- 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)).
- method
a character string indicating which method to be used for
comparing means.
- paired
a logical indicating whether you want a paired test. Used only
in t.test and in wilcox.test.
- method.args
a list of additional arguments used for the test method.
For example one might use method.args = list(alternative = "greater")
for wilcoxon test.
- ref.group
a character string specifying the reference group. If
specified, for a given grouping variable, each of the group levels will be
compared to the reference group (i.e. control group).
ref.group can be also ".all.". In this case, each of the
grouping variable levels is compared to all (i.e. basemean).
- comparisons
A list of length-2 vectors. The entries in the vector are
either the names of 2 values on the x-axis or the 2 integers that correspond
to the index of the groups of interest, to be compared.
- hide.ns
logical value. If TRUE, hide ns symbol when displaying
significance levels.
- label.sep
a character string to separate the terms. Default is ", ", to
separate the correlation coefficient and the p.value.
- label
character string specifying label type. Allowed values include
"p.signif" (shows the significance levels), "p.format" (shows the formatted
p 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.
- vjust
move the text up or down relative to the bracket.
- tip.length
numeric vector with the fraction of total height that the
bar goes down to indicate the precise column. Default is 0.03. Can be of
same length as the number of comparisons to adjust specifically the tip
lenth of each comparison. For example tip.length = c(0.01, 0.03).
If too short they will be recycled.
- bracket.size
Width of the lines of the bracket.
- step.increase
numeric vector with the increase in fraction of total
height for every additional comparison to minimize overlap.
- symnum.args
a list of arguments to pass to the function
symnum for symbolic number coding of p-values. For
example, symnum.args <- 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.
- ...
other arguments to pass to geom_text or
geom_label.