ggstatsplot v0.0.7

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'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

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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 (0.0.7):

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

You can get the development version of the package from GitHub (0.0.7.9000). 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:

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 = NULL, point.height.jitter = NULL, 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, 
#>     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: 0x0000000029fea220>
#> <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:

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 = datasets::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 = datasets::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("Animation", "Documentary")),
  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/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("Animation", "Documentary")), 
  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/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 = datasets::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/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 = datasets::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 = datasets::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.

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("Animation", "Documentary")), 
  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/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 faciliate to 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: In the correlation matrix,
#> the upper triangle: p-values adjusted for multiple comparisons
#> the lower triangle: unadjusted p-values.

Note that if there are NAs 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 = datasets::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"
)
#> Note: In the correlation matrix,
#> the upper triangle: p-values adjusted for multiple comparisons
#> the lower triangle: unadjusted p-values.
#> # 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"
)
#> # 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

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
# 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/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 = datasets::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 = datasets::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/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_extractor Convenience function to extract bayes factors and details about posterior (mean, median, HDI, etc.) from BayesFactor model object.
chisq_v_ci Chi-squared test of association with confidence interval for effect size (Cramer's V).
bartlett_message Display homogeneity of variance test as a message
Titanic_full Titanic dataset.
effsize_ci_message Message to display when bootstrapped confidence intervals are shown for effect size measure.
ggcorrmat Visualization of a correlalogram (or correlation matrix)
ggcoefstats_label_maker Create labels with statistical details for ggcoefstats.
ggstatsplot-package ggstatsplot: 'ggplot2' Based Plots with Statistical Details
gghistostats Histogram for distribution of a numeric variable
effsize_type_switch Switch function to determine which effect size is to computed.
grouped_ggbetweenstats Violin plots for group or condition comparisons in between-subjects designs repeated across all levels of a grouping variable.
ggpiestats Pie charts with statistical tests
games_howell Games-Howell post-hoc test
histo_labeller Custom function for adding labelled lines for x-axis variable.
grouped_ggscatterstats Scatterplot with marginal distributions for all levels of a grouping variable
intent_morality Moral judgments about third-party moral behavior.
numdf_summary Compute minimum, maximum, and median across all numeric columns in a dataframe.
grouped_message grouped_message
ggbetweenstats Box/Violin plots for group or condition comparisons in between-subjects designs.
ggcorrmat_matrix_message Message to display when adjusted p-values are displayed in correlation matrix.
palette_message Message if palette doesn't have enough number of colors.
reexports Objects exported from other packages
bf_oneway_anova Bayesian one-way analysis of variance.
ggdotplotstats Dot plot/chart for labeled numeric data.
bf_contingency_tab Bayesian contingency table analysis.
iris_long Edgar Anderson's Iris Data in long format.
kw_eta_h_ci Confidence interval for effect size for Kruskal-Wallis test.
bf_corr_test Bayesian correlation test.
bf_two_sample_ttest Bayesian two-samples t-test.
movies_wide Movie information and user ratings from IMDB.com (wide format).
normality_message Display normality test result as a message.
combine_plots Combining and arranging multiple plots in a grid
grouped_ggdotplotstats Grouped histograms for distribution of a labelled numeric variable
grouped_gghistostats Grouped histograms for distribution of a numeric variable
mean_labeller Create a dataframe with mean per group and a formatted label for display in ggbetweenstats plot.
cor_test_ci A correlation test with confidence interval for effect size.
ggbetweenstats_switch Switch function to use helper function to create subtitle for the ggbetweenstats plot.
grouped_ggpiestats Grouped pie charts with statistical tests
grouped_ggcorrmat Visualization of a correlalogram (or correlation matrix) for all levels of a grouping variable
movies_long Movie information and user ratings from IMDB.com (long format).
subtitle_mann_nonparametric Making text subtitle for the Mann-Whitney U-test (between-/within-subjects designs).
subtitle_anova_parametric Making text subtitle for the between-subject anova designs.
subtitle_anova_robust Making text subtitle for the robust ANOVA (between-subjects designs).
robcor_ci Robust correlation coefficient and its confidence interval
p.adjust.method.description Preparing text to describe which p-value adjustment method was used.
subtitle_anova_bayes Making text subtitle for the between-subject one-way anova designs.
subtitle_onesample_proptest Making text subtitle for Proportion Test (N Outcomes), a chi-squared Goodness of fit test.
theme_corrmat Default theme used for correlation matrix
theme_ggstatsplot Default theme used in all ggstatsplot package plots
subtitle_t_bayes Making text subtitle for the bayesian t-test.
t1way_ci A heteroscedastic one-way ANOVA for trimmed means with confidence interval for effect size.
subtitle_ggscatterstats Making text subtitle for the correlation test.
tfz_labeller Prepare labels with statistic for ggcoefstats function.
subtitle_kw_nonparametric Making text subtitle for the Kruskal-Wallis test (nonparametric ANOVA) (between-subjects designs).
yuend_ci Paired samples robust t-tests with confidence interval for effect size.
theme_pie Default theme used for pie chart
tibble Anticipate use of tibbles
ggcoefstats Model coefficients for fitted models with the model summary as a caption.
ggscatterstats Scatterplot with marginal distributions
subtitle_t_onesample Making text subtitle for one sample t-test and its nonparametric and robust equivalents.
ggsignif_position_calculator Calculating y coordinates for the ggsignif comparison bars.
lm_effsize_standardizer Standardize a dataframe with effect sizes for aov, lm, aovlist, etc. objects.
long_to_wide_converter Converts long-format dataframe to wide-format dataframe
pairwise_p Pairwise comparison tests
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)
pairwise_p_caption Preparing caption in case pairwise comparisons are displayed.
subtitle_friedman_nonparametric Making text subtitle for the Friedman Rank Sum Test (nonparametric ANOVA) (within-subjects designs).
subtitle_t_parametric Making text subtitle for the t-test (between-/within-subjects designs).
subtitle_t_robust Making text subtitle for the robust t-test (between- and within-subjects designs).
check_outlier Finding the outliers in the dataframe using Tukey's interquartile range rule
bf_one_sample_ttest Bayesian one-sample t-test.
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Vignettes of ggstatsplot

Name
web_only/combine_plots.Rmd
web_only/gallery.Rmd
web_only/ggbetweenstats.Rmd
web_only/ggcorrmat.Rmd
web_only/gghistostats.Rmd
web_only/ggpiestats.Rmd
web_only/ggscatterstats.Rmd
web_only/ggstatsplot_paper.Rmd
web_only/session_info.Rmd
web_only/theme_ggstatsplot.Rmd
additional.Rmd
ggcoefstats.Rmd
purrr_examples.Rmd
tests_and_coverage.Rmd
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