前言
所谓一图胜千言： ""Information-rich graphic is worth a thousand words""
ggstatsplot的理念非常简单：把数据的可视化与统计分析一块做了
简单易用： ggplot2很强大， 但是，但是，太多的参数，细节。。,统计知识比较差的你表示：（
--ggstatsplot 就是你的救星了。。。
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1. 软件安装
Install the ggstatsplot package from CRAN:
utils::install.packages("ggstatsplot")
Then you can get the development version of the package from Github:
library(remotes)remotes::install_github("IndrajeetPatil/ggstatsplot", dependencies = FALSE)
Load the needed packages-
library(ggstatsplot)library(ggplot2)
You are recommended to use the RStudioIDE, but you don't have to.
2. 使用
2.1 ggbetweenstats：分组数据分析
2.1.1 ggbetweenstats - defaults
ggbetweenstats(
data = movies_long,
x = mpaa, # > 2 groups
y = rating,
type = "p", # default
messages = FALSE
)
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Changing the type of test
- "p" → parametric
- "np" → non-parametric
- "r" → robust
- "bf" → bayes factor
2.1.2. ggbetweenstats - little code, rich details
ggbetweenstats(
data = movies_long,
x = mpaa,
y = rating
)
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Default information:
- statistical details
- Bayes Factor
- sample sizes
- distribution summary
2.1.3. ggbetweenstats - pairwise comparisons
ggbetweenstats(
data = movies_long,
x = mpaa,
y = rating,
type = "np",
mean.ci = TRUE,
pairwise.comparisons = TRUE,
pairwise.display = "ns",
p.adjust.method = "fdr",
messages = FALSE
)
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Changing pairwise comparisons displayed
- "ns" → only non-significant
- "s" → only significant
- "all" → everything
2.1.4. ggbetweenstats - (aesthetic) changes & outlier
ggbetweenstats(
data = movies_long,
x = mpaa,
y = rating,
type = "r",
conf.level = 0.99,
pairwise.comparisons = TRUE,
pairwise.annotation = "p",
outlier.tagging = TRUE,
outlier.label = title,
outlier.coef = 2,
ggtheme = hrbrthemes::theme_ipsum_tw(),
palette = "Darjeeling2",
package = "wesanderson",
messages = FALSE
)
Aesthetic preferences are not an excuse to not use ggstatsplot 😻
The default palette used iscolorblind-
2.1.5. ggbetweenstats - modification with ggplot2
ggbetweenstats(
data = movies_long,
x = mpaa,
y = rating,
type = "bf",
messages = FALSE
) +
scale_y_continuous(sec.axis = dup_axis())
Note: You can modify all ggstatsplot plots further using ggplot2 functions. Yaay!
2.1.6. Summary of tests - ggbetweenstats
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Effect sizes + CI - ggbetweenstats
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Pairwise comparion tests - ggbetweenstats
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2.2. ggwithinstats ：分组、条件数据分析，
For within group/condition comparisons
2.2.1. ggwithinstats - repeated measures equivalent
ggwithinstats(
data = WRS2::WineTasting,
x = Wine,
y = Taste,
pairwise.comparisons = TRUE,
pairwise.annotation = "p",
ggtheme = hrbrthemes::theme_ipsum_tw(),
ggstatsplot.layer = FALSE,
messages = FALSE
)
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Changing the type of test
- "p" → parametric
- "np" → non-parametric
- "r" → robust
- "bf" → bayes factor
2.2.2. ggwithinstats - little code, rich details
ggwithinstats(
data = WRS2::WineTasting,
x = Wine, # > 2 groups
y = Taste,
pairwise.comparisons = TRUE,
pairwise.annotation = "p",
ggtheme = hrbrthemes::theme_ipsum_tw(),
ggstatsplot.layer = FALSE,
messages = FALSE
)
Default information:
- statistical details
- pairwise comparisons
- sample sizes
- distribution summary
2.2.3. ggwithinstats - two groups，
ggwithinstats(
data = iris_long,
x = attribute, # 2 groups
y = value,
type = "r",
messages = FALSE
)
Changing the type of test
- "p" → parametric
- "np" → non-parametric
- "r" → robust
- "bf" → bayes factor
2.3 ggscatterstats-散点图，双变量相关性分析
Association between two numeric variables
2.3.1 ggscatterstats - defaults
ggscatterstats(
data = movies_long,
x = budget,
y = rating,
type = "p", # default #<<<
conf.level = 0.99,
messages = FALSE
)
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Changing the type of test
- "p" → parametric
- "np" → non-parametric
- "r" → robust
- "bf" → bayes factor
2.3.2. ggscatterstats - little code, rich details
ggscatterstats(
data = movies_long,
x = budget,
y = rating,
conf.level = 0.99
)
Default information:
- distribution
- Bayes Factor
- statistical details
2.3.3. ggscatterstats - conditional point tagging
ggscatterstats(
data = movies_long,
x = budget,
y = rating,
type = "r",
centrality.para = "mean",
label.var = title,
label.expression = budget > 150
& rating > 7.5,
marginal.type = "density",
messages = FALSE
)
Changing the marginal type
- histogram
- boxplot
- density
- violin
- densigram
2.3.4. ggscatterstats - changing smoothing functions
gscatterstats(
data = movies_long,
x = budget,
y = rating,
marginal = FALSE,
method = "gam",
formula = y ~ s(x, k = 3),
centrality.para = "mean",
messages = FALSE
)
Available centrality parameters
- mean
- median
2.4 ggcorrmat ：数据交叉相关性分析
2.4.1. ggcorrmat - defaults
ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_cycle:bodywt,
type = "r",
matrix.type = "upper",
p.adjust.method = "holm",
colors = NULL,
package = "yarrr",
palette = "southpark"
)
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Changing the type of test
- "p" → parametric
- "np" → non-parametric
- "r" → robust
- "bf" → not implemented
2.4.2. ggcorrmat - little code, rich details
ggcorrmat(data = dplyr::starwars)
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Default information:
statistical details
sample sizes
details about test
Note: Informative label about sample sizes in case NAs are present.
2.4.4. ggcorrmat - changing defaults
ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_cycle:bodywt,
type = "r",
matrix.type = "upper",
p.adjust.method = "holm",
colors = NULL,
package = "yarrr",
palette = "southpark"
)
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In addition to output = "plot", this function can also be used to get a dataframe of results:
- "r" → correlation
- "p" → p-values
-"n" → sample sizes- "ci" → confidence intervals
2.4.5. ggcorrmat - dataframe outputs
correlation coefficients
data = ggplot2::msleep,
cor.vars = sleep_cycle:bodywt,
type = "np",
output = "r",
p.adjust.method = "fdr",
messages = FALSE
)
** p-values**
ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_cycle:bodywt,
type = "np",
output = "p",
p.adjust.method = "none",
messages = FALSE
)
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** sample sizes**
ggcorrmat(
data = ggplot2::msleep,
cor.vars = sleep_cycle:bodywt,
type = "np",
output = "n",
p.adjust.method = "fdr",
messages = FALSE
)
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confidence intervals
options(digits = 3)
ggcorrmat(
data = ggplot2::msleep,
cor.vars = awake:bodywt,
type = "np",
output = "ci",
p.adjust.method = "fdr",
messages = FALSE
)
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2.5 gghistostats：密度图
Distribution of a numeric variable
2.5.1
2.5.2. gghistostats - further customization
gghistostats(
data = movies_long,
x = budget,
effsize.type = "d",
test.value = 50,
bar.measure = "mix",
centrality.para = "median",
test.value.line = TRUE,
normal.curve = TRUE,
ggtheme = hrbrthemes::theme_ipsum_tw(),
ggstatsplot.layer = FALSE,
messages = FALSE
)
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Available bar measures
- count
- proportion
- both (of the above)
- density
2.5.3. gghistostats - little code, rich details
gghistostats(
data = movies_long,
x = budget,
effsize.type = "d",
test.value = 50,
test.value.size = TRUE,
bar.measure = "mix",
centrality.para = "median",
test.value.line = TRUE,
normal.curve = TRUE
)
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Default information:
- statistical details
- Bayes Factor
- frequency
- distribution summary
2.6. ggdotplotstats- 点图
Distribution of a numeric variable with labels
2.6.1. ggdotplotstats - defaults
ggdotplotstats(
data = movies_long,
x = budget,
y = genre,
effsize.type = "d",
test.value = 52,
centrality.para = "median",
test.value.line = TRUE,
test.value.color = "red",
ggtheme = ggthemes::theme_par(),
messages = FALSE
)
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Changing the type of test
- "p" → parametric
- "np" → non-parametric
- "r" → robust
- "bf" → bayes factor
2.6.2. ggdotplotstats - little code, rich details
ggdotplotstats(
data = movies_long,
x = budget,
y = genre,
effsize.type = "d",
test.value = 52,
centrality.para = "median",
test.value.line = TRUE,
test.value.color = "red"
)
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Default information:
- statistical details
- Bayes Factor
- distribution summary
2.6.3 Summary of tests - gghistostats/ggdotplotstats
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2.7 ggpiestats： 饼图
For composition of categorical variables
2.7.1 ggpiestats - defaults
# let's use subset of data
ggpiestats(
data = dplyr::filter(.data = movies_long,
genre %in% c("Drama", "Comedy", "Animated")),
x = genre,
y = mpaa,
paired = FALSE, # default
conf.level = 0.99,
package = "ggsci",
palette = "default_ucscgb",
messages = FALSE
)
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Test by design
- paired = FALSE → Pearson's χ2
- paired = TRUE → McNemar
2.7.2 ggpiestats - little code, rich details
# let's use subset of data
ggpiestats(
data = dplyr::filter(movies_long,
genre %in% c("Drama", "Comedy", "Animated")),
x = genre,
y = mpaa,
conf.level = 0.99
)
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Default information:
- statistical details
- Bayes Factor
- sample sizes
- proportion test results
2.7.3 ggpiestats - proportion test
ggpiestats(
data = as.data.frame(Titanic),
x = Survived,
counts = Freq,
slice.label = "both",
messages = FALSE
)
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Note: If the data is in tabled format, you can use the counts argument.
Test by analysis
- condition != NULL → contingency table
- y = = NULL → goodness of fit
2.8. ggbarstats: 条形图-不同变量比较
For composition of categorical variables
2.8.1 ggbarstats - defaults
ggbarstats(
data = movies_long,
x = genre,
y = mpaa,
paired = FALSE, # default
package = "ggsci",
palette = "default_igv",
caption = substitute(
paste(italic("Source"), ": www.imdb.com")
),
messages = FALSE
)
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Note: Even if you display Bayes Factor message in a caption, you can still use the caption argument.
Label information
- percentage (default)
- counts
- both (of the above)
2.8.2. ggbarstats - little code, rich details
ggbarstats(
data = movies_long,
x = genre,
y = mpaa
)
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Default information:
- statistical details
- Bayes Factor
- sample sizes
- proportion test results
2.8.3 Test summary - ggpiestats/ggbarstats
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2.9. ggcoefstats: 数据拟合、建模
Displaying results from regression analyses
2.9.1 ggcoefstats - defaults
# model
mod <- stats::aov(
formula = rating ~ mpaa * genre,
data = movies_long
)
# plot
ggcoefstats(x = mod)
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In addition to output = "plot", this function can also be used to get a dataframe of results:
- "tidy" → estimates
- "glance" → model summary
- "augment" → predictions
2.9.2 ggcoefstats - little code, rich details
Default information:
- estimate + 95% CI
-model summarystatistical details
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2.9.3. ggcoefstats - dataframe outputs
model summary
library(lme4)
# model
mod1 <-
lme4::lmer(formula = Reaction ~ Days + (Days | Subject),
data = sleepstudy)
# dataframe
ggcoefstats(x = mod1,
output = "glance")
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augmented dataframe
library(ordinal)
# model
mod2 <- clm(formula = rating ~ temp * contact,
data = wine)
# dataframe
ggcoefstats(x = mod2,
output = "augment") %>%
head(5)
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2.9.4. ggcoefstats: Supported models
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2.9.5. ggcoefstats: If not implemented, use a dataframe
# dataframe with results
df <- tibble::tribble(
~term, ~estimate, ~std.error, ~statistic, ~p.value,
"(Intercept)", 3.77, 0.165, 22.9, 1.49e-20,
"x", -1.36, 0.258, -5.26, 1.13e-5
)
# plot
# `statistic` argument decides label format
ggcoefstats(
x = df,
statistic = "z",
exclude.intercept = FALSE
)
Supported statistic (for dataframe objects):
- t
-z- F
At the minimum, two columns needed - term and estimate.
2.9.6 ggcoefstats: You can also do meta-analysis!
# made up data
meta_df <- tibble::tribble(
~term, ~estimate, ~std.error,
"study_1", 0.111, 0.065,
"study_2", -0.003, 0.258,
"study_3", 0.001, 0.120,
"study_4", 0.032, 0.022,
"study_5", -0.765, 0.650,
"study_6", -0.032, 0.058
)
# plot
ggcoefstats(
x = meta_df,
meta.analytic.effect = TRUE,
bf.message = TRUE,
xlab = "estimate"
)
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Frequentist random-effects meta-analysis from
metafor
Bayesian random-effects meta-analysis frommetaBMA
2.10. grouped_ variants of all functions
Running the same function for all levels of a single grouping variable
2.10.1. grouped_ functions
# only one additional argument
grouped_ggpiestats(
data = mtcars,
x = cyl,
grouping.var = am,
results.subtitle = FALSE,
messages = FALSE
)
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vailable grouped_ variants
- grouped_ggdotplotstats
- grouped_ggbarstats
- grouped_ggscatterstats
- grouped_gghistostats
- grouped_ggpiestats
- grouped_ggbetweenstats
- grouped_ggwithinstats
- grouped_ggcorrmat
2.11 Utility beyond ggstatsplot
What if I don't like the default plots but still want to display statistical results?
2.11.1 Using as helper functions
ggstatsplot can also be used just to get the statistical details.
# using `ggstatsplot` for stats
results <-
ggstatsplot::ggpiestats(
data = Titanic_full,
x = Survived,
y = Sex,
return = "subtitle",
messages = FALSE
)
# using `ggiraphExtra` for plot
ggiraphExtra::ggSpine(
data = Titanic_full,
aes(x = Sex, fill = Survived),
addlabel = TRUE,
interactive = FALSE
) + labs(subtitle = results)
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All included analyses have their corresponding helper functions for preparing subtitles with statistical details.
2.12 Glossary
Statistical reporting in ggstatsplot
2.12.1. Best practices in reporting statistical details
- As discussed before, the details included in statistical analyses follow the APA gold standard.
- The default tests follow the best practices. For example,
ggbetweenstatsfunction by default runs Welch's t-test and Welch's ANOVA - and not Student's t-test and Fisher's ANOVA - based on recent work (Delacre et al., 2017, 2018).- No p-value error
(Lilienfeld et al., 2015)
2.12.2 Avoiding errors
Since the plot and the statistical analysis are yoked together, the chances of making an error in reporting the results are minimized. You never have to write the results manually or copy-paste them from someplace else.
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2.12.3 Making sense of null results
Combination of frequentist and Bayesian statistics for each analysis to properly interpret the null results.
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2.12.4. Toggling between type of statistics
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3. Types of statistical analyses supported
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4. Effect sizes + CI available?
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5. Benefits of using ggstatsplot
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 if something about the data changes.
Minimal amount of code needed for all functions (typically only data, x, and y). This minimizes chances of error.
6. Limitations
Limited kinds of plots available.
Limited number of statistical tests (and effect sizes) available.
Faceting (or small multiples) not implemented.
Default plots can be too complicated for effectively communicating results in time-constrained presentation settings (e.g., conference talks).
Bulky API (in terms of number of function arguments to keep in mind).
(Saving grace: Defaults are sufficient most of the time.)
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