boxplot
gg_boxplot.Rd
boxplot
Usage
gg_boxplot(
data,
x,
y,
method = "wilcox.test",
label = "p.signif",
ref.group = NULL,
comparisons = NULL,
...
)
Arguments
- data
data frame
- x
x
- y
y
- method
stat method, default is 'wilcox.test'
- label
default is 'p.signif'
- 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.
- ...
Arguments passed on to
ggpubr::stat_compare_means
mapping
Set of aesthetic mappings created by
aes()
. If specified andinherit.aes = TRUE
(the default), it is combined with the default mapping at the top level of the plot. You must supplymapping
if there is no plot mapping.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.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.x.npc,label.y.npc
can be
numeric
orcharacter
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, either as a
ggproto
Geom
subclass or as a string naming the geom stripped of thegeom_
prefix (e.g."point"
rather than"geom_point"
)position
Position adjustment, either as a string naming the adjustment (e.g.
"jitter"
to useposition_jitter
), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.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, andTRUE
always includes. It can also be a named logical vector to finely select the aesthetics to display.inherit.aes
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()
.
Examples
data("PlantGrowth")
gg_boxplot(PlantGrowth, group, weight, ref.group = "ctrl")
gg_boxplot(PlantGrowth,group, weight, ref.group = "ctrl",
method = "t.test", label = "p.format")