CitFuns/man/ggstats_add_xy.Rd

\name{ggstats_add_xy}
\alias{ggstats_add_xy}
\title{ggstats_add_xy}
\usage{
ggstats_add_xy(table_stat, table, group, xcol=NULL, y="max", bracket.offset=0.05, bracket.inspace=0.05, exclude_group=NULL)
}
\arguments{
  \item{table_stat}{A table generated by a rstatix funcion such as t_test() or wilcox_test().}
  \item{table}{The original table that was introduced to ggplot.}
  \item{group}{The grouping variable.}
  \item{xcol}{The X-axis variable. If null (the default), the function will pick the first column. This is intended when exclude_group is null.}
  \item{y}{The algorithm used to calculate the y height. Is useful to adapt to plots that show all events, bars with the mean, etc... Options are "max" (default), "mean", "mean+sd", "mean+sem".}
  \item{bracket.offset}{Increasing this parameter incresases the y position of the brackets.}
  \item{bracket.inspace}{Increasing this parameter increases the space between brackets.}
  \item{exclude_group}{Variable(s) that will not be grouped. This aims to preserve the variable in order to facet.}
}
\description{
Generates a table with the coordinates that is required by the ggpubr function "stat_pvalue_manual".
}
\examples{
library(tidyverse)
library(ggpubr)
library(rstatix)


df<-data.frame("pats"=paste0("PAT", 1:20), "Group"=rep(c("A","B"),each=10),"CytA"=rnorm(20,5), "CytB"=rnorm(20,5),"CytC"=c(rnorm(5,10),rnorm(5,10),rnorm(5,5),rnorm(5,5)),"CytD"=rnorm(20,5),"CytE"=c(rnorm(5,10),rnorm(5,5),rnorm(5,10),rnorm(5,5)),"CytF"=rnorm(20,5),"CytG"=c(rnorm(5,5),rnorm(5,5),rnorm(5,7),rnorm(5,7)))

mdf<-gather(df, "Cytokine","Value",-c(pats,Group))

g<-ggplot(mdf, aes(Cytokine, Value, color=Group))+
  geom_boxplot()+
  geom_point(position=position_dodge(width = 0.75))

stat.test<-mdf \%>\% group_by(Cytokine) \%>\% t_test(Value~Group)
g+stat_pvalue_manual(ggstats_add_xy(stat.test, mdf, "Group"),  label = "p", tip.length = 0.02, hide.ns = T)
}