- mapping
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.
- data
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)).
- wid
(factor) column name containing individuals/subjects identifier.
Should be unique per individual. Required only for repeated measure tests
("one_way_repeated", "two_way_repeated", "friedman_test", etc).
- group.by
(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.
- label
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.
- label.x.npc, label.y.npc
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.
- label.x, label.y
numeric Coordinates (in data units) to be used
for absolute positioning of the label. If too short they will be recycled.
- step.increase
numeric vector with the increase in fraction of total
height for every additional comparison to minimize overlap.
- p.adjust.method
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".
- significance
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
- geom
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.
- position
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.
- na.rm
If FALSE (the default), removes missing values with a warning. If
TRUE silently removes missing values.
- show.legend
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.
- inherit.aes
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.
- parse
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()