the null
hypothesis can’t be rejected with the NHST approach, the Bayesian
approach can help index evidence in favor of the null hypothesis (i.e.,
`BF01`

).

By default, Bayes Factor quantifies the support for the alternative
hypothesis (H1) over the null hypothesis (H0) (i.e., `BF10`

is
displayed). Natural logarithms are shown because BF values can be pretty
large. This also makes it easy to compare evidence in favor alternative
(`BF10`

) versus null (`BF01`

) hypotheses (since ```
log(BF10) = -
log(BF01)
```

).

Additionally, there is also a `grouped_`

variant of this function that
makes it easy to repeat the same operation across a **single** grouping
variable:

```
# for reproducibility
set.seed(123)
# let's exclude animation and documentary genres since there are not many
# datapoints for these genres
# plot
ggstatsplot::grouped_ggbetweenstats(
data = dplyr::filter(.data = ggstatsplot::movies_long,
genre %in% c("Action", "Action Comedy", "Action Drama", "Comedy")),
x = mpaa,
y = length,
grouping.var = genre, # grouping variable
pairwise.comparisons = TRUE, # display significant pairwise comparisons
pairwise.annotation = "p.value", # how do you want to annotate the pairwise comparisons
p.adjust.method = "bonferroni", # method for adjusting p-values for multiple comparisons
bf.message = TRUE, # display Bayes Factor in favor of the null hypothesis
conf.level = 0.99, # changing confidence level to 99%
k = 3,
title.prefix = "Movie genre",
caption = substitute(paste(italic("Source"),
":IMDb (Internet Movie Database)")),
palette = "default_jama",
package = "ggsci",
messages = FALSE,
nrow = 2,
ncol = 2,
title.text = "Differences in movie length by mpaa ratings for different genres"
)
```

For more, see the `ggbetweenstats`

vignette:
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggbetweenstats.html

**This function is not appropriate for within-subjects designs.**

Variant of this function `ggwithinstats`

is currently under work. You
*can* still use this function just to prepare the **plot** for
exploratory data analysis, but the statistical details displayed in the
subtitle will be incorrect. You can remove them by adding ```
+
ggplot2::labs(subtitle = NULL)
```

to your function call.

As a **temporary solution**, you can use the helper function from
`ggstatsplot`

to display results from within-subjects version of the
test in question. Here is an example-

```
# for reproducibility
set.seed(123)
# getting text results using a helper function
custom_subtitle <-
ggstatsplot::subtitle_t_parametric(
data = ggstatsplot::iris_long,
x = attribute,
y = value,
paired = TRUE
)
# displaying the subtitle on the plot
ggstatsplot::ggbetweenstats(
data = ggstatsplot::iris_long,
x = attribute,
y = value,
results.subtitle = FALSE, # turn off the default subtitle
subtitle = custom_subtitle, # add the custom subtitle prepared using helper function
messages = FALSE
)
```

`ggscatterstats`

This function creates a scatterplot with marginal
histograms/boxplots/density/violin/densigram plots from
`ggExtra::ggMarginal`

and results from statistical tests in the
subtitle:

```
ggstatsplot::ggscatterstats(
data = ggplot2::msleep,
x = sleep_rem,
y = awake,
xlab = "REM sleep (in hours)",
ylab = "Amount of time spent awake (in hours)",
title = "Understanding mammalian sleep",
bf.message = TRUE,
messages = FALSE
)
```

Number of other arguments can be specified to modify this basic plot-

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::ggscatterstats(
data = dplyr::filter(.data = ggstatsplot::movies_long, genre == "Action"),
x = budget,
y = rating,
type = "robust", # type of test that needs to be run
conf.level = 0.99, # confidence level
xlab = "Movie budget (in million/ US$)", # label for x axis
ylab = "IMDB rating", # label for y axis
label.var = "title", # variable for labeling data points
label.expression = "rating < 5 & budget > 150", # expression that decides which points to label
line.color = "yellow", # changing regression line color line
title = "Movie budget and IMDB rating (action)",# title text for the plot
caption = expression( # caption text for the plot
paste(italic("Note"), ": IMDB stands for Internet Movie DataBase")
),
ggtheme = hrbrthemes::theme_ipsum_ps(), # choosing a different theme
ggstatsplot.layer = FALSE, # turn off ggstatsplot theme layer
marginal.type = "density", # type of marginal distribution to be displayed
xfill = "#0072B2", # color fill for x-axis marginal distribution
yfill = "#009E73", # color fill for y-axis marginal distribution
xalpha = 0.6, # transparency for x-axis marginal distribution
yalpha = 0.6, # transparency for y-axis marginal distribution
centrality.para = "median", # central tendency lines to be displayed
point.width.jitter = 0.2, # amount of horizontal jitter for data points
point.height.jitter = 0.4, # amount of vertical jitter for data points
messages = FALSE # turn off messages and notes
)
```

Additionally, there is also a `grouped_`

variant of this function that
makes it easy to repeat the same operation across a **single** grouping
variable:

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::grouped_ggscatterstats(
data = dplyr::filter(.data = ggstatsplot::movies_long,
genre %in% c("Action", "Action Comedy", "Action Drama", "Comedy")),
x = rating,
y = length,
bf.message = TRUE, # display bayes factor message
conf.level = 0.99,
k = 3, # no. of decimal places in the results
xfill = "#E69F00",
yfill = "#8b3058",
xlab = "IMDB rating",
grouping.var = genre, # grouping variable
title.prefix = "Movie genre",
ggtheme = ggplot2::theme_grey(),
messages = FALSE,
nrow = 2,
ncol = 2,
title.text = "Relationship between movie length by IMDB ratings for different genres"
)
```

For more, see the `ggscatterstats`

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

`ggpiestats`

This function creates a pie chart for categorical or nominal variables
with results from contingency table analysis (Pearson’s chi-squared test
for between-subjects design and McNemar’s test for within-subjects
design) included in the subtitle of the plot. If only one categorical
variable is entered, results from one-sample **proportion test** will be
displayed as a subtitle.

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::ggpiestats(
data = ggplot2::msleep,
main = vore,
title = "Composition of vore types among mammals",
messages = FALSE
)
```

This function can also be used to study an interaction between two
categorical variables. Additionally, this basic plot can further be
modified with additional arguments and the function returns a `ggplot2`

object that can further be modified with `ggplot2`

syntax:

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::ggpiestats(
data = mtcars,
main = am,
condition = cyl,
conf.level = 0.99, # confidence interval for effect size measure
title = "Dataset: Motor Trend Car Road Tests", # title for the plot
stat.title = "interaction: ", # title for the results
bf.message = TRUE, # display bayes factor in favor of null
legend.title = "Transmission", # title for the legend
factor.levels = c("1 = manual", "0 = automatic"), # renaming the factor level names (`main`)
facet.wrap.name = "No. of cylinders", # name for the facetting variable
slice.label = "counts", # show counts data instead of percentages
package = "ggsci", # package from which color palette is to be taken
palette = "default_jama", # choosing a different color palette
caption = substitute( # text for the caption
paste(italic("Source"), ": 1974 Motor Trend US magazine")
),
messages = FALSE # turn off messages and notes
)
```

In case of within-subjects designs, setting `paired = TRUE`

will produce
results from McNemar test-

```
# for reproducibility
set.seed(123)
# data
survey.data <- data.frame(
`1st survey` = c('Approve', 'Approve', 'Disapprove', 'Disapprove'),
`2nd survey` = c('Approve', 'Disapprove', 'Approve', 'Disapprove'),
`Counts` = c(794, 150, 86, 570),
check.names = FALSE
)
# plot
ggstatsplot::ggpiestats(
data = survey.data,
main = `1st survey`,
condition = `2nd survey`,
counts = Counts,
paired = TRUE, # within-subjects design
conf.level = 0.99, # confidence interval for effect size measure
stat.title = "McNemar Test: ",
package = "wesanderson",
palette = "Royal1"
)
#> Note: Results from faceted one-sample proportion tests:
#> # A tibble: 2 x 7
#> condition Approve Disapprove `Chi-squared` df `p-value` significance
#> <fct> <chr> <chr> <dbl> <dbl> <dbl> <chr>
#> 1 Approve 90.23% 9.77% 570. 1 0 ***
#> 2 Disapprove 20.83% 79.17% 245 1 0 ***
```

Additionally, there is also a `grouped_`

variant of this function that
makes it easy to repeat the same operation across a **single** grouping
variable:

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::grouped_ggpiestats(
data = ggstatsplot::movies_long,
main = mpaa,
grouping.var = genre, # grouping variable
title.prefix = "Movie genre", # prefix for the facetted title
slice.label = "both", # show both counts and percentage data
perc.k = 1, # no. of decimal places for percentages
palette = "BrightPastel",
package = "quickpalette",
messages = FALSE,
nrow = 2,
ncol = 2,
title.text = "Composition of MPAA ratings for different genres"
)
```

For more, including information about the variant of this function
`grouped_ggpiestats`

, see the `ggpiestats`

vignette:
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggpiestats.html

`gghistostats`

In case you would like to see the distribution of one variable and check if it is significantly different from a specified value with a one sample test, this function will let you do that.

The `type`

(of test) argument also accepts the following abbreviations:
`"p"`

(for *parametric*) or `"np"`

(for *nonparametric*) or `"r"`

(for
*robust*) or `"bf"`

(for *Bayes Factor*).

```
ggstatsplot::gghistostats(
data = ToothGrowth, # dataframe from which variable is to be taken
x = len, # numeric variable whose distribution is of interest
title = "Distribution of Sepal.Length", # title for the plot
fill.gradient = TRUE, # use color gradient
test.value = 10, # the comparison value for t-test
test.value.line = TRUE, # display a vertical line at test value
type = "bf", # bayes factor for one sample t-test
bf.prior = 0.8, # prior width for calculating the bayes factor
messages = FALSE # turn off the messages
)
```

The aesthetic defaults can be easily modified-

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::gghistostats(
data = iris, # dataframe from which variable is to be taken
x = Sepal.Length, # numeric variable whose distribution is of interest
title = "Distribution of Iris sepal length", # title for the plot
caption = substitute(paste(italic("Source:", "Ronald Fisher's Iris data set"))),
type = "parametric", # one sample t-test
conf.level = 0.99, # changing confidence level for effect size
bar.measure = "mix", # what does the bar length denote
test.value = 5, # default value is 0
test.value.line = TRUE, # display a vertical line at test value
test.value.color = "#0072B2", # color for the line for test value
centrality.para = "mean", # which measure of central tendency is to be plotted
centrality.color = "darkred", # decides color for central tendency line
binwidth = 0.10, # binwidth value (experiment)
bf.message = TRUE, # display bayes factor for null over alternative
bf.prior = 0.8, # prior width for computing bayes factor
messages = FALSE, # turn off the messages
ggtheme = hrbrthemes::theme_ipsum_tw(), # choosing a different theme
ggstatsplot.layer = FALSE # turn off ggstatsplot theme layer
)
```

As can be seen from the plot, bayes factor can be attached (```
bf.message
= TRUE
```

) to assess evidence in favor of the null hypothesis.

`grouped_`

variant of this function that
makes it easy to repeat the same operation across a **single** grouping
variable:

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::grouped_gghistostats(
data = dplyr::filter(.data = ggstatsplot::movies_long,
genre %in% c("Action", "Action Comedy", "Action Drama", "Comedy")),
x = budget,
xlab = "Movies budget (in million US$)",
type = "robust", # use robust location measure
grouping.var = genre, # grouping variable
title.prefix = "Movie genre",
ggtheme = ggthemes::theme_tufte(),
messages = FALSE,
nrow = 2,
title.text = "Movies budgets for different genres"
)
```

For more, including information about the variant of this function
`grouped_gghistostats`

, see the `gghistostats`

vignette:
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/gghistostats.html

`ggdotplotstats`

This function is similar to `gghistostats`

, but is intended to be used
when numeric variable also has a label.

```
# for reproducibility
set.seed(123)
# plot
ggdotplotstats(
data = dplyr::filter(.data = gapminder::gapminder, continent == "Asia"),
y = country,
x = lifeExp,
test.value = 55,
test.value.line = TRUE,
test.line.labeller = TRUE,
test.value.color = "red",
centrality.para = "median",
centrality.k = 0,
title = "Distribution of life expectancy in Asian continent",
xlab = "Life expectancy",
bf.message = TRUE,
messages = FALSE,
caption = substitute(
paste(
italic("Source"),
": Gapminder dataset from https://www.gapminder.org/"
)
)
)
```

As with the rest of the functions in this package, there is also a
`grouped_`

variant of this function to facilitateto repeat the same
operation across a grouping variable.

```
# for reproducibility
set.seed(123)
# removing factor level with very few no. of observations
df <- dplyr::filter(.data = ggplot2::mpg, cyl %in% c("4", "6"))
# plot
ggstatsplot::grouped_ggdotplotstats(
data = df,
x = cty,
y = manufacturer,
xlab = "city miles per gallon",
ylab = "car manufacturer",
type = "np", # non-parametric test
grouping.var = cyl, # grouping variable
test.value = 15.5,
title.prefix = "cylinder count",
point.color = "red",
point.size = 5,
point.shape = 13,
test.value.line = TRUE,
ggtheme = ggthemes::theme_par(),
messages = FALSE,
title.text = "Fuel economy data"
)
```

`ggcorrmat`

`ggcorrmat`

makes a correlalogram (a matrix of correlation coefficients)
with minimal amount of code. Just sticking to the defaults itself
produces publication-ready correlation matrices. But, for the sake of
exploring the available options, let’s change some of the defaults. For
example, multiple aesthetics-related arguments can be modified to change
the appearance of the correlation matrix.

```
# for reproducibility
set.seed(123)
# as a default this function outputs a correlalogram plot
ggstatsplot::ggcorrmat(
data = ggplot2::msleep,
corr.method = "robust", # correlation method
sig.level = 0.001, # threshold of significance
p.adjust.method = "holm", # p-value adjustment method for multiple comparisons
cor.vars = c(sleep_rem, awake:bodywt), # a range of variables can be selected
cor.vars.names = c("REM sleep", # variable names
"time awake",
"brain weight",
"body weight"),
matrix.type = "upper", # type of visualization matrix
colors = c("#B2182B", "white", "#4D4D4D"),
title = "Correlalogram for mammals sleep dataset",
subtitle = "sleep units: hours; weight units: kilograms"
)
```

Note that if there are `NA`

s present in the selected dataframe, the
legend will display minimum, median, and maximum number of pairs used
for correlation matrices.

Alternatively, you can use it just to get the correlation matrices and
their corresponding *p*-values (in a `tibble`

format). Also, note that
if `cor.vars`

are not specified, all numeric variables will be used.

```
# for reproducibility
set.seed(123)
# show four digits in a tibble
options(pillar.sigfig = 4)
# getting the correlation coefficient matrix
ggstatsplot::ggcorrmat(
data = iris, # all numeric variables from data will be used
corr.method = "robust",
output = "correlations", # specifying the needed output ("r" or "corr" will also work)
digits = 3 # number of digits to be dispayed for correlation coefficient
)
#> # A tibble: 4 x 5
#> variable Sepal.Length Sepal.Width Petal.Length Petal.Width
#> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 Sepal.Length 1 -0.143 0.878 0.837
#> 2 Sepal.Width -0.143 1 -0.426 -0.373
#> 3 Petal.Length 0.878 -0.426 1 0.966
#> 4 Petal.Width 0.837 -0.373 0.966 1
# getting the p-value matrix
ggstatsplot::ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_total:bodywt,
corr.method = "robust",
output = "p.values", # only "p" or "p-values" will also work
p.adjust.method = "holm"
)
#> # A tibble: 6 x 7
#> variable sleep_total sleep_rem sleep_cycle awake brainwt bodywt
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 sleep_to~ 0. 5.291e-12 9.138e- 3 0. 3.170e- 5 2.568e- 6
#> 2 sleep_rem 4.070e-13 0. 1.978e- 2 5.291e-12 9.698e- 3 3.762e- 3
#> 3 sleep_cy~ 2.285e- 3 1.978e- 2 0. 9.138e- 3 1.637e- 9 1.696e- 5
#> 4 awake 0. 4.070e-13 2.285e- 3 0. 3.170e- 5 2.568e- 6
#> 5 brainwt 4.528e- 6 4.849e- 3 1.488e-10 4.528e- 6 0. 4.509e-17
#> 6 bodywt 2.568e- 7 7.524e- 4 2.120e- 6 2.568e- 7 3.221e-18 0.
# getting the confidence intervals for correlations
ggstatsplot::ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_total:bodywt,
corr.method = "kendall",
output = "ci",
p.adjust.method = "holm"
)
#> Note: In the correlation matrix,
#> the upper triangle: p-values adjusted for multiple comparisons
#> the lower triangle: unadjusted p-values.
#> # A tibble: 15 x 7
#> pair r lower upper p lower.adj upper.adj
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 1 0.5922 0.4000 0.7345 4.981e- 7 0.3027 0.7817
#> 2 2 -0.3481 -0.6214 0.0006818 5.090e- 2 -0.6789 0.1002
#> 3 3 -1 -1 -1 0. -1 -1
#> 4 4 -0.4293 -0.6220 -0.1875 9.621e- 4 -0.6858 -0.07796
#> 5 5 -0.3851 -0.5547 -0.1847 3.247e- 4 -0.6050 -0.1106
#> 6 6 -0.2066 -0.5180 0.1531 2.566e- 1 -0.5180 0.1531
#> 7 7 -0.5922 -0.7345 -0.4000 4.981e- 7 -0.7832 -0.2990
#> 8 8 -0.2636 -0.5096 0.02217 7.022e- 2 -0.5400 0.06404
#> 9 9 -0.3163 -0.5262 -0.07004 1.302e- 2 -0.5662 -0.01317
#> 10 10 0.3481 -0.0006818 0.6214 5.090e- 2 -0.1145 0.6867
#> 11 11 0.7125 0.4739 0.8536 1.001e- 5 0.3239 0.8954
#> 12 12 0.6545 0.3962 0.8168 4.834e- 5 0.2459 0.8656
#> 13 13 0.4293 0.1875 0.6220 9.621e- 4 0.08322 0.6829
#> 14 14 0.3851 0.1847 0.5547 3.247e- 4 0.1049 0.6087
#> 15 15 0.8378 0.7373 0.9020 8.181e-16 0.6716 0.9238
# getting the sample sizes for all pairs
ggstatsplot::ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_total:bodywt,
corr.method = "robust",
output = "n" # note that n is different due to NAs
)
#> # A tibble: 6 x 7
#> variable sleep_total sleep_rem sleep_cycle awake brainwt bodywt
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 sleep_total 83 61 32 83 56 83
#> 2 sleep_rem 61 61 32 61 48 61
#> 3 sleep_cycle 32 32 32 32 30 32
#> 4 awake 83 61 32 83 56 83
#> 5 brainwt 56 48 30 56 56 56
#> 6 bodywt 83 61 32 83 56 83
```

`grouped_`

variant of this function that
makes it easy to repeat the same operation across a **single** grouping
variable:

```
# for reproducibility
set.seed(123)
# plot
# let's use only 50% of the data to speed up the process
ggstatsplot::grouped_ggcorrmat(
data = dplyr::sample_frac(ggstatsplot::movies_long, size = 0.5),
cor.vars = length:votes,
corr.method = "np",
colors = c("#cbac43", "white", "#550000"),
grouping.var = genre, # grouping variable
title.prefix = "Movie genre",
messages = FALSE,
nrow = 2,
ncol = 2
)
```

For examples and more information, see the `ggcorrmat`

vignette:
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcorrmat.html

`ggcoefstats`

`ggcoefstats`

creates a lot with the regression coefficients’ point
estimates as dots with confidence interval whiskers.

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::ggcoefstats(x = stats::lm(formula = mpg ~ am * cyl,
data = mtcars))
```

The basic can be further modified to one’s liking with additional arguments (also, let’s use a robust linear model instead of a simple linear model now):

```
# for reproducibility
set.seed(123)
# plot
ggstatsplot::ggcoefstats(
x = MASS::rlm(formula = mpg ~ am * cyl,
data = mtcars),
point.color = "red",
point.shape = 15,
vline.color = "#CC79A7",
vline.linetype = "dotdash",
stats.label.size = 3.5,
stats.label.color = c("#0072B2", "#D55E00", "darkgreen"),
title = "Car performance predicted by transmission & cylinder count",
subtitle = "Source: 1974 Motor Trend US magazine",
ggtheme = ggthemes::theme_stata(),
ggstatsplot.layer = FALSE
) +
# further modification with the ggplot2 commands
# note the order in which the labels are entered
ggplot2::scale_y_discrete(labels = c("transmission", "cylinders", "interaction")) +
ggplot2::labs(x = "regression coefficient",
y = NULL)
```

All the regression model classes that are supported in the `broom`

package with `tidy`

and `glance`

methods
(https://broom.tidyverse.org/articles/available-methods.html) are also
supported by `ggcoefstats`

. Additionally, we can make a number of
aesthetic modifications by changing the defaults for theme and palette.

Let’s see a couple more examples:

```
# for reproducibility
set.seed(123)
library(quantreg)
library(nlme)
# loading dataframe needed for the analyses below
data(stackloss)
# combining plots together
ggstatsplot::combine_plots(
# quantile regression
ggstatsplot::ggcoefstats(
x = quantreg::rq(
formula = stack.loss ~ stack.x,
data = stackloss,
method = "br"
),
se.type = "iid",
title = "quantile regression"
),
# linear model using generalized least squares
ggstatsplot::ggcoefstats(
x = nlme::gls(
model = follicles ~ sin(2 * pi * Time) + cos(2 * pi * Time),
data = Ovary,
correlation = corAR1(form = ~ 1 | Mare)
),
point.color = "red",
stats.label.color = "black",
ggtheme = hrbrthemes::theme_ipsum_ps(),
ggstatsplot.layer = FALSE,
exclude.intercept = FALSE,
title = "generalized least squares model"
),
labels = c("(a)", "(b)"),
nrow = 2
)
```

This is by no means an exhaustive list of models supported by
`ggcoefstats`

. For a more thorough discussion about all regression
models supported, see the associated vignette-
https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcoefstats.html

`combine_plots`

The full power of `ggstatsplot`

can be leveraged with a functional
programming package like `purrr`

that
replaces `for`

loops with code that is both more succinct and easier to
read and, therefore, `purrr`

should be preferrred

## Functions in ggstatsplot

Name | Description | |

bf_corr_test | Bayesian correlation test. | |

ggbetweenstats | Box/Violin plots for group or condition comparisons in between-subjects designs. | |

ggbetweenstats_switch | Switch function to use helper function to create subtitle for the ggbetweenstats plot. | |

bf_two_sample_ttest | Bayesian two-samples t-test. | |

bartlett_message | Display homogeneity of variance test as a message | |

check_outlier | Finding the outliers in the dataframe using Tukey's interquartile range rule | |

Titanic_full | Titanic dataset. | |

ggcoefstats | Model coefficients for fitted models with the model summary as a caption. | |

ggcoefstats_label_maker | Create labels with statistical details for ggcoefstats. | |

cor_test_ci | A correlation test with confidence interval for effect size. | |

ggsignif_position_calculator | Calculating y coordinates for the ggsignif comparison bars. | |

ggstatsplot-package | ggstatsplot: 'ggplot2' Based Plots with Statistical Details | |

intent_morality | Moral judgments about third-party moral behavior. | |

effsize_ci_message | Message to display when bootstrapped confidence intervals are shown for effect size measure. | |

ggcorrmat | Visualization of a correlalogram (or correlation matrix) | |

iris_long | Edgar Anderson's Iris Data in long format. | |

mean_labeller | Create a dataframe with mean per group and a formatted label for display in ggbetweenstats plot. | |

movies_long | Movie information and user ratings from IMDB.com (long format). | |

robcor_ci | Robust correlation coefficient and its confidence interval | |

stats_type_switch | Switch function to determine which type of statistics is to be run. | |

subtitle_t_parametric | Making text subtitle for the t-test (between-/within-subjects designs). | |

ggcorrmat_matrix_message | Message to display when adjusted p-values are displayed in correlation matrix. | |

subtitle_t_robust | Making text subtitle for the robust t-test (between- and within-subjects designs). | |

grouped_ggpiestats | Grouped pie charts with statistical tests | |

numdf_summary | Compute minimum, maximum, and median across all numeric columns in a dataframe. | |

grouped_ggscatterstats | Scatterplot with marginal distributions for all levels of a grouping variable | |

p.adjust.method.description | Preparing text to describe which p-value adjustment method was used. | |

bf_one_sample_ttest | Bayesian one-sample t-test. | |

normality_message | Display normality test result as a message. | |

bf_oneway_anova | Bayesian one-way analysis of variance. | |

movies_wide | Movie information and user ratings from IMDB.com (wide format). | |

effsize_type_switch | Switch function to determine which effect size is to computed. | |

subtitle_friedman_nonparametric | Making text subtitle for the Friedman Rank Sum Test (nonparametric ANOVA) (within-subjects designs). | |

bf_caption_maker | Prepare caption with bayes factor in favor of null | |

subtitle_ggscatterstats | Making text subtitle for the correlation test. | |

bf_contingency_tab | Bayesian contingency table analysis. | |

subtitle_meta_ggcoefstats | Prepare subtitle with meta-analysis results | |

combine_plots | Combining and arranging multiple plots in a grid | |

chisq_v_ci | Chi-squared test of association with confidence interval for effect size (Cramer's V). | |

games_howell | Games-Howell post-hoc test | |

subtitle_t_bayes | Making text subtitle for the bayesian t-test. | |

subtitle_onesample_proptest | Making text subtitle for Proportion Test (N Outcomes), a chi-squared Goodness of fit test. | |

grouped_ggbetweenstats | Violin plots for group or condition comparisons in between-subjects designs repeated across all levels of a grouping variable. | |

subtitle_t_onesample | Making text subtitle for one sample t-test and its nonparametric and robust equivalents. | |

ggdotplotstats | Dot plot/chart for labeled numeric data. | |

grouped_ggcorrmat | Visualization of a correlalogram (or correlation matrix) for all levels of a grouping variable | |

grouped_ggdotplotstats | Grouped histograms for distribution of a labelled numeric variable | |

gghistostats | Histogram for distribution of a numeric variable | |

grouped_message | grouped_message | |

histo_labeller | Custom function for adding labelled lines for x-axis variable. | |

subtitle_anova_bayes | Making text subtitle for the between-subject one-way anova designs. | |

subtitle_anova_parametric | Making text subtitle for the between-subject anova designs. | |

subtitle_kw_nonparametric | Making text subtitle for the Kruskal-Wallis test (nonparametric ANOVA) (between-subjects designs). | |

subtitle_mann_nonparametric | Making text subtitle for the Mann-Whitney U-test (between-/within-subjects designs). | |

grouped_gghistostats | Grouped histograms for distribution of a numeric variable | |

long_to_wide_converter | Converts long-format dataframe to wide-format dataframe | |

matrix_to_tibble | Convert a matrix to a tibble dataframe. | |

subtitle_anova_robust | Making text subtitle for the robust ANOVA (between-subjects designs). | |

subtitle_contingency_tab | Making text subtitle for contingency analysis (Pearson's chi-square test for independence for between-subjects design or McNemar's test for within-subjects design) | |

tfz_labeller | Prepare labels with statistic for ggcoefstats function. | |

theme_ggstatsplot | Default theme used in all ggstatsplot package plots | |

theme_corrmat | Default theme used for correlation matrix | |

theme_pie | Default theme used for pie chart | |

ggpiestats | Pie charts with statistical tests | |

ggscatterstats | Scatterplot with marginal distributions | |

kw_eta_h_ci | Confidence interval for effect size for Kruskal-Wallis test. | |

lm_effsize_standardizer | Standardize a dataframe with effect sizes for aov, lm, aovlist, etc. objects. | |

pairwise_p | Pairwise comparison tests | |

pairwise_p_caption | Preparing caption in case pairwise comparisons are displayed. | |

palette_message | Message if palette doesn't have enough number of colors. | |

reexports | Objects exported from other packages | |

subtitle_template | Template for subtitles with statistical details for tests with a single parameter (e.g., t, chi-squared, etc.) | |

t1way_ci | A heteroscedastic one-way ANOVA for trimmed means with confidence interval for effect size. | |

tibble | Anticipate use of tibbles | |

yuend_ci | Paired samples robust t-tests with confidence interval for effect size. | |

bf_extractor | Convenience function to extract bayes factors and details about posterior (mean, median, HDI, etc.) from BayesFactor model object. | |

No Results! |

## Vignettes of ggstatsplot

## Last month downloads

## Details

#### Include our badge in your README

```
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```