Create significance layer
stat_signif(mapping = NULL, data = NULL, position = "identity",
na.rm = FALSE, show.legend = NA, inherit.aes = TRUE,
comparisons = NULL, test = "wilcox.test", test.args = NULL,
annotations = NULL, map_signif_level = FALSE, y_position = NULL,
xmin = NULL, xmax = NULL, margin_top = 0.05, step_increase = 0,
tip_length = 0.03, size = 0.5, textsize = 3.88, family = "",
vjust = 0, parse = FALSE, manual = FALSE, ...)geom_signif(mapping = NULL, data = NULL, stat = "signif",
position = "identity", na.rm = FALSE, show.legend = NA,
inherit.aes = TRUE, comparisons = NULL, test = "wilcox.test",
test.args = NULL, annotations = NULL, map_signif_level = FALSE,
y_position = NULL, xmin = NULL, xmax = NULL, margin_top = 0.05,
step_increase = 0, tip_length = 0.03, size = 0.5,
textsize = 3.88, family = "", vjust = 0, parse = FALSE,
manual = FALSE, ...)
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)
).
Position adjustment, either as a string, or the result of a call to a position adjustment function.
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.
If FALSE
, 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, e.g. borders()
.
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 columns of interest
the name of the statistical test that is applied to the values of the 2 columns (e.g. `t.test`, `wilcox.test` etc.). If you implement a custom test make sure that it returns a list that has an entry called `p.value`.
additional arguments for the test method
character vector with alternative annotations, if not null test is ignored
boolean value, if the p-value are directly written as annotation or asterisks are used instead. Alternatively one can provide a named numeric vector to create custom mappings from p-values to annotation: For example: c("***"=0.001, "**"=0.01, "*"=0.05) Alternatively, one can provide a function that takes a numeric argument (the p-value) and returns a string
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 how much higher that the maximum value that bars start as fraction of total height
numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.
numeric vector with the fraction of total height that the bar goes down to indicate the precise column
change the width of the lines of the bracket
change the size of the text
change the font used for the text
move the text up or down relative to the bracket
If `TRUE`, the labels will be parsed into expressions and displayed as described in `?plotmath`.
boolean flag that indicates that the parameters are provided with a data.frame. This option is necessary if one wants to plot different annotations per facet.
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, as a string.
# NOT RUN {
library(ggplot2)
library(ggsignif)
ggplot(mpg, aes(class, hwy)) +
geom_boxplot() +
geom_signif(comparisons = list(c("compact", "pickup"),
c("subcompact", "suv")))
ggplot(mpg, aes(class, hwy)) +
geom_boxplot() +
geom_signif(comparisons = list(c("compact", "pickup"),
c("subcompact", "suv")),
map_signif_level=function(p)sprintf("p = %.2g", p))
ggplot(mpg, aes(class, hwy)) +
geom_boxplot() +
geom_signif(annotations = c("First", "Second"),
y_position = c(30, 40), xmin=c(4,1), xmax=c(5,3))
# }
# NOT RUN {
# }
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