Stacked bar charts with statistical tests

Bar charts for categorical data with statistical details included in the plot as a subtitle.

Usage

ggbarstats(
  data,
  x,
  y = NULL,
  counts = NULL,
  type = "parametric",
  paired = FALSE,
  results.subtitle = TRUE,
  label = "percentage",
  label.args = list(alpha = 1, fill = "white"),
  sample.size.label.args = list(size = 4),
  digits = 2L,
  proportion.test = results.subtitle,
  digits.perc = 0L,
  bf.message = TRUE,
  ratio = NULL,
  alternative = "two.sided",
  conf.level = 0.95,
  p.adjust.method = "holm",
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  legend.title = NULL,
  xlab = NULL,
  ylab = NULL,
  ggtheme = ggstatsplot::theme_ggstatsplot(),
  palette = "ggthemes::gdoc",
  ggplot.component = NULL,
  ...
)

Arguments

data

A data frame (or a tibble) from which variables specified are to be taken. Other data types (e.g., matrix,table, array, etc.) will not be accepted. Additionally, grouped data frames from {dplyr} should be ungrouped before they are entered as data.

x

The variable to use as the rows in the contingency table. Please note that if there are empty factor levels in your variable, they will be dropped.

y

The variable to use as the columns in the contingency table. Please note that if there are empty factor levels in your variable, they will be dropped. Default is NULL. If NULL, one-sample proportion test (a goodness of fit test) will be run for the x variable. Otherwise an appropriate association test will be run.

counts

The variable in data containing counts, or NULL if each row represents a single observation.

type

A character specifying the type of statistical approach:

• "parametric"

• "nonparametric"

• "robust"

• "bayes"

You can specify just the initial letter.

paired

Logical indicating whether data came from a within-subjects or repeated measures design study (Default: FALSE).

results.subtitle

Decides whether the results of statistical tests are to be displayed as a subtitle (Default: TRUE). If set to FALSE, only the plot will be returned.

label

Character decides what information needs to be displayed on the label in each pie slice. Possible options are "percentage" (default), "counts", "both".

label.args

Additional aesthetic arguments that will be passed to ggplot2::geom_label().

sample.size.label.args

Additional aesthetic arguments that will be passed to ggplot2::geom_text().

digits

Number of digits for rounding or significant figures. May also be "signif" to return significant figures or "scientific" to return scientific notation. Control the number of digits by adding the value as suffix, e.g. digits = "scientific4" to have scientific notation with 4 decimal places, or digits = "signif5" for 5 significant figures (see also signif()).

proportion.test

Decides whether proportion test for x variable is to be carried out for each level of y. Defaults to results.subtitle. In ggbarstats(), only p-values from this test will be displayed.

digits.perc

Numeric that decides number of decimal places for percentage labels (Default: 0L).

bf.message

Logical that decides whether to display Bayes Factor in favor of the null hypothesis. This argument is relevant only for parametric test (Default: TRUE).

ratio

A vector of proportions: the expected proportions for the proportion test (should sum to 1). Default is NULL, which means the null is equal theoretical proportions across the levels of the nominal variable. E.g., ratio = c(0.5, 0.5) for two levels, ratio = c(0.25, 0.25, 0.25, 0.25) for four levels, etc.

alternative

a character string specifying the alternative hypothesis, must be one of "two.sided" (default), "greater" or "less". You can specify just the initial letter.

conf.level

Scalar between 0 and 1 (default: 95% confidence/credible intervals, 0.95). If NULL, no confidence intervals will be computed.

p.adjust.method

Adjustment method for p-values for multiple comparisons. Possible methods are: "holm" (default), "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none".

title

The text for the plot title.

subtitle

The text for the plot subtitle. Will work only if results.subtitle = FALSE.

caption

The text for the plot caption. This argument is relevant only if bf.message = FALSE.

legend.title

Title text for the legend.

xlab

Label for x axis variable. If NULL (default), variable name for x will be used.

ylab

Labels for y axis variable. If NULL (default), variable name for y will be used.

ggtheme

A {ggplot2} theme. Default value is theme_ggstatsplot(). Any of the {ggplot2} themes (e.g., ggplot2::theme_bw()), or themes from extension packages are allowed (e.g., ggthemes::theme_fivethirtyeight(), hrbrthemes::theme_ipsum_ps(), etc.). But note that sometimes these themes will remove some of the details that {ggstatsplot} plots typically contains. For example, if relevant, ggbetweenstats() shows details about multiple comparison test as a label on the secondary Y-axis. Some themes (e.g. ggthemes::theme_fivethirtyeight()) will remove the secondary Y-axis and thus the details as well.

palette

Name of the palette in "package::palette" format to be used for coloring. Passed to paletteer::scale_color_paletteer_d(). Run View(paletteer::palettes_d_names) to see all available options.

ggplot.component

A ggplot component to be added to the plot prepared by {ggstatsplot}. This argument is primarily helpful for grouped_ variants of all primary functions. Default is NULL. The argument should be entered as a {ggplot2} function or a list of {ggplot2} functions.

...

Currently ignored.

Details

For details, see: https://www.indrapatil.com/ggstatsplot/articles/web_only/ggpiestats.html

Summary of graphics

graphical element	geom used	argument for further modification
bars	ggplot2::geom_bar()	NA
descriptive labels	ggplot2::geom_label()	label.args
sample size labels	ggplot2::geom_text()	sample.size.label.args

Contingency table analyses

The table below provides summary about:

• statistical test carried out for inferential statistics

• type of effect size estimate and a measure of uncertainty for this estimate

• functions used internally to compute these details

two-way table

Hypothesis testing

Type	Design	Test	Function used
Parametric/Non-parametric	Unpaired	Pearson's chi-squared test	stats::chisq.test()
Bayesian	Unpaired	Bayesian Pearson's chi-squared test	BayesFactor::contingencyTableBF()
Parametric/Non-parametric	Paired	McNemar's chi-squared test	stats::mcnemar.test()
Bayesian	Paired	No	No

Effect size estimation

Type	Design	Effect size	CI available?	Function used
Parametric/Non-parametric	Unpaired	Cramer's V	Yes	effectsize::cramers_v()
Bayesian	Unpaired	Cramer's V	Yes	effectsize::cramers_v()
Parametric/Non-parametric	Paired	Cohen's g	Yes	effectsize::cohens_g()
Bayesian	Paired	No	No	No

one-way table

Hypothesis testing

Type	Test	Function used
Parametric/Non-parametric	Goodness of fit chi-squared test	stats::chisq.test()
Bayesian	Bayesian Goodness of fit chi-squared test	(custom)

Effect size estimation

Type	Effect size	CI available?	Function used
Parametric/Non-parametric	Pearson's C	Yes	effectsize::pearsons_c()
Bayesian	No	No	No

Pairwise comparisons

When there is a two-way table and x has more than two levels, pairwise contingency table analyses (Fisher's exact tests) are computed using statsExpressions::pairwise_contingency_table(). These pairwise results are not displayed in the plot because bar and pie charts lack a natural visual representation for pairwise significance annotations (unlike box/violin plots, which use bracket annotations). Additionally, there is no established convention for overlaying pairwise comparisons on pie charts, and both ggpiestats() and ggbarstats() are designed to remain visually congruent. The pairwise results are available as a data frame via extract_stats(plot)$pairwise_comparisons_data.

See also

grouped_ggbarstats, ggpiestats, grouped_ggpiestats

Examples

# for reproducibility
set.seed(123)

# one sample goodness of fit proportion test
p <- ggbarstats(mtcars, vs)

# looking at the plot
p


# extracting details from statistical tests
extract_stats(p)
#> $subtitle_data
#> # A tibble: 1 × 13
#>   statistic    df p.value method                                   effectsize 
#>       <dbl> <dbl>   <dbl> <chr>                                    <chr>      
#> 1       0.5     1   0.480 Chi-squared test for given probabilities Pearson's C
#>   estimate conf.level conf.low conf.high conf.method conf.distribution n.obs
#>      <dbl>      <dbl>    <dbl>     <dbl> <chr>       <chr>             <int>
#> 1    0.124       0.95        0     0.426 ncp         chisq                32
#>   expression
#>   <list>    
#> 1 <language>
#> 
#> $caption_data
#> # A tibble: 1 × 4
#>    bf10 prior.scale method                                      expression
#>   <dbl>       <dbl> <chr>                                       <list>    
#> 1 0.180           1 Bayesian one-way contingency table analysis <language>
#> 
#> $pairwise_comparisons_data
#> NULL
#> 
#> $descriptive_data
#> # A tibble: 2 × 4
#>   vs    counts  perc .label
#>   <fct>  <int> <dbl> <chr> 
#> 1 0         18  56.2 56%   
#> 2 1         14  43.8 44%   
#> 
#> $one_sample_data
#> NULL
#> 
#> $tidy_data
#> NULL
#> 
#> $glance_data
#> NULL
#> 
#> attr(,"class")
#> [1] "ggstatsplot_stats" "list"             

# association test (or contingency table analysis)
ggbarstats(mtcars, vs, cyl)


# with 3+ x levels, pairwise comparisons are available
ggbarstats(mtcars, cyl, am)


# Bayesian test
ggbarstats(mtcars, vs, cyl, type = "bayes")


# using pre-aggregated data with counts
ggbarstats(as.data.frame(Titanic), x = Survived, y = Sex, counts = Freq)