R/cr_eqn.R

In mssm-msf-2019/BiostatsALL:

#' A function that returns an equation with the pearson correlation coef and the pvalue  
#' @description This function calls with(db,cor(x,y,method='Pearson')) and constructs an equation with the estimates. Use to add equation to scatterplot
#' @param df : data base
#' @param x : name of the independent variable
#' @param y : name of the dependent variable
#' @examples 
#' cr_eqn(data,'x','y')

cr_eqn = function(df,x,y){
  cp<-with(data.frame(x=df[,x],y=df[,y]),cor.test(x,y,use='p'))
  db<-list(rc = format(cp$estimate, digits = 2),
           pc = format(cp$p.value, digits = 2),
           pc.exponent=floor(log10(cp$p.value)),
           pc.base =round(cp$p.value/(10^floor(log10(cp$p.value))), digits=1)
  )
  if  (cp$p.value==0)  eq <- substitute(~italic(r)~"="~rc~", "~italic(p)~"<"*10^-16, db)
  else  if  (db[['pc.base']]==1)  eq <- substitute(~italic(r)~"="~rc~", "~italic(p)~"="~10^pc.exponent, db)
  else  if  (db[['pc.exponent']]==(-1))  eq <- substitute(~italic(r)~"="~rc~", "~italic(p)~"="~pc, db)
  else   eq <- substitute(~italic(r)~"="~rc~", "~italic(p)~"="~pc.base%*%10^pc.exponent, db)
  
  paste(as.character(as.expression(eq)));                 
}