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:
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.
To get the latest, stable CRAN release (0.0.8
):
utils::install.packages(pkgs = "ggstatsplot")
Note: If you are on a linux machine, you will need to have OpenGL libraries installed (specifically, libx11
, mesa
and Mesa OpenGL Utility library - glu
) for the dependency package rgl
to work.
You can get the development version of the package from GitHub (0.0.8.9000
). 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upgrade_dependencies = TRUE # updates any out of date dependencies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:
If you want to cite this package in a scientific journal or in any other context, run the following code in your R
console:
There is currently a publication in preparation corresponding this package and the citation will be updated once it’s published.
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/.
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 = 0, point.height.jitter = 0, 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,
#> ggplot.component = NULL, 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 ggstatsplot-specific layer is to be added on top of the default theme
#> 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: 0x0000000022d9b3e8>
#> <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-
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 = 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 = 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)
# plot
ggstatsplot::grouped_ggbetweenstats(
data = dplyr::filter(.data = ggstatsplot::movies_long,
genre %in% c("Action", "Action Comedy", "Action Drama", "Comedy")),
x = mpaa,
y = length,
grouping.var = genre, # grouping variable
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%
ggplot.component = list( # adding new components to `ggstatsplot` default
ggplot2::scale_y_continuous(sec.axis = ggplot2::dup_axis())
),
k = 3,
title.prefix = "Movie genre",
caption = substitute(paste(italic("Source"),
":IMDb (Internet Movie Database)")),
palette = "default_jama",
package = "ggsci",
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/web_only/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,
title = "repeated measures design",
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("Action", "Action Comedy", "Action Drama", "Comedy")
),
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(),
ggplot.component = list(
ggplot2::scale_x_continuous(breaks = seq(2, 9, 1), limits = (c(2, 9)))
),
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/web_only/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 = 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/web_only/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 = 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 = 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("Action", "Action Comedy", "Action Drama", "Comedy")
),
x = budget,
xlab = "Movies budget (in million US$)",
type = "robust", # use robust location measure
grouping.var = genre, # grouping variable
normal.curve = TRUE, # superimpose a normal distribution curve
normal.curve.color = "red",
title.prefix = "Movie genre",
ggtheme = ggthemes::theme_tufte(),
ggplot.component = list( # modify the defaults from `ggstatsplot` for each plot
ggplot2::scale_x_continuous(breaks = seq(0, 200, 50), limits = (c(0, 200)))
),
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/web_only/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 facilitateto 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 that if there are NA
s 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 = 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"
)
#> # 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"
)
#> Note: In the correlation matrix,
#> the upper triangle: p-values adjusted for multiple comparisons
#> the lower triangle: unadjusted p-values.
#> # 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/web_only/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 = 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 = 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/web_only/ggcoefstats.html
combine_plots
The full power of ggstatsplot
can be leveraged with a functional programming package like purrr
that replaces for
loops with code that is both more succinct and easier to read and, therefore, purrr
should be preferrred 😻. (Another old school option to do this effectively is using the plyr
package.)
In such cases, ggstatsplot
contains a helper function combine_plots
to combine multiple plots, which can be useful for combining a list of plots produced with purrr
. This is a wrapper around cowplot::plot_grid
and lets you combine multiple plots and add a combination of title, caption, and annotation texts with suitable defaults.
For examples (both with plyr
and purrr
), see the associated vignette- https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/combine_plots.html
theme_ggstatsplot
All plots from ggstatsplot
have a default theme: theme_ggstatsplot
. You can change this theme by using the argument ggtheme
for all functions.
It is important to note that irrespective of which ggplot
theme you choose, ggstatsplot
in the backdrop adds a new layer with its idiosyncratic theme settings, chosen to make the graphs more readable or aesthetically pleasing. Let’s see an example with gghistostats
and see how a certain theme from hrbrthemes
package looks with and without the ggstatsplot
layer.
# to use hrbrthemes themes, first make sure you have all the necessary fonts
library(hrbrthemes)
# extrafont::ttf_import()
# extrafont::font_import()
# try this yourself
ggstatsplot::combine_plots(
# with the ggstatsplot layer
ggstatsplot::gghistostats(
data = iris,
x = Sepal.Width,
messages = FALSE,
title = "Distribution of Sepal Width",
test.value = 5,
ggtheme = hrbrthemes::theme_ipsum(),
ggstatsplot.layer = TRUE
),
# without the ggstatsplot layer
ggstatsplot::gghistostats(
data = iris,
x = Sepal.Width,
messages = FALSE,
title = "Distribution of Sepal Width",
test.value = 5,
ggtheme = hrbrthemes::theme_ipsum_ps(),
ggstatsplot.layer = FALSE
),
nrow = 1,
labels = c("(a)", "(b)"),
title.text = "Behavior of ggstatsplot theme layer with chosen ggtheme"
)
For more on how to modify it, see the associated vignette- https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/theme_ggstatsplot.html
ggstatsplot
helpers to display text resultsSometimes you may not like the default plot produced by ggstatsplot
. In such cases, you can use other custom plots (from ggplot2
or other plotting packages) and still use ggstatsplot
(subtitle) helper functions to display results from relevant statistical test. For example, in the following chunk, we will use pirateplot from yarrr
package and use ggstatsplot
helper function to display the results.
# for reproducibility
set.seed(123)
# loading the needed libraries
library(yarrr)
library(ggstatsplot)
# using `ggstatsplot` to prepare text with statistical results
stats_results <-
ggstatsplot::subtitle_anova_parametric(
data = ChickWeight,
x = Time,
y = weight,
messages = FALSE
)
# using `yarrr` to create plot
yarrr::pirateplot(
formula = weight ~ Time,
data = ChickWeight,
theme = 1,
main = stats_results
)
As the code stands right now, here is the code coverage for all primary functions involved: https://codecov.io/gh/IndrajeetPatil/ggstatsplot/tree/master/R
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.
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.