knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
ggstatsplot::ggpiestats can be used for quick data
exploration and/or to prepare publication-ready pie charts to summarize
the statistical relationship(s) among one or more categorical variables. We will
see examples of how to use this function in this vignette.
To begin with, here are some instances where you would want to use
to check if the proportion of observations matches our hypothesized proportion, this is typically known as a "Goodness of Fit" test
to see if the frequency distribution of two categorical variables are independent of each other using the contingency table analysis
to check if the proportion of observations at each level of a categorical variable is equal
Note: The following demo uses the pipe operator (
%>%), if you are not
familiar with this operator, here is a good explanation:
ggpiestats only works with data organized in dataframes or tibbles. It
will not work with other data structures like base R tables or matrices. It can
operate on dataframes that are organized with one row per observation or
dataframes that have one column containing counts. This vignette provides
examples of both (see examples below).
To help demonstrate how
ggpiestats can be used with categorical (also known as
nominal) data, a modified version of the original
Titanic dataset (from the
datasets library) has been provided in the
ggstatsplot package with the name
Titanic_full. The Titanic Passenger Survival Dataset provides information "on
the fate of passengers on the fatal maiden voyage of the ocean liner Titanic,
including economic status (class), sex, age, and survival."
Let's have a look at the structure of both.
library(datasets) library(dplyr) library(ggstatsplot) # looking at the original data in tabular format dplyr::glimpse(x = Titanic) # looking at the dataset as a tibble or dataframe dplyr::glimpse(x = ggstatsplot::Titanic_full)
Goodness of Fit with
The simplest use case for
ggpiestats is that we want to display information
about one categorical or nominal variable. As part of that display or plot,
we may also choose to execute a chi-squared goodness of fit test to see whether
the proportions (or percentages) in categories of the single variable appear to
line up with our hypothesis or model. To start simple and then expand, let's say
that we'd like to display a piechart with the percentages of passengers who did
or did not survive. Our initial hypothesis is that it was no different than
flipping a coin. People had a 50/50 chance of surviving.
# since effect size confidence intervals are computed using bootstrapping, let's # set seed for reproducibility set.seed(123) # to speed up the process, let's use only half of the dataset Titanic_full_50 <- dplyr::sample_frac(tbl = ggstatsplot::Titanic_full, size = 0.5) # plot ggstatsplot::ggpiestats( data = Titanic_full_50, main = Survived, title = "Passenger survival on the Titanic", # title for the entire plot caption = "Source: Titanic survival dataset", # caption for the entire plot legend.title = "Survived?", # legend title messages = FALSE # turn off messages )
Note: equal proportions per category are the default, e.g. 50/50, but you
can specify any hypothesized ratio you like with
ratio so if our hypothesis
was that 80% died and 20% survived we would add
ratio = c(.80,.20) when we
entered the code.
Let's move on to a more complex example statistically and in terms of the
features we will use in
Independence (or association) with
Let's next investigate whether the passenger's gender was independent of, or
associated with, gender. The test is whether the proportion of people who
survived was different between the sexes using
We'll modify a number of arguments to change the appearance of this plot and
showcase the flexibility of
ggpiestats. We will:
Change the plot theme to
Change our color palette to
We'll customize the subtitle by being more precise about which chi squared test this is
stat.title = "chi squared test of independence: "
Finally, we'll make a call to
ggplot2to modify the size of our plot title and to make it right justified
# since effect size confidence intervals are computed using bootstrapping, let's # set seed for reproducibility set.seed(123) # to speed up the process, let's use only half of the dataset Titanic_full_50 <- dplyr::sample_frac(tbl = ggstatsplot::Titanic_full, size = 0.5) # plot ggstatsplot::ggpiestats( data = Titanic_full_50, main = Survived, condition = Sex, title = "Passenger survival on the Titanic by gender", # title for the entire plot caption = "Source: Titanic survival dataset", # caption for the entire plot legend.title = "Survived?", # legend title bf.message = TRUE, # show resuls from bayes factor in favor of null ggtheme = ggplot2::theme_grey(), # changing plot theme palette = "category10_d3", # choosing a different color palette package = "ggsci", # package to which color palette belongs stat.title = "Pearson's chi-squared test: ", # title for statistical test k = 2, # decimal places in result perc.k = 1, # decimal places in percentage labels nboot = 10, # no. of bootstrap sample for effect size CI messages = FALSE ) + # further modification with `ggplot2` commands ggplot2::theme(plot.title = ggplot2::element_text( color = "black", size = 14, hjust = 0 ))
The plot clearly shows that survival rates were very different between males and
females. The Pearson's chi-square test of independence is significant given our
large sample size. Additionally, for both females and males, the survival rates
were significantly different than 50% as indicated by the
*** which is
equivalent to a goodness of fit test for each gender.
Grouped analysis with
What if we want to do the same analysis of gender but also factor in the
passenger's age (Age)? We have information that classifies the passengers as
Child or Adult, perhaps that makes a difference to their survival rate? We could
for loop or use
ggstatsplot provides a special helper
function for such instances:
It is a convenient wrapper function around
ggpiestats across all levels of a specified grouping variable
and then combines the list of individual plots into a single plot. Note that the
grouping variable can be anything: conditions in a given study, groups in a
study sample, different studies, etc.
# since effect size confidence intervals are computed using bootstrapping, let's # set seed for reproducibility set.seed(123) # plot ggstatsplot::grouped_ggpiestats( # arguments relevant for ggstatsplot::gghistostats data = ggstatsplot::Titanic_full, grouping.var = Age, title.prefix = "Child or Adult?: ", main = Survived, condition = Sex, bf.message = TRUE, nboot = 10, k = 2, perc.k = 1, package = "ggsci", palette = "category10_d3", messages = FALSE, # arguments relevant for ggstatsplot::combine_plots title.text = "Passenger survival on the Titanic by gender and age", caption.text = "Asterisks denote results from proportion tests; \n***: p < 0.001, ns: non-significant", nrow = 2, ncol = 1 )
The resulting pie charts and statistics make the story clear. For adults gender very much matters. Women survived at much higher rates than men. For children gender is not significantly associated with survival and both male and female children have a survival rate that is not significantly different from 50/50.
Grouped analysis with
grouped_ggpiestats provides a quick way to explore the data, it
leaves much to be desired. For example, we may want to add different captions,
titles, themes, or palettes for each level of the grouping variable, etc. For
cases like these, it would be better to use
See the associated vignette here: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/purrr_examples.html
Working with data organized by
ggpiestats can also work with dataframe containing counts (aka tabled data),
i.e., when each row doesn't correspond to a unique observation. For example,
consider the following notional
fishing dataframe containing data from two
B) about the number of different types fish they caught in the
March. In this dataframe, each row corresponds to a
unique combination of
# for reproducibility set.seed(123) # creating a dataframe # (this is completely fictional; I don't know first thing about fishing!) ( fishing <- data.frame( Boat = c(rep("B", 4), rep("A", 4), rep("A", 4), rep("B", 4)), Month = c(rep("February", 2), rep("March", 2), rep("February", 2), rep("March", 2)), Fish = c( "Bass", "Catfish", "Cod", "Haddock", "Cod", "Haddock", "Bass", "Catfish", "Bass", "Catfish", "Cod", "Haddock", "Cod", "Haddock", "Bass", "Catfish" ), SumOfCaught = c(25, 20, 35, 40, 40, 25, 30, 42, 40, 30, 33, 26, 100, 30, 20, 20) ) %>% # converting to a tibble dataframe tibble::as_data_frame(x = .) )
When the data is organized this way, we make a slightly different call to the
ggpiestats function: we use the
counts argument. If we want to investigate
the relationship of type of fish by month (a test of independence), our command
# running `ggpiestats` with counts information ggstatsplot::ggpiestats( data = fishing, main = Fish, condition = Month, counts = SumOfCaught, package = "ggsci", palette = "default_jama", title = "Type fish caught by month", caption = "Source: completely made up", legend.title = "Type fish caught: ", messages = FALSE )
The results support our hypothesis that the type of fish caught is related to the month in which we're fishing. The chi squared independence test results at the top of the plot. In February we catch significantly more Haddock than we would hypothesize for an equal distribution. Whereas in March our results indicate there's no strong evidence that the distribution isn't equal.
For our final example let's imagine we're conducting clinical trials for some
new imaginary wonder drug. We have 134 subjects entering the trial. Some of them
enter healthy (N=96), some of them enter the trial already being sick (N=38).
All of them receive our treatment or intervention. Then we check back in a month
to see if they are healthy or sick. A classic pre/post experimental design.
We're interested in seeing the change in both groupings. In the case of
within-subjects designs, you can set
paired = TRUE, which will display results
from McNemar test in the subtitle.
(Note: If you forget to set
paired = TRUE, the results you get will be
# seed for reproducibility set.seed(123) # create our imaginary data clinical_trial <- tibble::tribble( ~SickBefore, ~SickAfter, ~Counts, "No", "Yes", 4, "Yes", "No", 25, "Yes", "Yes", 13, "No", "No", 92 ) # display it as a simple table stats::xtabs( formula = Counts ~ SickBefore + SickAfter, subset = NULL, data = clinical_trial ) # plot ggstatsplot::ggpiestats( data = clinical_trial, condition = SickBefore, main = SickAfter, counts = Counts, paired = TRUE, stat.title = "McNemar test: ", title = "Results from imaginary clinical trial", package = "ggsci", palette = "default_ucscgb", direction = -1, messages = FALSE )
The results bode well for our experimental wonder drug. Of the 96 who started out healthy only 4% were sick after a month. Ideally, we would have hoped for zero but reality is seldom perfect. On the other side of the 38 who started out sick that number has reduced to just 13 or 34% which is a marked improvement.
If you find any bugs or have any suggestions/remarks, please file an issue on GitHub: https://github.com/IndrajeetPatil/ggstatsplot/issues