`ggstatsplot`: `ggplot2` Based Plots with Statistical Details

Package	Status	Usage	GitHub	References

Raison d’être

“What is to be sought in designs for the display of information is the clear portrayal of complexity. Not the complication of the simple; rather … the revelation of the complex.”

Edward R. Tufte

ggstatsplot is an extension of ggplot2 package for creating graphics with details from statistical tests included in the information-rich plots themselves. In a typical exploratory data analysis workflow, data visualization and statistical modeling are two different phases: visualization informs modeling, and modeling 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.

Summary of available plots

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

Function	Plot	Description
`ggbetweenstats`	violin plots	for comparisons between groups/conditions
`ggwithinstats`	violin plots	for comparisons within groups/conditions
`gghistostats`	histograms	for distribution about numeric variable
`ggdotplotstats`	dot plots/charts	for distribution about labeled numeric variable
`ggpiestats`	pie charts	for categorical data
`ggbarstats`	bar charts	for categorical data
`ggscatterstats`	scatterplots	for correlations between two variables
`ggcorrmat`	correlation matrices	for correlations between multiple variables
`ggcoefstats`	dot-and-whisker plots	for regression models and meta-analysis

In addition to these basic plots, ggstatsplot also provides grouped_ versions (see below) that makes it easy to repeat the same analysis for any grouping variable.

Summary of types of statistical analyses

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

The table below summarizes all the different types of analyses currently supported in this package-

Functions	Description	Parametric	Non-parametric	Robust	Bayes Factor
`ggbetweenstats`	Between group/condition comparisons	Yes	Yes	Yes	Yes
`ggwithinstats`	Within group/condition comparisons	Yes	Yes	Yes	Yes
`gghistostats`, `ggdotplotstats`	Distribution of a numeric variable	Yes	Yes	Yes	Yes
`ggcorrmat`	Correlation matrix	Yes	Yes	Yes	Yes
`ggscatterstats`	Correlation between two variables	Yes	Yes	Yes	Yes
`ggpiestats`, `ggbarstats`	Association between categorical variables	Yes	`NA`	`NA`	Yes
`ggpiestats`, `ggbarstats`	Equal proportions for categorical variable levels	Yes	`NA`	`NA`	Yes
`ggcoefstats`	Regression model coefficients	Yes	Yes	Yes	Yes
`ggcoefstats`	Random-effects meta-analysis	Yes	`NA`	Yes	Yes

Summary of Bayesian analysis

Analysis	Hypothesis testing	Estimation
(one/two-sample) t-test	Yes	Yes
one-way ANOVA	Yes	Yes
correlation	Yes	Yes
(one/two-way) contingency table	Yes	Yes
random-effects meta-analysis	Yes	Yes

Statistical reporting

For all statistical tests reported in the plots, the default template abides by the APA gold standard for statistical reporting. For example, here are results from Yuen’s test for trimmed means (robust t-test):

Summary of statistical tests and effect sizes

Here is a summary table of all the statistical tests currently supported across various functions: https://indrajeetpatil.github.io/statsExpressions/articles/stats_details.html

Installation

To get the latest, stable CRAN release:

install.packages("ggstatsplot")

Note:

Linux users may encounter some installation problems, as several R packages require external libraries on the system, especially for PMCMRplus package. The following README file briefly describes the installation procedure: https://CRAN.R-project.org/package=PMCMRplus/readme/README.html

You can get the development version of the package from GitHub.

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

# needed package to download from GitHub repo
install.packages("remotes")

# downloading the package from GitHub (needs `remotes` package to be installed)
remotes::install_github(
  repo = "IndrajeetPatil/ggstatsplot", # package path on GitHub
  dependencies = FALSE, # assumes you have already installed needed packages
  quick = TRUE # skips docs, demos, and vignettes
)

If time is not a constraint-

remotes::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
)

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

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:

citation("ggstatsplot")
#> 
#>   Patil, I. (2018). ggstatsplot: 'ggplot2' Based Plots with Statistical
#>   Details. CRAN. Retrieved from
#>   https://cran.r-project.org/web/packages/ggstatsplot/index.html
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Article{,
#>     title = {{ggstatsplot}: 'ggplot2' Based Plots with Statistical Details},
#>     author = {Indrajeet Patil},
#>     year = {2018},
#>     journal = {CRAN},
#>     url = {https://CRAN.R-project.org/package=ggstatsplot},
#>     doi = {10.5281/zenodo.2074621},
#>   }

There is currently a publication in preparation corresponding to 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:

Website: https://indrajeetpatil.github.io/ggstatsplot/
README: https://CRAN.R-project.org/package=ggstatsplot/readme/README.html
Presentation: https://indrajeetpatil.github.io/ggstatsplot_slides/slides/ggstatsplot_presentation.html#1
Vignettes: https://CRAN.R-project.org/package=ggstatsplot/vignettes/additional.html

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/.

Primary functions

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: https://CRAN.R-project.org/package=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-

# for reproducibility
set.seed(123)
library(ggstatsplot)

# plot
ggstatsplot::ggbetweenstats(
  data = iris,
  x = Species,
  y = Sepal.Length,
  title = "Distribution of sepal length across Iris species"
)

Note that this function returns object of class ggplot and thus can be further modified using ggplot2 functions.

A number of other arguments can be specified to make this plot even more informative or change some of the default options. Additionally, this time we will use a grouping variable that has only two levels. The function will automatically switch from carrying out an ANOVA analysis to a t-test.

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.

# for reproducibility
set.seed(123)
library(ggplot2)

# plot
ggstatsplot::ggbetweenstats(
  data = ToothGrowth,
  x = supp,
  y = len,
  mean.ci = TRUE, # whether to display confidence interval for means
  k = 3, # number of decimal places for statistical results
  outlier.tagging = TRUE, # whether outliers need to be tagged
  outlier.label = dose, # variable to be used for tagging outliers
  xlab = "Supplement type", # label for the x-axis variable
  ylab = "Tooth length", # label for the y-axis variable
  title = "The Effect of Vitamin C on Tooth Growth", # 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
)

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_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
  ggsignif.args = list(textsize = 4, tip_length = 0.01),
  p.adjust.method = "bonferroni", # method for adjusting p-values for multiple comparisons
  # adding new components to `ggstatsplot` default
  ggplot.component = list(ggplot2::scale_y_continuous(sec.axis = ggplot2::dup_axis())),
  k = 3,
  title.prefix = "Movie genre",
  caption = substitute(paste(italic("Source"), ": IMDb (Internet Movie Database)")),
  palette = "default_jama",
  package = "ggsci",
  plotgrid.args = list(nrow = 2),
  title.text = "Differences in movie length by mpaa ratings for different genres"
)

Summary of tests

Following (between-subjects) tests are carried out for each type of analyses-

Type	No. of groups	Test	Function
Parametric	> 2	Fisher’s or Welch’s one-way ANOVA	`stats::oneway.test`
Non-parametric	> 2	Kruskal–Wallis one-way ANOVA	`stats::kruskal.test`
Robust	> 2	Heteroscedastic one-way ANOVA for trimmed means	`WRS2::t1way`
Bayes Factor	> 2	Fisher’s ANOVA	`BayesFactor::anovaBF`
Parametric	2	Student’s or Welch’s t-test	`stats::t.test`
Non-parametric	2	Mann–Whitney U test	`stats::wilcox.test`
Robust	2	Yuen’s test for trimmed means	`WRS2::yuen`
Bayes Factor	2	Student’s t-test	`BayesFactor::ttestBF`

Following effect sizes (and confidence intervals/CI) are available for each type of test-

Type	No. of groups	Effect size	CI?	Function
Parametric	> 2	$\eta_{p}^2$ , $\omega_{p}^2$	Yes	`effectsize::omega_squared`, `effectsize::eta_squared`
Non-parametric	> 2	$\eta_{H}^2$ (H-statistic based eta-squared)	Yes	`rcompanion::epsilonSquared`
Robust	> 2	$\xi$ (Explanatory measure of effect size)	Yes	`WRS2::t1way`
Bayes Factor	> 2	$R_{posterior}^2$	Yes	`performance::r2_bayes`
Parametric	2	Cohen’s d, Hedge’s g	Yes	`effectsize::cohens_d`, `effectsize::hedges_g`
Non-parametric	2	r (computed as $Z/\sqrt{N}$ )	Yes	`rcompanion::wilcoxonR`
Robust	2	$\xi$ (Explanatory measure of effect size)	Yes	`WRS2::yuen.effect.ci`
Bayes Factor	2	$\delta_{posterior}$	Yes	`bayestestR::describe_posterior`

Here is a summary of multiple pairwise comparison tests supported in ggbetweenstats-

Type	Equal variance?	Test	p-value adjustment?	Function
Parametric	No	Games-Howell test	Yes	`stats::pairwise.t.test`
Parametric	Yes	Student’s t-test	Yes	`PMCMRplus::gamesHowellTest`
Non-parametric	No	Dunn test	Yes	`PMCMRplus::kwAllPairsDunnTest`
Robust	No	Yuen’s trimmed means test	Yes	`WRS2::lincon`
Bayes Factor	`NA`	Student’s t-test	`NA`	`BayesFactor::ttestBF`

For more, see the ggbetweenstats vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggbetweenstats.html

`ggwithinstats`

ggbetweenstats function has an identical twin function ggwithinstats for repeated measures designs that behaves in the same fashion with a few minor tweaks introduced to properly visualize the repeated measures design. As can be seen from an example below, the only difference between the plot structure is that now the group means are connected by paths to highlight the fact that these data are paired with each other.

# for reproducibility and data
set.seed(123)
library(WRS2)

# plot
ggstatsplot::ggwithinstats(
  data = WineTasting,
  x = Wine,
  y = Taste,
  title = "Wine tasting",
  caption = "Data source: `WRS2` R package",
  ggtheme = ggthemes::theme_fivethirtyeight(),
  ggstatsplot.layer = FALSE
)

As with the ggbetweenstats, this function also has a grouped_ variant that makes repeating the same analysis across a single grouping variable quicker. We will see an example with only repeated measurements-

# common setup
set.seed(123)

# plot
ggstatsplot::grouped_ggwithinstats(
  data = dplyr::filter(
    .data = ggstatsplot::bugs_long,
    region %in% c("Europe", "North America"),
    condition %in% c("LDLF", "LDHF")
  ),
  x = condition,
  y = desire,
  xlab = "Condition",
  ylab = "Desire to kill an artrhopod",
  grouping.var = region,
  outlier.tagging = TRUE,
  outlier.label = education,
  ggtheme = hrbrthemes::theme_ipsum_tw(),
  ggstatsplot.layer = FALSE
)

Summary of tests

Following (within-subjects) tests are carried out for each type of analyses-

Type	No. of groups	Test
Parametric	> 2	One-way repeated measures ANOVA
Non-parametric	> 2	Friedman rank sum test
Robust	> 2	Heteroscedastic one-way repeated measures ANOVA for trimmed means
Bayes Factor	> 2	One-way repeated measures ANOVA
Parametric	2	Student’s t-test
Non-parametric	2	Wilcoxon signed-rank test
Robust	2	Yuen’s test on trimmed means for dependent samples
Bayes Factor	2	Student’s t-test

Following effect sizes (and confidence intervals/CI) are available for each type of test-

Type	No. of groups	Effect size	CI?	Function
Parametric	> 2	$\eta_{p}^2$ , $\omega_{p}^2$	Yes	`effectsize::omega_squared`, `effectsize::eta_squared`
Non-parametric	> 2	$W_{Kendall}$ (Kendall’s coefficient of concordance)	Yes	`rcompanion::kendallW`
Robust	> 2	No	No	`NA`
Bayes Factor	> 2	$R_{posterior}^2$	Yes	`performance::r2_bayes`
Parametric	2	Cohen’s d, Hedge’s g	Yes	`effectsize::cohens_d`, `effectsize::hedges_g`
Non-parametric	2	r (computed as $Z/\sqrt{N}$ )	Yes	`rcompanion::wilcoxonR`
Robust	2	$\delta_{R}$ (robust standardized difference)	Yes	`WRS2::dep.effect`
Bayes Factor	2	$\delta_{posterior}$	Yes	`bayestestR::describe_posterior`

Here is a summary of multiple pairwise comparison tests supported in ggwithinstats-

Type	Test	p-value adjustment?	Function
Parametric	Student’s t-test	Yes	`stats::pairwise.t.test`
Non-parametric	Durbin-Conover test	Yes	`PMCMRplus::durbinAllPairsTest`
Robust	Yuen’s trimmed means test	Yes	`WRS2::rmmcp`
Bayes Factor	Student’s t-test	`NA`	`BayesFactor::ttestBF`

For more, see the ggwithinstats vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggwithinstats.html

`ggscatterstats`

This function creates a scatterplot with marginal distributions overlaid on the axes (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"
)

The available marginal distributions are-

histograms
boxplots
density
violin
densigram (density + histogram)

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
  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 > 100, # expression that decides which points to label
  title = "Movie budget and IMDB rating (action)", # title text for the plot
  caption = expression(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 = "pink", # color fill for x-axis marginal distribution
  yfill = "#009E73" # color fill for y-axis marginal distribution
)

Additionally, there is also a grouped_ variant of this function that makes it easy to repeat the same operation across a single grouping variable. Also, note that, as opposed to the other functions, this function does not return a ggplot object and any modification you want to make can be made in advance using ggplot.component argument (available for all functions, but especially useful for this particular function):

# 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,
  grouping.var = genre, # grouping variable
  label.var = title,
  label.expression = length > 200,
  xlab = "IMDB rating",
  title.prefix = "Movie genre",
  ggtheme = ggplot2::theme_grey(),
  ggplot.component = list(
    ggplot2::scale_x_continuous(breaks = seq(2, 9, 1), limits = (c(2, 9)))
  ),
  plotgrid.args = list(nrow = 2),
  title.text = "Relationship between movie length by IMDB ratings for different genres"
)

Summary of tests

Following tests are carried out for each type of analyses. Additionally, the correlation coefficients (and their confidence intervals) are used as effect sizes-

Type	Test	CI?	Function
Parametric	Pearson’s correlation coefficient	Yes	`correlation::correlation`
Non-parametric	Spearman’s rank correlation coefficient	Yes	`correlation::correlation`
Robust	Percentage bend correlation coefficient	Yes	`correlation::correlation`
Bayes Factor	Pearson’s correlation coefficient	Yes	`correlation::correlation`

For more, see the ggscatterstats vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html

`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 correlation matrix plot
ggstatsplot::ggcorrmat(
  data = ggplot2::msleep,
  type = "robust", # correlation method
  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"
  ),
  colors = c("#B2182B", "white", "#4D4D4D"),
  title = "Correlalogram for mammals sleep dataset",
  subtitle = "sleep units: hours; weight units: kilograms",
  caption = "Source: `ggplot2` R package"
)

Two things to note:

If there are NAs present in the selected variables, the legend will display minimum, median, and maximum number of pairs used for correlation tests.
If cor.vars are not specified, all numeric variables will be used.

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_ggcorrmat(
  data = dplyr::filter(
    .data = ggstatsplot::movies_long,
    genre %in% c("Action", "Action Comedy", "Action Drama", "Comedy")
  ),
  cor.vars = length:votes,
  colors = c("#cbac43", "white", "#550000"),
  grouping.var = genre, # grouping variable
  matrix.type = "lower", # type of visualization matrix
  title.prefix = "Movie genre",
  plotgrid.args = list(nrow = 2)
)

You can also get a dataframe containing all relevant details from the statistical tests:

# setup
set.seed(123)

# dataframe in long format
ggcorrmat(
  data = ggplot2::msleep,
  type = "bayes",
  output = "dataframe"
)
#> # A tibble: 15 x 13
#>    parameter1  parameter2  estimate conf.low conf.high    pd rope.percentage
#>    <chr>       <chr>          <dbl>    <dbl>     <dbl> <dbl>           <dbl>
#>  1 sleep_total sleep_rem      0.731    0.617    0.810  1              0     
#>  2 sleep_total sleep_cycle   -0.432   -0.678   -0.223  0.995          0.0173
#>  3 sleep_total awake         -1.00    -1.00    -1.00   1              0     
#>  4 sleep_total brainwt       -0.339   -0.523   -0.156  0.996          0.028 
#>  5 sleep_total bodywt        -0.300   -0.458   -0.142  0.997          0.0292
#>  6 sleep_rem   sleep_cycle   -0.306   -0.535   -0.0555 0.965          0.091 
#>  7 sleep_rem   awake         -0.734   -0.824   -0.638  1              0     
#>  8 sleep_rem   brainwt       -0.202   -0.410    0.0130 0.927          0.212 
#>  9 sleep_rem   bodywt        -0.315   -0.481   -0.120  0.994          0.0362
#> 10 sleep_cycle awake          0.441    0.226    0.662  0.995          0.0158
#> 11 sleep_cycle brainwt        0.823    0.720    0.911  1              0     
#> 12 sleep_cycle bodywt         0.386    0.145    0.610  0.992          0.0392
#> 13 awake       brainwt        0.341    0.154    0.524  0.992          0.0253
#> 14 awake       bodywt         0.299    0.139    0.454  0.998          0.0265
#> 15 brainwt     bodywt         0.926    0.896    0.957  1              0     
#>    prior.distribution prior.location prior.scale bayes.factor method          
#>    <chr>                       <dbl>       <dbl>        <dbl> <chr>           
#>  1 cauchy                          0       0.707     3.00e+ 9 Bayesian Pearson
#>  2 cauchy                          0       0.707     8.85e+ 0 Bayesian Pearson
#>  3 cauchy                          0       0.707    NA        Bayesian Pearson
#>  4 cauchy                          0       0.707     7.29e+ 0 Bayesian Pearson
#>  5 cauchy                          0       0.707     9.28e+ 0 Bayesian Pearson
#>  6 cauchy                          0       0.707     1.42e+ 0 Bayesian Pearson
#>  7 cauchy                          0       0.707     3.01e+ 9 Bayesian Pearson
#>  8 cauchy                          0       0.707     6.54e- 1 Bayesian Pearson
#>  9 cauchy                          0       0.707     4.80e+ 0 Bayesian Pearson
#> 10 cauchy                          0       0.707     8.85e+ 0 Bayesian Pearson
#> 11 cauchy                          0       0.707     3.80e+ 6 Bayesian Pearson
#> 12 cauchy                          0       0.707     3.76e+ 0 Bayesian Pearson
#> 13 cauchy                          0       0.707     7.29e+ 0 Bayesian Pearson
#> 14 cauchy                          0       0.707     9.27e+ 0 Bayesian Pearson
#> 15 cauchy                          0       0.707     1.58e+22 Bayesian Pearson
#>    n.obs
#>    <int>
#>  1    61
#>  2    32
#>  3    83
#>  4    56
#>  5    83
#>  6    32
#>  7    61
#>  8    48
#>  9    61
#> 10    32
#> 11    30
#> 12    32
#> 13    56
#> 14    83
#> 15    56

Summary of tests

This is same as ggscatterstats.

For examples and more information, see the ggcorrmat vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcorrmat.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 chi-squared 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 (i.e., a chi-squared goodness of fit test) will be displayed as a subtitle.

To study an interaction between two categorical variables:

# for reproducibility
set.seed(123)

# plot
ggstatsplot::ggpiestats(
  data = mtcars,
  x = am,
  y = cyl,
  title = "Dataset: Motor Trend Car Road Tests", # title for the plot
  legend.title = "Transmission", # title for the legend
  caption = substitute(paste(italic("Source"), ": 1974 Motor Trend US magazine"))
)

In case of repeated measures designs, setting paired = TRUE will produce results from McNemar’s chi-squared test-

# for reproducibility
set.seed(123)

# data
df_paired <-
  data.frame(
    "before" = c("Approve", "Approve", "Disapprove", "Disapprove"),
    "after" = c("Approve", "Disapprove", "Approve", "Disapprove"),
    counts = c(794, 150, 86, 570),
    check.names = FALSE
  )

# plot
ggstatsplot::ggpiestats(
  data = df_paired,
  x = before,
  y = after,
  counts = counts,
  title = "Survey results before and after the intervention",
  label = "both",
  paired = TRUE, # within-subjects design
  package = "wesanderson",
  palette = "Royal1"
)

Additionally, there is also a grouped_ variant of this function that makes it easy to repeat the same operation across a single grouping variable. Following example is a case where the theoretical question is about proportions for different levels of a single nominal variable:

# for reproducibility
set.seed(123)

# plot
ggstatsplot::grouped_ggpiestats(
  data = ggstatsplot::movies_long,
  x = genre,
  grouping.var = mpaa, # grouping variable
  title.prefix = "Movie genre", # prefix for the faceted title
  label.repel = TRUE, # repel labels (helpful for overlapping labels)
  package = "ggsci", # package from which color palette is to be taken
  palette = "default_ucscgb", # choosing a different color palette
  title.text = "Composition of MPAA ratings for different genres"
)

Summary of tests

Following tests are carried out for each type of analyses-

Type of data	Design	Test	Function
Unpaired	$n \times p$ contingency table	Pearson’s $\chi^2$ test	`stats::chisq.test`
Paired	$n \times p$ contingency table	McNemar’s $\chi^2$ test	`stats::mcnemar.tests`
Frequency	$n \times 1$ contingency table	Goodness of fit ( $\chi^2$ test)	`stats::chisq.test`

Following effect sizes (and confidence intervals/CI) are available for each type of test-

Test	Effect size	CI?	Function
Pearson’s $\chi^2$ test	Cramer’s	Yes	`effectsize::cramers_v`
McNemar’s test	Cohen’s	Yes	`effectsize::cohens_g`
Goodness of fit	Cramer’s	Yes	`effectsize::cramers_v`

For more, see the ggpiestats vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggpiestats.html

`ggbarstats`

In case you are not a fan of pie charts (for very good reasons), you can alternatively use ggbarstats function which has a similar syntax-

# for reproducibility
set.seed(123)
library(ggplot2)

# plot
ggstatsplot::ggbarstats(
  data = ggstatsplot::movies_long,
  x = mpaa,
  y = genre,
  title = "MPAA Ratings by Genre",
  xlab = "movie genre",
  legend.title = "MPAA rating",
  ggtheme = hrbrthemes::theme_ipsum_pub(),
  ggplot.component = list(ggplot2::scale_x_discrete(guide = ggplot2::guide_axis(n.dodge = 2))),
  palette = "Set2"
)

(The p-values from one-sample proportion test are displayed on top of each bar.)

And, needless to say, there is also a grouped_ variant of this function-

# setup
set.seed(123)

# smaller dataset
df <-
  dplyr::filter(
    .data = forcats::gss_cat,
    race %in% c("Black", "White"),
    relig %in% c("Protestant", "Catholic", "None"),
    !partyid %in% c("No answer", "Don't know", "Other party")
  )

# plot
ggstatsplot::grouped_ggbarstats(
  data = df,
  x = relig,
  y = partyid,
  grouping.var = race,
  title.prefix = "Race",
  label = "both",
  xlab = "Party affiliation",
  package = "wesanderson",
  palette = "Darjeeling2",
  ggtheme = ggthemes::theme_tufte(base_size = 12),
  ggstatsplot.layer = FALSE,
  title.text = "Race, religion, and political affiliation",
  plotgrid.args = list(nrow = 2)
)

Summary of tests

This is identical to the ggpiestats function summary of tests.

`gghistostats`

To visualize the distribution of a single variable and check if its mean is significantly different from a specified value with a one-sample test, gghistostats can be used.

# for reproducibility
set.seed(123)

# plot
ggstatsplot::gghistostats(
  data = ggplot2::msleep, # dataframe from which variable is to be taken
  x = awake, # numeric variable whose distribution is of interest
  title = "Amount of time spent awake", # title for the plot
  caption = substitute(paste(italic("Source: "), "Mammalian sleep data set")),
  test.value = 12, # default value is 0
  test.value.line = TRUE, # display a vertical line at test value
  centrality.parameter = "median", # which measure of central tendency is to be plotted
  centrality.line.args = list(color = "darkred"), # aesthetics for central tendency line
  binwidth = 1, # binwidth value (experiment)
  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.

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_gghistostats(
  data = dplyr::filter(
    .data = ggstatsplot::movies_long,
    genre %in% c("Action", "Action Comedy", "Action Drama", "Comedy")
  ),
  x = budget,
  test.value = 50,
  xlab = "Movies budget (in million US$)",
  type = "nonparametric",
  grouping.var = genre, # grouping variable
  normal.curve = TRUE, # superimpose a normal distribution curve
  normal.curve.args = list(color = "red", size = 1),
  title.prefix = "Movie genre",
  ggtheme = ggthemes::theme_tufte(),
  # modify the defaults from `ggstatsplot` for each plot
  ggplot.component = ggplot2::scale_x_continuous(
    breaks = seq(0, 200, 50),
    limits = (c(0, 200))
  ),
  plotgrid.args = list(nrow = 2),
  title.text = "Movies budgets for different genres"
)

Summary of tests

Following tests are carried out for each type of analyses-

Type	Test	Function
Parametric	One-sample Student’s t-test	`stats::t.test`
Non-parametric	One-sample Wilcoxon test	`stats::wilcox.test`
Robust	One-sample percentile bootstrap	`WRS2::onesampb`
Bayes Factor	One-sample Student’s t-test	`BayesFactor::ttestBF`

Following effect sizes (and confidence intervals/CI) are available for each type of test-

Type	Effect size	CI?	Function
Parametric	Cohen’s d, Hedge’s g	Yes	`effectsize::cohens_d`, `effectsize::hedges_g`
Non-parametric	r	Yes	`rcompanion::wilcoxonOneSampleR`
Robust	robust location measure	Yes	`WRS2::onesampb`
Bayes Factor	$\delta_{posterior}$	Yes	`bayestestR::describe_posterior`

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 the 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,
  centrality.parameter = "median",
  centrality.k = 0,
  title = "Distribution of life expectancy in Asian continent",
  xlab = "Life expectancy",
  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 facilitate looping the same operation for all levels of a single grouping variable.

# for reproducibility
set.seed(123)

# plot
ggstatsplot::grouped_ggdotplotstats(
  data = dplyr::filter(.data = ggplot2::mpg, cyl %in% c("4", "6")),
  x = cty,
  y = manufacturer,
  xlab = "city miles per gallon",
  ylab = "car manufacturer",
  type = "nonparametric", # non-parametric test
  grouping.var = cyl, # grouping variable
  test.value = 15.5,
  test.value.line = TRUE,
  title.prefix = "cylinder count",
  point.args = list(color = "red", size = 5, shape = 13),
  title.text = "Fuel economy data"
)

Summary of tests

This is identical to summary of tests for gghistostats.

`ggcoefstats`

The function ggstatsplot::ggcoefstats generates dot-and-whisker plots for regression models saved in a tidy data frame. The tidy dataframes are prepared using parameters::model_parameters. Additionally, if available, the model summary indices are also extracted from performance::model_performance.

Although the statistical models displayed in the plot may differ based on the class of models being investigated, there are few aspects of the plot that will be invariant across models:

The dot-whisker plot contains a dot representing the estimate and their confidence intervals (95% is the default). The estimate can either be effect sizes (for tests that depend on the F statistic) or regression coefficients (for tests with t and z statistic), etc. The function will, by default, display a helpful x-axis label that should clear up what estimates are being displayed. The confidence intervals can sometimes be asymmetric if bootstrapping was used.
The caption will always contain diagnostic information, if available, about models that can be useful for model selection: The smaller the Akaike’s Information Criterion (AIC) and the Bayesian Information Criterion (BIC) values, the “better” the model is.
The output of this function will be a ggplot2 object and, thus, it can be further modified (e.g., change themes, etc.) with ggplot2 functions.

# for reproducibility
set.seed(123)

# model
mod <- stats::lm(formula = mpg ~ am * cyl, data = mtcars)

# plot
ggstatsplot::ggcoefstats(mod)

This default plot can be further modified to one’s liking with additional arguments (also, let’s use a different model now):

# for reproducibility
set.seed(123)

# model
mod <- MASS::rlm(formula = mpg ~ am * cyl, data = mtcars)

# plot
ggstatsplot::ggcoefstats(
  x = mod,
  point.args = list(color = "red", size = 3, shape = 15),
  vline.args = list(size = 1, color = "#CC79A7", linetype = "dotdash"),
  title = "Car performance predicted by transmission & cylinder count",
  subtitle = "Source: 1974 Motor Trend US magazine",
  ggtheme = hrbrthemes::theme_ipsum_ps(),
  ggstatsplot.layer = FALSE
) + # 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)

Supported models

Most of the regression models that are supported in the underlying packages are also supported by ggcoefstats. For example-

aareg, anova, aov, aovlist, Arima, bam, bayesx, bayesGARCH, BBmm, BBreg, bcplm, betamfx, betaor, BFBayesFactor, bglmerMod, bife, bigglm, biglm, blavaan, bmlm, blmerMod, bracl, brglm, brglm2, brmsfit, brmultinom, btergm, cch, censReg, cgam, cgamm, cglm, clm, clm2, clmm, clmm2, coeftest, complmrob, confusionMatrix, coxme, coxph, coxph.penal, cpglm, cpglmm, crch, crq, DirichReg, drc, emmGrid, epi.2by2, ergm, feis, felm, fitdistr, flexsurvreg, gam, Gam, gamlss, garch, geeglm, glmc, glmerMod, glmmTMB, gls, glht, glm, glmm, glmmadmb, glmmPQL, glmRob, glmrob, glmx, gmm, HLfit, hurdle, ivreg, iv_robust, lavaan, lm, lm.beta, lmerMod, lmerModLmerTest, lmodel2, lmRob, lmrob, lm_robust, logitmfx, logitor, logitsf, LORgee, lqm, lqmm, lrm, manova, maov, margins, mcmc, mcmc.list, MCMCglmm, mclogit, mice, mmclogit, mediate, metafor, merMod, merModList, metaplus, mixor, mjoint, mle2, mlm, multinom, negbin, negbinmfx, negbinirr, nlmerMod, nlrq, nlreg, nls, orcutt, orm, plm, poissonmfx, poissonirr, polr, ridgelm, rjags, rlm, rlmerMod, robmixglm, rq, rqss, rrvglm, scam, semLm, semLme, slm, speedglm, speedlm, stanfit, stanreg, survreg, svyglm, svyolr, svyglm, tobit, truncreg, vgam, vglm, wbgee, wblm, zeroinfl, etc.

Although not shown here, this function can also be used to carry out both frequentist, robust, and Bayesian random-effects meta-analysis.

Summary of meta-analysis tests

Type	Test	Effect size	95% CI available?	Function
Parametric	Meta-analysis via random-effects models	$\beta$	Yes	`metafor::metafor`
Robust	Meta-analysis via robust random-effects models	$\beta$	Yes	`metaplus::metaplus`
Bayes	Meta-analysis via robust random-effects models	$\beta$	Yes	`metaBMA::meta_random`

For a more exhaustive account of this function, 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 😻. (Another old school option to do this effectively is using the plyr package.)

In such cases, ggstatsplot contains a helper function combine_plots to combine multiple plots, which can be useful for combining a list of plots produced with purrr. This is a wrapper around cowplot::plot_grid and lets you combine multiple plots and add a combination of title, caption, and annotation texts with suitable defaults.

For examples (both with plyr and purrr), see the associated vignette- https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/combine_plots.html

Using `ggstatsplot` statistical details with custom plots

Sometimes you may not like the default plots produced by ggstatsplot. In such cases, you can use other custom plots (from ggplot2 or other plotting packages) and still use ggstatsplot functions to display results from relevant statistical test.

For example, in the following chunk, we will create plot (ridgeplot) using ggridges package and use ggstatsplot function for extracting results.

# loading the needed libraries
set.seed(123)
library(ggridges)
library(ggplot2)
library(ggstatsplot)

# using `ggstatsplot` to get call with statistical results
stats_results <-
  ggstatsplot::ggbetweenstats(
    data = morley,
    x = Expt,
    y = Speed,
    output = "subtitle"
  )

# using `ggridges` to create plot
ggplot(morley, aes(x = Speed, y = as.factor(Expt), fill = as.factor(Expt))) +
  geom_density_ridges(
    jittered_points = TRUE,
    quantile_lines = TRUE,
    scale = 0.9,
    alpha = 0.7,
    vline_size = 1,
    vline_color = "red",
    point_size = 0.4,
    point_alpha = 1,
    position = position_raincloud(adjust_vlines = TRUE)
  ) + # adding annotations
  labs(
    title = "Michelson-Morley experiments",
    subtitle = stats_results,
    x = "Speed of light",
    y = "Experiment number"
  ) + # remove the legend
  theme(legend.position = "none")

Usage and syntax simplicity

As seen from these examples, ggstatsplot relies on non-standard evaluation (NSE) - implemented via rlang - i.e., rather than looking at the values of arguments (x, y), it instead looks at their expressions. Therefore, the syntax is simpler and follows the following principles-

When a given function depends on variables in a dataframe, data argument must always be specified.
The $ operator cannot be used to specify variables in a dataframe.
All functions accept both string (x = "var1") and symbol (x = var1) arguments.

These set principles combined with the fact that almost all functions produce publication-ready plots that require very few arguments if one finds the aesthetic and statistical defaults satisfying make the syntax much less cognitively demanding and easy to remember/reconstruct.

Most functions share a type (of test) argument that is helpful to specify the type of statistical analysis:

"p" (for parametric)
"np" (for non-parametric)
"r" (for robust)
"bf" (for Bayes Factor)

All relevant functions in ggstatsplot have a output argument which can be used to not only return plots (which is the default), but also to return a subtitle or caption, which are objects of type call and can be used to display statistical details in conjunction with a custom plot and at a custom location in the plot.

Additionally, all functions share the ggtheme and palette arguments that can be used to specify your favorite ggplot theme and color palette.

`ggstatsverse`: Components of `ggstatsplot`

To make the maintenance and development of ggstatsplot more manageable, it is being broken into smaller pieces. Currently, the package internally relies on the following packages that manage different aspects of statistical analyses:

`statsExpressions`

The statsExpressions package forms the statistical backend that processes data and creates expressions containing results from statistical tests and are by default displayed in as plot subtitle.

For more exhaustive documentation for this package, see: https://indrajeetpatil.github.io/statsExpressions/

`tidyBF`

The tidyBF package forms the backend that processes data and creates expressions containing results from Bayes Factor tests and are by default displayed in as plot caption.

For more exhaustive documentation for this package, see: https://indrajeetpatil.github.io/tidyBF/

`pairwiseComparisons`

The pairwiseComparisons package forms the pairwise comparison backend for creating results that are used to display post hoc multiple comparisons displayed in ggbetweenstats and ggwithinstats functions.

For more exhaustive documentation for this package, see: https://indrajeetpatil.github.io/pairwiseComparisons/

`ipmisc`

The ipmisc package contains some of the data wrangling/cleaning functions and a few other miscellaneous functions.

For more exhaustive documentation for this package, see: https://indrajeetpatil.github.io/ipmisc/

Extensions

In case you use the GUI software jamovi, you can install a module called jjstatsplot, which is a wrapper around ggstatsplot.

Acknowledgments

I would like to thank all the contributors to ggstatsplot who pointed out bugs or requested features I hadn’t considered. I would especially like to thank other package developers (especially Daniel Lüdecke, Dominique Makowski, Mattan S. Ben-Shachar, Patrick Mair, Salvatore Mangiafico, etc.) who have patiently and diligently answered my relentless number of questions and added feature requests I wanted. I also want to thank Chuck Powell for his initial contributions to the package.

The hexsticker was generously designed by Sarah Otterstetter (Max Planck Institute for Human Development, Berlin). This package has also benefited from the larger rstats community on Twitter and StackOverflow.

Thanks are also due to my postdoc advisers (Mina Cikara and Fiery Cushman at Harvard University; Iyad Rahwan at Max Planck Institute for Human Development) who patiently supported me spending hundreds of hours working on this package rather than what I was paid to do. 😄

Code coverage

As the code stands right now, here is the code coverage for all primary functions involved: https://codecov.io/gh/IndrajeetPatil/ggstatsplot/tree/master/R

Contributing

I’m happy to receive bug reports, suggestions, questions, and (most of all) contributions to fix problems and add features. I personally prefer using the GitHub issues system over trying to reach out to me in other ways (personal e-mail, Twitter, etc.). Pull Requests for contributions are encouraged.

Here are some simple ways in which you can contribute (in the increasing order of commitment):

Read and correct any inconsistencies in the documentation
Raise issues about bugs or wanted features
Review code
Add new functionality (in the form of new plotting functions or helpers for preparing subtitles)

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Session Information

For reproducibility purposes, the details about the session information in which this document was rendered, see- https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/session_info.html

andersonjaraujo / ggstatsplot Goto Github PK

ggstatsplot's Introduction

ggstatsplot: ggplot2 Based Plots with Statistical Details

Raison d’être

Summary of available plots

Summary of types of statistical analyses

Statistical reporting

Summary of statistical tests and effect sizes

Installation

Citation

Documentation and Examples

Primary functions

ggbetweenstats

Summary of tests

ggwithinstats

Summary of tests

ggscatterstats

Summary of tests

ggcorrmat

Summary of tests

ggpiestats

Summary of tests

ggbarstats

Summary of tests

gghistostats

Summary of tests

ggdotplotstats

Summary of tests

ggcoefstats

Supported models

Summary of meta-analysis tests

combine_plots

Using ggstatsplot statistical details with custom plots

Usage and syntax simplicity

ggstatsverse: Components of ggstatsplot

statsExpressions

tidyBF

pairwiseComparisons

ipmisc

Extensions

Acknowledgments

Code coverage

Contributing

Session Information

ggstatsplot's People

Contributors

Recommend Projects

Recommend Topics

Recommend Org

`ggstatsplot`: `ggplot2` Based Plots with Statistical Details

`ggbetweenstats`

`ggwithinstats`

`ggscatterstats`

`ggcorrmat`

`ggpiestats`

`ggbarstats`

`gghistostats`

`ggdotplotstats`

`ggcoefstats`

`combine_plots`

Using `ggstatsplot` statistical details with custom plots

`ggstatsverse`: Components of `ggstatsplot`

`statsExpressions`

`tidyBF`

`pairwiseComparisons`

`ipmisc`