add_pval {ggpval}

Add p-values to ggplot objects.

Description

Add p-values to ggplot objects.

Usage

add_pval(
  ggplot_obj,
  pairs = NULL,
  test = "wilcox.test",
  heights = NULL,
  barheight = NULL,
  textsize = 5,
  pval_text_adj = NULL,
  annotation = NULL,
  log = FALSE,
  pval_star = FALSE,
  plotly = FALSE,
  fold_change = FALSE,
  parse_text = NULL,
  response = "infer",
  ...
)

Arguments

ggplot_obj

ggplot object

pairs

a list pairs of comparison. Groups indicated by integer numbers counted from left to right. e.g. list(c(1, 2), c(2, 3)) will compare first group with second, second group with third

test

character of statistical testing method. e.g. t.test, wilcox.test. Default wilcox.test

heights

integer or vector of integers. The heights of the p-value/annotation. Default maximum value from the data

barheight

tip bar height of the annotation. Default calculated by range_y / 20

textsize

p-value/annotation text size

pval_text_adj

distance of p-value/annotation from annotation bar. Default barheight/2

annotation

text to annotate. If specified, statistical test will not be done

log

whether y axis is log transformed. Default FALSE

pval_star

whether transform pval numbers to stars

plotly

set to TRUE if wrap the plot with 'ggploty'

fold_change

whether also compute and show fold changes. Default FALSE.

parse_text

whether parse the annotation text (NULL, TRUE, FALSE). If NULL, p-values will be parsed, text annotations will not. Default NULL.

response

the column that contains the data for statistical testing. Default infer from ggplot object.

...

additional arguments for statistical testing function (e.g. alternative = "less").

Examples

library(ggplot2)
library(ggpval)
data("PlantGrowth")
plt <- ggplot(PlantGrowth, aes(group, weight)) +
  geom_boxplot()
add_pval(plt, pairs = list(c(1, 3)), test='wilcox.test')