R/plot.SurvSurv.R

In Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

plot.SurvSurv <- function(x, Trial.Level=TRUE, Weighted=TRUE, 
Indiv.Level.By.Trial=TRUE, Xlab.Indiv, Ylab.Indiv, Xlab.Trial, 
Ylab.Trial, Main.Trial, Main.Indiv, 
Par=par(oma=c(0, 0, 0, 0), mar=c(5.1, 4.1, 4.1, 2.1)),...){
 
  Object <- x 
   
  if (Trial.Level==TRUE){ 
    if (missing(Xlab.Trial)) {Xlab.Trial <- expression(paste("Treatment effect on the surrogate endpoint ", (alpha[i])))}
    if (missing(Ylab.Trial)) {Ylab.Trial <- expression(paste("Treatment effect on the true endpoint  ",(beta[i])))}
    if (missing(Main.Trial)) {Main.Trial <- c("Trial-level surrogacy")}
    dev.new()
    par=Par
    if (Weighted==TRUE){
      plot(Object$Results.Stage.1$LogHazard_True, Object$Results.Stage.1$LogHazard_Surr, 
           cex=(Object$Results.Stage.1$Trial.Size/max(Object$Results.Stage.1$Trial.Size))*8, 
           xlab=Xlab.Trial, ylab=Ylab.Trial, main=Main.Trial, ...)
      abline(lm(Object$Results.Stage.1$LogHazard_True ~ Object$Results.Stage.1$LogHazard_Surr))}
    
    if (Weighted==FALSE){
      plot(Object$Results.Stage.1$LogHazard_True, Object$Results.Stage.1$LogHazard_Surr, 
           cex=1, xlab=Xlab.Trial, ylab=Ylab.Trial, main=Main.Trial, ...)
      abline(lm(Object$Results.Stage.1$LogHazard_True ~ Object$Results.Stage.1$LogHazard_Surr))}
  }
 
  if (Indiv.Level.By.Trial==TRUE){ 
    if (missing(Xlab.Indiv)) {Xlab.Indiv <- expression(paste("LRF"[a]))}
    if (missing(Ylab.Indiv)) {Ylab.Indiv <- "Trial"}
    if (missing(Main.Indiv)) {Main.Indiv <- c("Individual-level surrogacy")}
    dev.new()
    par=Par
    plot(y=(1:dim(Object$R2.hInd.By.Trial)[1]), x=Object$R2.hInd.By.Trial[,2], yaxt = "n",
         xlab=Xlab.Indiv, ylab=Ylab.Indiv, main=Main.Indiv, xlim=c(0, 1), ...)
    axis(2, at=(1:dim(Object$R2.hInd.By.Trial)[1]), labels=Object$R2.hInd.By.Trial[,1])
    for (i in 1: dim(Object$R2.hInd.By.Trial)[1]){
      segments(y0 = i, x0 = Object$R2.hInd.By.Trial[i,3], y1 = i, x1 = Object$R2.hInd.By.Trial[i,4], lty=2)
    }
    
  }    
  
}