Add Kruskal-Wallis test p-values to a ggplot, such as box blots, dot plots and stripcharts.
stat_kruskal_test(
mapping = NULL,
data = NULL,
group.by = NULL,
label = "{method}, p = {p.format}",
label.x.npc = "left",
label.y.npc = "top",
label.x = NULL,
label.y = NULL,
step.increase = 0.1,
p.adjust.method = "holm",
significance = list(),
geom = "text",
position = "identity",
na.rm = FALSE,
show.legend = FALSE,
inherit.aes = TRUE,
parse = FALSE,
...
)
Set of aesthetic mappings created by aes()
. If specified and
inherit.aes = TRUE
(the default), it is combined with the default mapping
at the top level of the plot. You must supply mapping
if there is no plot
mapping.
The data to be displayed in this layer. There are three options:
If NULL
, the default, the data is inherited from the plot
data as specified in the call to ggplot()
.
A data.frame
, or other object, will override the plot
data. All objects will be fortified to produce a data frame. See
fortify()
for which variables will be created.
A function
will be called with a single argument,
the plot data. The return value must be a data.frame
, and
will be used as the layer data. A function
can be created
from a formula
(e.g. ~ head(.x, 10)
).
(optional) character vector specifying the grouping variable; it should be used only for grouped plots. Possible values are :
"x.var"
: Group by the x-axis variable and perform the test
between legend groups. In other words, the p-value is compute between legend
groups at each x position
"legend.var"
: Group by the legend
variable and perform the test between x-axis groups. In other words, the
test is performed between the x-groups for each legend level.
the column containing the label (e.g.: label = "p" or label =
"p.adj"), where p
is the p-value. Can be also an expression that can
be formatted by the glue()
package. For example, when
specifying label = "t-test, p = {p}", the expression {p} will be
replaced by its value.
can be numeric
or character
vector of the same length as the number of groups and/or panels. If too
short they will be recycled.
If numeric
, value should
be between 0 and 1. Coordinates to be used for positioning the label,
expressed in "normalized parent coordinates".
If character
,
allowed values include: i) one of c('right', 'left', 'center', 'centre',
'middle') for x-axis; ii) and one of c( 'bottom', 'top', 'center', 'centre',
'middle') for y-axis.
numeric
Coordinates (in data units) to be used
for absolute positioning of the label. If too short they will be recycled.
numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.
method for adjusting p values (see
p.adjust
). Has impact only in a situation, where
multiple pairwise tests are performed; or when there are multiple grouping
variables. Allowed values include "holm", "hochberg", "hommel",
"bonferroni", "BH", "BY", "fdr", "none". If you don't want to adjust the p
value (not recommended), use p.adjust.method = "none".
a list of arguments specifying the signifcance cutpoints
and symbols. For example, significance <- list(cutpoints = c(0,
0.0001, 0.001, 0.01, 0.05, Inf), symbols = c("****", "***", "**", "*",
"ns"))
.
In other words, we use the following convention for symbols indicating statistical significance:
ns
: p > 0.05
*
: p <= 0.05
**
: p <= 0.01
***
: p <= 0.001
****
: p <= 0.0001
The geometric object to use to display the data for this layer.
When using a stat_*()
function to construct a layer, the geom
argument
can be used to override the default coupling between stats and geoms. The
geom
argument accepts the following:
A Geom
ggproto subclass, for example GeomPoint
.
A string naming the geom. To give the geom as a string, strip the
function name of the geom_
prefix. For example, to use geom_point()
,
give the geom as "point"
.
For more information and other ways to specify the geom, see the layer geom documentation.
A position adjustment to use on the data for this layer. This
can be used in various ways, including to prevent overplotting and
improving the display. The position
argument accepts the following:
The result of calling a position function, such as position_jitter()
.
This method allows for passing extra arguments to the position.
A string naming the position adjustment. To give the position as a
string, strip the function name of the position_
prefix. For example,
to use position_jitter()
, give the position as "jitter"
.
For more information and other ways to specify the position, see the layer position documentation.
If FALSE (the default), removes missing values with a warning. If TRUE silently removes missing values.
logical. Should this layer be included in the legends?
NA
, the default, includes if any aesthetics are mapped.
FALSE
never includes, and TRUE
always includes.
It can also be a named logical vector to finely select the aesthetics to
display. To include legend keys for all levels, even
when no data exists, use TRUE
. If NA
, all levels are shown in legend,
but unobserved levels are omitted.
If FALSE
(the default for most ggpubr functions),
overrides the default aesthetics, rather than combining with them. This is
most useful for helper functions that define both data and aesthetics and
shouldn't inherit behaviour from the default plot specification. Set to
TRUE
to inherit aesthetics from the parent ggplot layer.
If TRUE, the labels will be parsed into expressions and displayed
as described in ?plotmath
.
other arguments passed to the function geom_bracket()
or
geom_text()
statistic: the Kruskal-Wallis rank sum chi-squared statistic used to compute the p-value.
p: p-value.
p.adj: Adjusted p-values.
p.signif: P-value significance.
p.adj.signif: Adjusted p-value significance.
p.format: Formated p-value.
p.adj.format: Formated adjusted p-value.
n: number of samples.
# Data preparation
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Transform `dose` into factor variable
df <- ToothGrowth
df$dose <- as.factor(df$dose)
# Add a random grouping variable
set.seed(123)
df$group <- sample(factor(rep(c("grp1", "grp2", "grp3"), 20)))
df$len <- ifelse(df$group == "grp2", df$len+2, df$len)
df$len <- ifelse(df$group == "grp3", df$len+7, df$len)
head(df, 3)
#> len supp dose group
#> 1 4.2 VC 0.5 grp1
#> 2 18.5 VC 0.5 grp3
#> 3 14.3 VC 0.5 grp3
# Basic boxplot
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Create a basic boxplot
# Add 5% and 10% space to the plot bottom and the top, respectively
bxp <- ggboxplot(df, x = "dose", y = "len") +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1)))
# Add the p-value to the boxplot
bxp + stat_kruskal_test()
# Change the label position
# Using coordinates in data units
bxp + stat_kruskal_test(label.x = "1", label.y = 10, hjust = 0)
# Format the p-value differently
custom_p_format <- function(p) {
rstatix::p_format(p, accuracy = 0.0001, digits = 3, leading.zero = FALSE)
}
bxp + stat_kruskal_test(
label = "Kruskal-Wallis, italic(p) = {custom_p_format(p)}{p.signif}"
)
#> Warning: Computation failed in `stat_compare_multiple_means()`.
#> Caused by error in `mutate()`:
#> ℹ In argument: `label = glue(label)`.
#> Caused by error:
#> ! Failed to evaluate glue component {custom_p_format(p)}
#> Caused by error in `custom_p_format()`:
#> ! could not find function "custom_p_format"
# Show a detailed label in italic
bxp + stat_kruskal_test(label = "as_detailed_italic")
# Faceted plots
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
# Create a ggplot facet
bxp <- ggboxplot(df, x = "dose", y = "len", facet.by = "supp") +
scale_y_continuous(expand = expansion(mult = c(0.05, 0.1)))
# Add p-values
bxp + stat_kruskal_test()
# Grouped plots
#%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
bxp2 <- ggboxplot(df, x = "group", y = "len", color = "dose", palette = "npg")
# For each x-position, computes tests between legend groups
bxp2 + stat_kruskal_test(aes(group = dose), label = "p = {p.format}{p.signif}")
# For each legend group, computes tests between x variable groups
bxp2 + stat_kruskal_test(aes(group = dose, color = dose), group.by = "legend.var")