ggdotplotstats
Indrajeet Patil
20211130
Source:vignettes/web_only/ggdotplotstats.Rmd
ggdotplotstats.Rmd
You can cite this package/vignette as:
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}},
}
The function ggdotplotstats
can be used for data exploration and to provide an easy way to make publicationready dot plots/charts with appropriate and selected statistical details embedded in the plot itself. In this vignette, we will explore several examples of how to use it.
This function is a sister function of gghistostats
with the difference being it expects a labeled numeric variable.
Distribution of a sample with ggdotplotstats
Let’s begin with a very simple example from the ggplot2 package (ggplot2::mpg
), a subset of the fuel economy data that the EPA makes available on http://fueleconomy.gov.
## looking at the structure of the data using glimpse
dplyr::glimpse(ggplot2::mpg)
#> Rows: 234
#> Columns: 11
#> $ manufacturer <chr> "audi", "audi", "audi", "audi", "audi", "audi", "audi", "…
#> $ model <chr> "a4", "a4", "a4", "a4", "a4", "a4", "a4", "a4 quattro", "…
#> $ displ <dbl> 1.8, 1.8, 2.0, 2.0, 2.8, 2.8, 3.1, 1.8, 1.8, 2.0, 2.0, 2.…
#> $ year <int> 1999, 1999, 2008, 2008, 1999, 1999, 2008, 1999, 1999, 200…
#> $ cyl <int> 4, 4, 4, 4, 6, 6, 6, 4, 4, 4, 4, 6, 6, 6, 6, 6, 6, 8, 8, …
#> $ trans <chr> "auto(l5)", "manual(m5)", "manual(m6)", "auto(av)", "auto…
#> $ drv <chr> "f", "f", "f", "f", "f", "f", "f", "4", "4", "4", "4", "4…
#> $ cty <int> 18, 21, 20, 21, 16, 18, 18, 18, 16, 20, 19, 15, 17, 17, 1…
#> $ hwy <int> 29, 29, 31, 30, 26, 26, 27, 26, 25, 28, 27, 25, 25, 25, 2…
#> $ fl <chr> "p", "p", "p", "p", "p", "p", "p", "p", "p", "p", "p", "p…
#> $ class <chr> "compact", "compact", "compact", "compact", "compact", "c…
Let’s say we want to visualize the distribution of mileage by car manufacturer.
## for reproducibility
set.seed(123)
library(ggstatsplot)
## removing factor level with very few no. of observations
df < dplyr::filter(ggplot2::mpg, cyl %in% c("4", "6"))
## creating a vector of colors using `paletteer` package
paletter_vector <
paletteer::paletteer_d(
palette = "palettetown::venusaur",
n = nlevels(as.factor(df$manufacturer)),
type = "discrete"
)
## plot
ggdotplotstats(
data = df,
x = cty,
y = manufacturer,
xlab = "city miles per gallon",
ylab = "car manufacturer",
test.value = 15.5,
point.args = list(
shape = 16,
color = paletter_vector,
size = 5
),
title = "Distribution of mileage of cars",
ggtheme = ggplot2::theme_dark()
)
Grouped analysis with grouped_ggdotplotstats
What if we want to do the same analysis separately for different engines with different numbers of cylinders?
ggstatsplot provides a special helper function for such instances: grouped_ggdotplotstats
. This is merely a wrapper function around combine_plots
. It applies ggdotplotstats
across all levels of a specified grouping variable and then combines the individual plots into a single plot.
Let’s see how we can use this function to apply ggdotplotstats
to accomplish our task.
## for reproducibility
set.seed(123)
## removing factor level with very few no. of observations
df < dplyr::filter(ggplot2::mpg, cyl %in% c("4", "6"))
## plot
grouped_ggdotplotstats(
## arguments relevant for ggdotplotstats
data = df,
grouping.var = cyl, ## grouping variable
x = cty,
y = manufacturer,
xlab = "city miles per gallon",
ylab = "car manufacturer",
type = "bayes", ## Bayesian test
test.value = 15.5,
## arguments relevant for `combine_plots`
annotation.args = list(title = "Fuel economy data"),
plotgrid.args = list(nrow = 2)
)
Grouped analysis with {purrr}
Although this is a quick and dirty way to explore a large amount of data with minimal effort, it does come with an important limitation: reduced flexibility. For example, if we wanted to add, let’s say, a separate test.value
argument for each gender, this is not possible with grouped_ggdotplotstats
. For cases like these, or to run separate kinds of tests (robust for some, parametric for other, while Bayesian for some other levels of the group) it would be better to use purrr.
See the associated vignette here: https://indrajeetpatil.github.io/ggstatsplot/articles/web_only/purrr_examples.html
Summary of tests
Central tendency measure
Type  Measure  Function used 

Parametric  mean  parameters::describe_distribution 
Nonparametric  median  parameters::describe_distribution 
Robust  trimmed mean  parameters::describe_distribution 
Bayesian  MAP (maximum a posteriori probability) estimate  parameters::describe_distribution 
Hypothesis testing
Type  Test  Function used 

Parametric  Onesample Student’s ttest  stats::t.test 
Nonparametric  Onesample Wilcoxon test  stats::wilcox.test 
Robust  Bootstrapt method for onesample test  WRS2::trimcibt 
Bayesian  Onesample Student’s ttest  BayesFactor::ttestBF 
Effect size estimation
Type  Effect size  CI?  Function used 

Parametric  Cohen’s d, Hedge’s g  ✅ 
effectsize::cohens_d , effectsize::hedges_g

Nonparametric  r (rankbiserial correlation)  ✅  effectsize::rank_biserial 
Robust  trimmed mean  ✅  WRS2::trimcibt 
Bayes Factor  \(\delta_{posterior}\)  ✅  bayestestR::describe_posterior 
Reporting
If you wish to include statistical analysis results in a publication/report, the ideal reporting practice will be a hybrid of two approaches:
the ggstatsplot approach, where the plot contains both the visual and numerical summaries about a statistical model, and
the standard narrative approach, which provides interpretive context for the reported statistics.
For example, let’s see the following example:
ggdotplotstats(morley, Speed, Expt, test.value = 800)
The narrative context (assuming type = "parametric"
) can complement this plot either as a figure caption or in the main text
Student’s ttest revealed that, across 5 experiments, the speed of light was significantly different than posited speed. The effect size \((g = 1.22)\) was very large, as per Cohen’s (1988) conventions. The Bayes Factor for the same analysis revealed that the data were 3.46 times more probable under the alternative hypothesis as compared to the null hypothesis. This can be considered moderate evidence (Jeffreys, 1961) in favor of the alternative hypothesis.
Suggestions
If you find any bugs or have any suggestions/remarks, please file an issue on GitHub: https://github.com/IndrajeetPatil/ggstatsplot/issues