add brackets with label annotation to a ggplot. Helpers for adding p-value or significance levels to a plot.
stat_bracket(
mapping = NULL,
data = NULL,
position = "identity",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE,
label = NULL,
type = c("text", "expression"),
y.position = NULL,
xmin = NULL,
xmax = NULL,
step.increase = 0,
step.group.by = NULL,
tip.length = 0.03,
bracket.nudge.y = 0,
bracket.shorten = 0,
size = 0.3,
label.size = 3.88,
family = "",
vjust = 0,
...
)
geom_bracket(
mapping = NULL,
data = NULL,
stat = "bracket",
position = "identity",
na.rm = FALSE,
show.legend = NA,
inherit.aes = TRUE,
label = NULL,
type = c("text", "expression"),
y.position = NULL,
xmin = NULL,
xmax = NULL,
step.increase = 0,
step.group.by = NULL,
tip.length = 0.03,
bracket.nudge.y = 0,
bracket.shorten = 0,
size = 0.3,
label.size = 3.88,
family = "",
vjust = 0,
coord.flip = 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)
).
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.
character vector with alternative label, if not null test is ignored
the label type. Can be one of "text" and "expression" (for parsing plotmath expression).
numeric vector with the y positions of the brackets
numeric vector with the positions of the left sides of the brackets
numeric vector with the positions of the right sides of the brackets
numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.
a variable name for grouping brackets before adding step.increase. Useful to group bracket by facet panel.
numeric vector with the fraction of total height that the bar goes down to indicate the precise column
Vertical adjustment to nudge brackets by. Useful to move up or move down the bracket. If positive value, brackets will be moved up; if negative value, brackets are moved down.
a small numeric value in [0-1] for shortening the with of bracket.
change the width of the lines of the bracket
change the size of the label text
change the font used for the text
move the text up or down relative to the bracket
other arguments passed on to layer()
). These are often
aesthetics, used to set an aesthetic to a fixed value, like color =
"red"
or size = 3
. They may also be parameters to the paired
geom/stat.
The statistical transformation to use on the data for this layer.
When using a geom_*()
function to construct a layer, the stat
argument can be used to override the default coupling between geoms and
stats. The stat
argument accepts the following:
A Stat
ggproto subclass, for example StatCount
.
A string naming the stat. To give the stat as a string, strip the
function name of the stat_
prefix. For example, to use stat_count()
,
give the stat as "count"
.
For more information and other ways to specify the stat, see the layer stat documentation.
logical. If TRUE
, flip x and y coordinates so that
horizontal becomes vertical, and vertical, horizontal. When adding the
p-values to a horizontal ggplot (generated using
coord_flip()
), you need to specify the option
coord.flip = TRUE
.
df <- ToothGrowth
df$dose <- factor(df$dose)
# Add bracket with labels
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
xmin = "0.5", xmax = "1", y.position = 30,
label = "t-test, p < 0.05"
)
# Customize bracket tip.length tip.length
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
xmin = "0.5", xmax = "1", y.position = 30,
label = "t-test, p < 0.05", tip.length = c(0.2, 0.02)
)
#Using plotmath expression
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
xmin = "0.5", xmax = "1", y.position = 30,
label = "list(~italic(p)<=0.001)", type = "expression",
tip.length = c(0.2, 0.02)
)
# Specify multiple brackets manually
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
xmin = c("0.5", "1"), xmax = c("1", "2"),
y.position = c(30, 35), label = c("***", "**"),
tip.length = 0.01
)
# Compute statistical tests and add p-values
stat.test <- compare_means(len ~ dose, ToothGrowth, method = "t.test")
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
aes(xmin = group1, xmax = group2, label = signif(p, 2)),
data = stat.test, y.position = 35
)
# Increase step length between brackets
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
aes(xmin = group1, xmax = group2, label = signif(p, 2)),
data = stat.test, y.position = 35, step.increase = 0.1
)
# Or specify the positions of each comparison
ggboxplot(df, x = "dose", y = "len") +
geom_bracket(
aes(xmin = group1, xmax = group2, label = signif(p, 2)),
data = stat.test, y.position = c(32, 35, 38)
)