ggstatsplot: ggplot2 Based Plots with Statistical Details
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, and robust versions of t-test, anova, and 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 (for hypothesis about distributions), and
- 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 (0.0.6):
utils::install.packages(pkgs = "ggstatsplot")You can get the development version of the package from GitHub
(0.0.6.9000). 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] TRUECitation
If you want to cite this package in a scientific journal or in any other
context, run the following code in your R console:
utils::citation(package = "ggstatsplot")There is currently a publication in preparation corresponding this package and the citation will be updated once it’s published.
Documentation and Examples
To see the detailed documentation for each function in the stable CRAN version of the package, see:
- README: https://cran.r-project.org/web/packages/ggstatsplot/readme/README.html
- Vignettes: https://cran.r-project.org/web/packages/ggstatsplot/vignettes/
To see the documentation relevant for the development version of the
package, see the dedicated website for ggstatplot, which is updated
after every new commit: https://indrajeetpatil.github.io/ggstatsplot/.
Help
In R, documentation for any function can be accessed with the standard
help command-
# primary functions
?ggbetweenstats
?ggscatterstats
?gghistostats
?ggpiestats
?ggcorrmat
?ggcoefstats
# grouped variants of primary functions
?grouped_ggbetweenstats
?grouped_ggscatterstats
?grouped_gghistostats
?grouped_ggpiestats
?grouped_ggcorrmat
# helper functions
?combine_plots
?theme_ggstatsplotAnother handy tool to see arguments to any of the functions is args.
For example-
args(name = ggstatsplot::ggscatterstats)
#> function (data, x, y, 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,
#> type = "pearson", results.subtitle = TRUE, title = NULL,
#> subtitle = NULL, caption = NULL, nboot = 100, beta = 0.1,
#> k = 3, axes.range.restrict = FALSE, ggtheme = ggplot2::theme_bw(),
#> ggstatsplot.layer = TRUE, messages = TRUE)
#> NULLIn 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 = 10, face = "bold"),
#> strip.text.x = ggplot2::element_text(size = 10, face = "bold"),
#> strip.text.y = ggplot2::element_text(size = 10, face = "bold"),
#> strip.text = ggplot2::element_text(size = 10, face = "bold"),
#> axis.title.y = ggplot2::element_text(size = 10, face = "bold"),
#> axis.text.x = ggplot2::element_text(size = 10, face = "bold"),
#> axis.text.y = ggplot2::element_text(size = 10, face = "bold"),
#> axis.line = ggplot2::element_line(),
#> legend.text = ggplot2::element_text(size = 10),
#> legend.title = ggplot2::element_text(size = 10, 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 = 10,
#> face = "plain",
#> hjust = 0.5
#> )
#> )
#> } else {
#> ggtheme
#> }
#> }
#> <bytecode: 0x000000002915e4f0>
#> <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,
which means you shouldn’t enter arguments in the following manner:
data = NULL, x = data$x, y = data$y. You must always specify the
data argument for all functions.
Additionally, ggstatsplot is a very chatty package and will by default
output information about references for tests, notes on assumptions
about linear models, and warnings. 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: 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 the vignettes on the site: https://cran.r-project.org/web/packages/ggstatsplot/vignettes/
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 in favor of the null
k = 2, # 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)
# plot
ggstatsplot::grouped_ggbetweenstats(
data = ggstatsplot::movies_long,
x = mpaa,
y = length,
grouping.var = genre, # grouping variable
title.prefix = "Movie genre",
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)
# creating a smaller dataframe
intent_short <- ggstatsplot::intent_morality %>%
dplyr::filter(.data = ., condition %in% c("accidental", "attempted"))
# getting text results using with a helper function
results_subtitle <- ggstatsplot::subtitle_ggbetween_t_parametric(
data = intent_short,
x = condition,
y = rating,
paired = TRUE
)
# displaying the subtitle on the plot
ggstatsplot::ggbetweenstats(
data = intent_short,
x = condition,
y = rating,
messages = FALSE
) +
ggplot2::labs(subtitle = results_subtitle)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",
messages = FALSE
)Number of other arguments can be specified to modify this basic plot-
library(datasets)
# 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 > 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", # which type of central tendency lines are 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 = ggstatsplot::movies_long,
x = rating,
y = length,
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,
title = "Dataset: Motor Trend Car Road Tests", # title for the plot
stat.title = "interaction: ", # title for the results from Pearson's chi-squared test
legend.title = "Transmission", # title for the legend
factor.levels = c("1 = manual", "0 = automatic"), # renaming the factor level names for 'main' variable
facet.wrap.name = "No. of cylinders", # name for the facetting variable
facet.proptest = FALSE, # turning of facetted proportion test results
package = "ggsci", # package from which color palette is to be taken
palette = "default_jama", # choosing a different color palette
caption = expression( # text for the caption
paste(italic("Note"), ": this is a demo")
),
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
stat.title = "McNemar Test: ",
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:
# for reproducibility
set.seed(123)
# plot
ggstatsplot::grouped_ggpiestats(
data = ggstatsplot::movies_long,
main = mpaa,
grouping.var = genre, # grouping variable
title.prefix = "Movie genre",
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-
Note: To use bar.measure = "mix" option, you will need to get the
development version of ggplot2 from GitHub.
# getting development version of ggplot2
# devtools::install_github(repo = "tidyverse/ggplot2", dependencies = FALSE)
# 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
type = "parametric", # one sample t-test
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 of vertical line representing central tendency
binwidth = 0.10, # binwidth value (experiment until you find the best one)
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 (using
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 = ggstatsplot::movies_long,
x = budget,
xlab = "Movies budget (in million US$)",
grouping.var = genre, # grouping variable
title.prefix = "Movie genre",
ggtheme = ggthemes::theme_tufte(),
messages = FALSE,
nrow = 2,
ncol = 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
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.
# 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 is based on p-values adjusted for multiple comparisons,
#> while the lower triangle is based on unadjusted p-values.Note that if there are NAs present in the selected dataframe, the
legend will display minimum and maximum number of pairs used for
correlation matrices.
Multiple aesthetics-related arguments can be modified to change the appearance of the correlation matrix.
Alternatively, you can use it just to get the correlation matrices and
their corresponding p-values (in a tibble format).
# show four digits in a tibble
options(pillar.sigfig = 4)
# getting the correlation coefficient matrix
ggstatsplot::ggcorrmat(
data = datasets::iris,
cor.vars = Sepal.Length:Petal.Width,
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 denotes p-values adjusted for multiple comparisons,
#> while the lower triangle denotes 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_t~ 0. 5.291e-12 9.138e- 3 0. 3.170e- 5 2.568e- 6
#> 2 sleep_r~ 4.070e-13 0. 1.978e- 2 5.291e-12 9.698e- 3 3.762e- 3
#> 3 sleep_c~ 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 sample sizes for all pairs
ggstatsplot::ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_total:bodywt,
corr.method = "robust",
output = "n"
)
#> # 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 83Additionally, 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.
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):
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:
library(dplyr)
library(lme4)
library(quantreg)
# for reproducibility
set.seed(200)
# creating dataframe needed for one of the analyses below
d <- as.data.frame(Titanic)
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 mmodel
ggstatsplot::ggcoefstats(
x = lme4::lmer(
formula = Reaction ~ Days + (Days | Subject),
data = lme4::sleepstudy
),
point.color = "red",
stats.label.color = "black",
ggtheme = hrbrthemes::theme_ipsum_ps(),
ggstatsplot.layer = FALSE,
exclude.intercept = FALSE,
title = "linear mixed-effects model"
),
labels = c("(a)", "(b)"),
nrow = 2,
ncol = 1
)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