stat_signif: Create significance layer

Description Usage Arguments Examples

View source: R/significance_annotation.R

Description

Create significance layer

Usage

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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, 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, manual = FALSE, ...)

Arguments

mapping

Set of aesthetic mappings created by aes or 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.

position

Position adjustment, either as a string, or the result of a call to a position adjustment function.

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.

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.

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 columns of interest

test

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'.

test.args

additional arguments for the test method

annotations

character vector with alternative annotations, if not null test is ignored

map_signif_level

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)

y_position

numeric vector with the y positions of the brackets

xmin

numeric vector with the positions of the left sides of the brackets

xmax

numeric vector with the positions of the right sides of the brackets

margin_top

numeric vector how much higher that the maximum value that bars start as fraction of total height

step_increase

numeric vector with the increase in fraction of total height for every additional comparison to minimize overlap.

tip_length

numeric vector with the fraction of total height that the bar goes down to indicate the precise column

size

change the width of the lines of the bracket

textsize

change the size of the text

family

change the font used for the text

vjust

move the text up or down relative to the bracket

manual

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.

stat

The statistical transformation to use on the data for this layer, as a string.

Examples

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## 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(annotations = c("First", "Second"),
              y_position = c(30, 40), xmin=c(4,1), xmax=c(5,3))

## End(Not run)

Artjom-Metro/ggsignif documentation built on Nov. 7, 2017, 5:07 a.m.