R/plot.MetaAnalyticMTS.R

In Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

plot.UnifixedContCont <- plot.BifixedContCont <- plot.UnimixedContCont <-
  function(x, Trial.Level=TRUE, Weighted=TRUE, Indiv.Level=TRUE, ICA=TRUE, Entropy.By.ICA=FALSE,
  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")}
    par=Par
    if (Weighted==TRUE){
      plot(Object$Results.Stage.1$Treatment.S, Object$Results.Stage.1$Treatment.T, cex=(Object$Results.Stage.1$Obs.per.trial/max(Object$Results.Stage.1$Obs.per.trial))*8, xlab=Xlab.Trial, ylab=Ylab.Trial, main=Main.Trial,...)
      abline(lm(Object$Results.Stage.1$Treatment.T ~ Object$Results.Stage.1$Treatment.S))}

    if (Weighted==FALSE){
      plot(Object$Results.Stage.1$Treatment.S, Object$Results.Stage.1$Treatment.T, xlab=Xlab.Trial, ylab=Ylab.Trial, main=Main.Trial, ...)
      abline(lm(Object$Results.Stage.1$Treatment.T ~ Object$Results.Stage.1$Treatment.S))}
  }


  if (ICA==TRUE){
    Fit <- MaxEntContCont(x=Object$ICA, T0T0 = Object$T0T0, T1T1 = Object$T1T1, S0S0 = Object$S0S0, S1S1 = Object$S1S1)
    plot(Fit, Main="Individual Causal Association")
    }

  if (Entropy.By.ICA==TRUE){
    Fit <- MaxEntContCont(x=Object$ICA, T0T0 = Object$T0T0, T1T1 = Object$T1T1, S0S0 = Object$S0S0, S1S1 = Object$S1S1)
    plot(Fit, Entropy.By.ICA = TRUE)
    points(x=Fit$Max.Ent, y=Fit$ICA.Max.Ent, col="red", pch=3, cex=2)
    }


  if (Indiv.Level==TRUE){
    if (missing(Xlab.Indiv)) {Xlab.Indiv <- expression(paste("Residuals for the surrogate endpoint ", (epsilon[Sij])))}
    if (missing(Ylab.Indiv)) {Ylab.Indiv <- expression(paste("Residuals for the true endpoint  ", (epsilon[Tij])))}
    if (missing(Main.Indiv)) {Main.Indiv <- c("Individual-level surrogacy")}
    par=Par
    plot(x=Object$Residuals.Stage.1$Residuals.Model.S, y=Object$Residuals.Stage.1$Residuals.Model.T, xlab=Xlab.Indiv, ylab=Ylab.Indiv, main=Main.Indiv, ...)
    abline(lm(Object$Residuals.Stage.1$Residuals.Model.T ~ -1 + Object$Residuals.Stage.1$Residuals.Model.S))
  }
}





plot.BimixedContCont <- function(x, Trial.Level=TRUE, Weighted=TRUE, Indiv.Level=TRUE, ICA=TRUE, Entropy.By.ICA=FALSE,
                                 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")}
    par=Par
    if (Weighted==TRUE){
      plot(data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.S, data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.T, cex=(data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Obs.per.trial / (max(data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Obs.per.trial)))*8, xlab=Xlab.Trial, ylab=Ylab.Trial, main=Main.Trial,...)
      abline(lm(data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.T ~ data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.S))
    }

    if (Weighted==FALSE){
      plot(data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.S, data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.T, xlab=Xlab.Trial, ylab=Ylab.Trial, main=Main.Trial, ...)
      abline(lm(data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.T ~ data.frame(Object$Trial.Spec.Results, stringsAsFactors = TRUE)$Treatment.S))
    }
  }

  if (ICA==TRUE){
    Fit <- MaxEntContCont(x=Object$ICA, T0T0 = Object$T0T0, T1T1 = Object$T1T1, S0S0 = Object$S0S0, S1S1 = Object$S1S1)
    plot(Fit, Main="Individual Causal Association")
  }

  if (Entropy.By.ICA==TRUE){
    Fit <- MaxEntContCont(x=Object$ICA, T0T0 = Object$T0T0, T1T1 = Object$T1T1, S0S0 = Object$S0S0, S1S1 = Object$S1S1)

    plot(Fit, Entropy.By.ICA = TRUE)
    points(x=Fit$Max.Ent, y=Fit$ICA.Max.Ent, col="red", pch=3, cex=2)
  }


  if (Indiv.Level==TRUE){
    if (missing(Xlab.Indiv)) {Xlab.Indiv <- expression(paste("Residuals for the surrogate endpoint ", (epsilon[Sij])))}
    if (missing(Ylab.Indiv)) {Ylab.Indiv <- expression(paste("Residuals for the true endpoint  ", (epsilon[Tij])))}
    if (missing(Main.Indiv)) {Main.Indiv <- c("Individual-level surrogacy")}
    par=Par
    plot(x=Object$Residuals$Residuals.S, y=Object$Residuals$Residuals.T, xlab=Xlab.Indiv, ylab=Ylab.Indiv, main=Main.Indiv, ...)
    abline(lm(Object$Residuals$Residuals.T ~ -1 + Object$Residuals$Residuals.S))
  }
}