| Status | Usage | Miscellaneous |
|---|---|---|
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“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.
| Type | Command |
|---|---|
| Release | install.packages("ggstatsplot") |
| Development | pak::pak("IndrajeetPatil/ggstatsplot") |
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")
To cite package 'ggstatsplot' in publications use:
Patil, I. (2021). Visualizations with statistical details: The
'ggstatsplot' approach. Journal of Open Source Software, 6(61), 3167,
doi:10.21105/joss.03167
A BibTeX entry for LaTeX users is
@Article{,
doi = {10.21105/joss.03167},
url = {https://doi.org/10.21105/joss.03167},
year = {2021},
publisher = {{The Open Journal}},
volume = {6},
number = {61},
pages = {3167},
author = {Indrajeet Patil},
title = {{Visualizations with statistical details: The {'ggstatsplot'} approach}},
journal = {{Journal of Open Source Software}},
}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, Brenton Wiernik,
Patrick Mair, Salvatore Mangiafico, etc.) who have patiently and
diligently answered my relentless questions and supported feature
requests in their projects. 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, LinkedIn, 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. 😁
To see the detailed documentation for each function in the stable CRAN version of the package, see:
| 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 |
ggscatterstats() |
scatterplots | for correlation between two variables |
ggcorrmat() |
correlation matrices | for correlations between multiple variables |
ggpiestats() |
pie charts | for categorical data |
ggbarstats() |
bar charts | for categorical data |
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.
The table below summarizes all the different types of analyses currently supported in this package-
| Functions | Description | Parametric | Non-parametric | Robust | Bayesian |
|---|---|---|---|---|---|
ggbetweenstats() |
Between group/condition comparisons | ✅ | ✅ | ✅ | ✅ |
ggwithinstats() |
Within group/condition comparisons | ✅ | ✅ | ✅ | ✅ |
gghistostats(), ggdotplotstats() |
Distribution of a numeric variable | ✅ | ✅ | ✅ | ✅ |
ggcorrmat |
Correlation matrix | ✅ | ✅ | ✅ | ✅ |
ggscatterstats() |
Correlation between two variables | ✅ | ✅ | ✅ | ✅ |
ggpiestats(), ggbarstats() |
Association between categorical variables | ✅ | ✅ | ❌ | ✅ |
ggpiestats(), ggbarstats() |
Equal proportions for categorical variable levels | ✅ | ✅ | ❌ | ✅ |
ggcoefstats() |
Regression model coefficients | ✅ | ✅ | ✅ | ✅ |
ggcoefstats() |
Random-effects meta-analysis | ✅ | ❌ | ✅ | ✅ |
Summary of Bayesian analysis
| Analysis | Hypothesis testing | Estimation |
|---|---|---|
| (one/two-sample) t-test | ✅ | ✅ |
| one-way ANOVA | ✅ | ✅ |
| correlation | ✅ | ✅ |
| (one/two-way) contingency table | ✅ | ✅ |
| random-effects meta-analysis | ✅ | ✅ |
For all statistical tests reported in the plots, the default template abides by the gold standard for statistical reporting. For example, here are results from Yuen’s test for trimmed means (robust t-test):
Statistical analysis is carried out by {statsExpressions} package, and
thus a summary table of all the statistical tests currently supported
across various functions can be found in article for that package:
https://indrajeetpatil.github.io/statsExpressions/articles/stats_details.html
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-
set.seed(123)
ggbetweenstats(
data = iris,
x = Species,
y = Sepal.Length,
title = "Distribution of sepal length across Iris species"
)
Defaults return
✅ raw data + distributions
✅ descriptive statistics
✅
inferential statistics
✅ effect size + CIs
✅ pairwise
comparisons
✅ Bayesian hypothesis-testing
✅ Bayesian
estimation
A number of other arguments can be specified to make this plot even more
informative or change some of the default options. Additionally, there
is also a grouped_ variant of this function that makes it easy to
repeat the same operation across a single grouping variable:
set.seed(123)
grouped_ggbetweenstats(
data = dplyr::filter(movies_long, genre %in% c("Action", "Comedy")),
x = mpaa,
y = length,
grouping.var = genre,
ggsignif.args = list(textsize = 4, tip_length = 0.01),
p.adjust.method = "bonferroni",
palette = "default_jama",
package = "ggsci",
plotgrid.args = list(nrow = 1),
annotation.args = list(title = "Differences in movie length by mpaa ratings for different genres")
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggbetweenstats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggbetweenstats.html
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.
set.seed(123)
library(WRS2) ## for data
library(afex) ## to run ANOVA
ggwithinstats(
data = WineTasting,
x = Wine,
y = Taste,
title = "Wine tasting"
)
Defaults return
✅ raw data + distributions
✅ descriptive statistics
✅
inferential statistics
✅ effect size + CIs
✅ pairwise
comparisons
✅ Bayesian hypothesis-testing
✅ Bayesian
estimation
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-
set.seed(123)
grouped_ggwithinstats(
data = dplyr::filter(bugs_long, region %in% c("Europe", "North America"), condition %in% c("LDLF", "LDHF")),
x = condition,
y = desire,
type = "np",
xlab = "Condition",
ylab = "Desire to kill an artrhopod",
grouping.var = region
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggwithinstats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggwithinstats.html
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.
set.seed(123)
gghistostats(
data = ggplot2::msleep,
x = awake,
title = "Amount of time spent awake",
test.value = 12,
binwidth = 1
)
Defaults return
✅ counts + proportion for bins
✅ descriptive statistics
✅
inferential statistics
✅ effect size + CIs
✅ Bayesian
hypothesis-testing
✅ Bayesian estimation
There is also a grouped_ variant of this function that makes it easy
to repeat the same operation across a single grouping variable:
set.seed(123)
grouped_gghistostats(
data = dplyr::filter(movies_long, genre %in% c("Action", "Comedy")),
x = budget,
test.value = 50,
type = "nonparametric",
xlab = "Movies budget (in million US$)",
grouping.var = genre,
ggtheme = ggthemes::theme_tufte(),
## modify the defaults from `{ggstatsplot}` for each plot
plotgrid.args = list(nrow = 1),
annotation.args = list(title = "Movies budgets for different genres")
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/gghistostats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/gghistostats.html
This function is similar to gghistostats(), but is intended to be used
when the numeric variable also has a label.
set.seed(123)
ggdotplotstats(
data = dplyr::filter(gapminder::gapminder, continent == "Asia"),
y = country,
x = lifeExp,
test.value = 55,
type = "robust",
title = "Distribution of life expectancy in Asian continent",
xlab = "Life expectancy"
)
Defaults return
✅ descriptives (mean + sample size)
✅ inferential statistics
✅ effect size + CIs
✅ Bayesian hypothesis-testing
✅
Bayesian estimation
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.
set.seed(123)
grouped_ggdotplotstats(
data = dplyr::filter(ggplot2::mpg, cyl %in% c("4", "6")),
x = cty,
y = manufacturer,
type = "bayes",
xlab = "city miles per gallon",
ylab = "car manufacturer",
grouping.var = cyl,
test.value = 15.5,
point.args = list(color = "red", size = 5, shape = 13),
annotation.args = list(title = "Fuel economy data")
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggdotplotstats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggdotplotstats.html
This function creates a scatterplot with marginal distributions overlaid on the axes and results from statistical tests in the subtitle:
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"
)
Defaults return
✅ raw data + distributions
✅ marginal distributions
✅
inferential statistics
✅ effect size + CIs
✅ Bayesian
hypothesis-testing
✅ Bayesian estimation
There is also a grouped_ variant of this function that makes it easy
to repeat the same operation across a single grouping variable.
set.seed(123)
grouped_ggscatterstats(
data = dplyr::filter(movies_long, genre %in% c("Action", "Comedy")),
x = rating,
y = length,
grouping.var = genre,
label.var = title,
label.expression = length > 200,
xlab = "IMDB rating",
ggtheme = ggplot2::theme_grey(),
ggplot.component = list(ggplot2::scale_x_continuous(breaks = seq(2, 9, 1), limits = (c(2, 9)))),
plotgrid.args = list(nrow = 1),
annotation.args = list(title = "Relationship between movie length and IMDB ratings")
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggscatterstats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggscatterstats.html
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.
set.seed(123)
## as a default this function outputs a correlation matrix plot
ggcorrmat(
data = ggplot2::msleep,
colors = c("#B2182B", "white", "#4D4D4D"),
title = "Correlalogram for mammals sleep dataset",
subtitle = "sleep units: hours; weight units: kilograms"
)
Defaults return
✅ effect size + significance
✅ careful handling of NAs
If there are NAs present in the selected variables, the legend will
display minimum, median, and maximum number of pairs used for
correlation tests.
There is also a grouped_ variant of this function that makes it easy
to repeat the same operation across a single grouping variable:
set.seed(123)
grouped_ggcorrmat(
data = dplyr::filter(movies_long, genre %in% c("Action", "Comedy")),
type = "robust",
colors = c("#cbac43", "white", "#550000"),
grouping.var = genre,
matrix.type = "lower"
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggcorrmat.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcorrmat.html
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:
set.seed(123)
ggpiestats(
data = mtcars,
x = am,
y = cyl,
package = "wesanderson",
palette = "Royal1",
title = "Dataset: Motor Trend Car Road Tests",
legend.title = "Transmission"
)
Defaults return
✅ descriptives (frequency + %s)
✅ inferential statistics
✅
effect size + CIs
✅ Goodness-of-fit tests
✅ Bayesian
hypothesis-testing
✅ Bayesian estimation
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:
set.seed(123)
grouped_ggpiestats(
data = mtcars,
x = cyl,
grouping.var = am,
label.repel = TRUE,
package = "ggsci",
palette = "default_ucscgb"
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggpiestats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggpiestats.html
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.
N.B. The p-values from one-sample proportion test are displayed on top of each bar.
set.seed(123)
library(ggplot2)
ggbarstats(
data = movies_long,
x = mpaa,
y = genre,
title = "MPAA Ratings by Genre",
xlab = "movie genre",
legend.title = "MPAA rating",
ggplot.component = list(ggplot2::scale_x_discrete(guide = ggplot2::guide_axis(n.dodge = 2))),
palette = "Set2"
)
Defaults return
✅ descriptives (frequency + %s)
✅ inferential statistics
✅
effect size + CIs
✅ Goodness-of-fit tests
✅ Bayesian
hypothesis-testing
✅ Bayesian estimation
And, needless to say, there is also a grouped_ variant of this
function-
## setup
set.seed(123)
grouped_ggbarstats(
data = mtcars,
x = am,
y = cyl,
grouping.var = vs,
package = "wesanderson",
palette = "Darjeeling2" # ,
# ggtheme = ggthemes::theme_tufte(base_size = 12)
)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggbarstats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggbarstats.html
The function ggcoefstats() generates dot-and-whisker plots for
regression models. The tidy data frames are prepared using
parameters::model_parameters(). Additionally, if available, the model
summary indices are also extracted from
performance::model_performance().
set.seed(123)
## model
mod <- stats::lm(formula = mpg ~ am * cyl, data = mtcars)
ggcoefstats(mod)
Defaults return
✅ inferential statistics
✅ estimate + CIs
✅ model summary
(AIC and BIC)
Details about underlying functions used to create graphics and statistical tests carried out can be found in the function documentation: https://indrajeetpatil.github.io/ggstatsplot/reference/ggcoefstats.html
For more, also read the following vignette: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/ggcoefstats.html
{ggstatsplot} also offers a convenience function to extract data
frames with statistical details that are used to create expressions
displayed in {ggstatsplot} plots.
set.seed(123)
p <- ggbetweenstats(mtcars, cyl, mpg)
# extracting expression present in the subtitle
extract_subtitle(p)
#> list(italic("F")["Welch"](2, 18.03) == "31.62", italic(p) ==
#> "1.27e-06", widehat(omega["p"]^2) == "0.74", CI["95%"] ~
#> "[" * "0.53", "1.00" * "]", italic("n")["obs"] == "32")
# extracting expression present in the caption
extract_caption(p)
#> list(log[e] * (BF["01"]) == "-14.92", widehat(italic(R^"2"))["Bayesian"]^"posterior" ==
#> "0.71", CI["95%"]^HDI ~ "[" * "0.57", "0.79" * "]", italic("r")["Cauchy"]^"JZS" ==
#> "0.71")
# a list of tibbles containing statistical analysis summaries
extract_stats(p)
#> $subtitle_data
#> # A tibble: 1 × 14
#> statistic df df.error p.value
#> <dbl> <dbl> <dbl> <dbl>
#> 1 31.6 2 18.0 0.00000127
#> method effectsize estimate
#> <chr> <chr> <dbl>
#> 1 One-way analysis of means (not assuming equal variances) Omega2 0.744
#> conf.level conf.low conf.high conf.method conf.distribution n.obs expression
#> <dbl> <dbl> <dbl> <chr> <chr> <int> <list>
#> 1 0.95 0.531 1 ncp F 32 <language>
#>
#> $caption_data
#> # A tibble: 6 × 17
#> term pd prior.distribution prior.location prior.scale bf10
#> <chr> <dbl> <chr> <dbl> <dbl> <dbl>
#> 1 mu 1 cauchy 0 0.707 3008850.
#> 2 cyl-4 1 cauchy 0 0.707 3008850.
#> 3 cyl-6 0.780 cauchy 0 0.707 3008850.
#> 4 cyl-8 1 cauchy 0 0.707 3008850.
#> 5 sig2 1 cauchy 0 0.707 3008850.
#> 6 g_cyl 1 cauchy 0 0.707 3008850.
#> method log_e_bf10 effectsize estimate std.dev
#> <chr> <dbl> <chr> <dbl> <dbl>
#> 1 Bayes factors for linear models 14.9 Bayesian R-squared 0.714 0.0503
#> 2 Bayes factors for linear models 14.9 Bayesian R-squared 0.714 0.0503
#> 3 Bayes factors for linear models 14.9 Bayesian R-squared 0.714 0.0503
#> 4 Bayes factors for linear models 14.9 Bayesian R-squared 0.714 0.0503
#> 5 Bayes factors for linear models 14.9 Bayesian R-squared 0.714 0.0503
#> 6 Bayes factors for linear models 14.9 Bayesian R-squared 0.714 0.0503
#> conf.level conf.low conf.high conf.method n.obs expression
#> <dbl> <dbl> <dbl> <chr> <int> <list>
#> 1 0.95 0.574 0.788 HDI 32 <language>
#> 2 0.95 0.574 0.788 HDI 32 <language>
#> 3 0.95 0.574 0.788 HDI 32 <language>
#> 4 0.95 0.574 0.788 HDI 32 <language>
#> 5 0.95 0.574 0.788 HDI 32 <language>
#> 6 0.95 0.574 0.788 HDI 32 <language>
#>
#> $pairwise_comparisons_data
#> # A tibble: 3 × 9
#> group1 group2 statistic p.value alternative distribution p.adjust.method
#> <chr> <chr> <dbl> <dbl> <chr> <chr> <chr>
#> 1 4 6 -6.67 0.00110 two.sided q Holm
#> 2 4 8 -10.7 0.0000140 two.sided q Holm
#> 3 6 8 -7.48 0.000257 two.sided q Holm
#> test expression
#> <chr> <list>
#> 1 Games-Howell <language>
#> 2 Games-Howell <language>
#> 3 Games-Howell <language>
#>
#> $descriptive_data
#> NULL
#>
#> $one_sample_data
#> NULL
#>
#> $tidy_data
#> NULL
#>
#> $glance_data
#> NULL
#>
#> attr(,"class")
#> [1] "ggstatsplot_stats" "list"Note that all of this analysis is carried out by {statsExpressions}
package: https://indrajeetpatil.github.io/statsExpressions/
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 our own plot using
{ggplot2} package, and use {ggstatsplot} function for extracting
expression:
## loading the needed libraries
set.seed(123)
library(ggplot2)
## using `{ggstatsplot}` to get expression with statistical results
stats_results <- ggbetweenstats(morley, Expt, Speed) %>% extract_subtitle()
## creating a custom plot of our choosing
ggplot(morley, aes(x = as.factor(Expt), y = Speed)) +
geom_boxplot() +
labs(
title = "Michelson-Morley experiments",
subtitle = stats_results,
x = "Speed of light",
y = "Experiment number"
)
-
No need to use scores of packages for statistical analysis (e.g., one to get stats, one to get effect sizes, another to get Bayes Factors, and yet another to get pairwise comparisons, etc.).
-
Minimal amount of code needed for all functions (typically only
data,x, andy), which minimizes chances of error and makes for tidy scripts. -
Conveniently toggle between statistical approaches.
-
Truly makes your figures worth a thousand words.
-
No need to copy-paste results to the text editor (MS-Word, e.g.).
-
Disembodied figures stand on their own and are easy to evaluate for the reader.
-
More breathing room for theoretical discussion and other text.
-
No need to worry about updating figures and statistical details separately.
This package is…
❌ an alternative to learning {ggplot2}
✅ (The better you know
{ggplot2}, the more you can modify the defaults to your liking.)
❌ meant to be used in talks/presentations
✅ (Default plots can be
too complicated for effectively communicating results in
time-constrained presentation settings, e.g. conference talks.)
❌ the only game in town
✅ (GUI software alternatives:
JASP and jamovi).
In case you use the GUI software jamovi,
you can install a module called
jjstatsplot, which is a
wrapper around {ggstatsplot}.
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.
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