- 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
ANOVA test methods. Possible values are one of
c("one_way", "one_way_repeated", "two_way", "two_way_repeated",
"two_way_mixed").
- 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.
- type
the type of sums of squares for ANOVA. Allowed values are either
1, 2 or 3. type = 2 is the default because this will yield identical
ANOVA results as type = 1 when data are balanced but type = 2 will
additionally yield various assumption tests where appropriate. When the data
are unbalanced the type = 3 is used by popular commercial softwares
including SPSS.
- effect.size
the effect size to compute and to show in the ANOVA
results. Allowed values can be either "ges" (generalized eta squared) or
"pes" (partial eta squared) or both. Default is "ges".
- error
(optional) for a linear model, an lm model object from which the
overall error sum of squares and degrees of freedom are to be calculated.
Read more in Anova() documentation.
- correction
character. Used only in repeated measures ANOVA test to
specify which correction of the degrees of freedom should be reported for
the within-subject factors. Possible values are:
"GG":
applies Greenhouse-Geisser correction to all within-subjects factors even if
the assumption of sphericity is met (i.e., Mauchly's test is not
significant, p > 0.05).
"HF": applies Hyunh-Feldt correction to all
within-subjects factors even if the assumption of sphericity is met,
"none": returns the ANOVA table without any correction and
"auto": apply automatically GG correction to only within-subjects
factors violating the sphericity assumption (i.e., Mauchly's test p-value is
significant, p <= 0.05).
- label
character string specifying label. Can be:
the
column containing the label (e.g.: label = "p" or label =
"p.adj"), where p is the p-value. Other possible values are
"p.signif", "p.adj.signif", "p.format", "p.adj.format".
an
expression that can be formatted by the glue() package.
For example, when specifying label = "Anova, p = \{p\}", the
expression {p} will be replaced by its value.
a combination of
plotmath expressions and glue expressions. You may want some of the
statistical parameter in italic; for example:label = "Anova, italic(p)
= {p}".
a constant: label = "as_italic": display statistical
parameters in italic; label = "as_detailed": detailed plain text;
label = "as_detailed_expression" or label =
"as_detailed_italic": detailed plotmath expression. Statistical parameters
will be displayed in italic.
.
- 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 value in with the increase in fraction of total
height for every additional comparison to minimize overlap. The step value
can be negative to reverse the order of groups.
- 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 to pass to
geom_text, such as: