Package 'ggpval'

Title: Annotate Statistical Tests for 'ggplot2'
Description: Automatically performs desired statistical tests (e.g. wilcox.test(), t.test()) to compare between groups, and adds the resulting p-values to the plot with an annotation bar. Visualizing group differences are frequently performed by boxplots, bar plots, etc. Statistical test results are often needed to be annotated on these plots. This package provides a convenient function that works on 'ggplot2' objects, performs the desired statistical test between groups of interest and annotates the test results on the plot.
Authors: Jun Cheng [aut, cre]
Maintainer: Jun Cheng <[email protected]>
License: GPL-3
Version: 0.2.5
Built: 2025-02-27 03:46:32 UTC
Source: https://github.com/s6juncheng/ggpval

Help Index

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')