R/plot_ICABinCont.R

In Surrogate: Evaluation of Surrogate Endpoints in Clinical Trials

#' @export
plot.ICA.BinCont <- function(x, Histogram.ICA=TRUE, Mixmean=TRUE, Mixvar=TRUE, Deviance=TRUE,
                             Type="Percent", Labels=FALSE, ...){

  Object <- x


  if (Histogram.ICA==TRUE){
    Xlab <- expression(R[H]^2)
    Main = " "


    if (Type=="Density"){
    plot(density(x$R2_H, na.rm = T), xlab=Xlab, ylab="Density", main=Main, lwd=2, ...)
    }
    if (Type=="Freq"){
      h <- hist(Object$R2_H, plot = FALSE, ...)
      h$density <- h$counts/sum(h$counts)
      cumulMidPoint <- ecdf(x=Object$R2_H)(h$mids)
      labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")

      if (Labels==FALSE){
        plot(h,freq=T, xlab=Xlab, ylab="Frequency", main=Main, col="grey", ...)
      }
      if (Labels==TRUE){
        plot(h,freq=T, xlab=Xlab, ylab="Frequency", main=Main, labels=labs, col="grey", ...)
      }
    }

    if (Type=="Percent"){

      h <- hist(Object$R2_H, plot = FALSE, ...)
      h$density <- h$counts/sum(h$counts)
      cumulMidPoint <- ecdf(x=Object$R2_H)(h$mids)
      labs <- paste(round((1-cumulMidPoint), digits=4)*100, "%", sep="")

      if (Labels==FALSE){
        plot(h, freq=F, xlab=Xlab, ylab="Percentage", main=Main, col="grey", ...)
      }
      if (Labels==TRUE){
        plot(h, freq=F, xlab=Xlab, ylab="Percentage", main=Main, labels=labs, col="grey", ...)
      }
      }

    if (Type=="CumPerc"){

      h <- hist(Object$R2_H, breaks=length(Object$R2_H), plot = FALSE, ...)
      h$density <- h$counts/sum(h$counts)
      cumulative <- cumsum(h$density)
      plot(x=h$mids, y=cumulative, xlab=Xlab, ylab="Cumulative percentage", col=0, main=Main, ...)
      lines(x=h$mids, y=cumulative)
    }
  } # end of histogram


if (Mixmean==TRUE){

Xlab <- expression(Run)
Ylab <- expression(Mean)
Main_S0 <- expression(S[0])
Main_S1 <- expression(S[1])

  par(mfrow=c(1,2))
  plot(Object$mean_Y_S0, type = "p", ylim = c(round(min(Object$mean_Y_S0, Object$mean.S0))-1,
                                              round(max(Object$mean_Y_S0, Object$mean.S0))+1),
       main = Main_S0, xlab = Xlab, ylab = Ylab, ...)
  abline(h = Object$mean.S0, col = "red", lty = 2, lwd = 4)

  plot(Object$mean_Y_S1, type = "p", ylim = c(round(min(Object$mean_Y_S1, Object$mean.S1))-1, round(max(Object$mean_Y_S1,Object$mean.S1))+1),
       main = Main_S1, xlab = Xlab, ylab = Ylab, ...)
  abline(h = Object$mean.S1, col = "red", lty = 2, lwd = 4)
  par(mfrow=c(1,1))

}


  if (Mixvar==TRUE){

    Xlab <- expression(Run)
    Ylab <- expression(Variance)
    Main_S0 <- expression(S[0])
    Main_S1 <- expression(S[1])

    par(mfrow=c(1,2))
    plot(Object$var_Y_S0, type = "p", ylim = c(round(min(Object$var_Y_S0, Object$var.S0))-1,
                                                round(max(Object$var_Y_S0, Object$var.S0))+1),
         main = Main_S0, xlab = Xlab, ylab = Ylab, ...)
    abline(h = Object$var.S0, col = "red", lty = 2, lwd = 4)

    plot(Object$var_Y_S1, type = "p", ylim = c(round(min(Object$var_Y_S1, Object$var.S1))-1, round(max(Object$var_Y_S1,Object$var.S1))+1),
         main = Main_S1, xlab = Xlab, ylab = Ylab, ...)
    abline(h = Object$var.S1, col = "red", lty = 2, lwd = 4)
    par(mfrow=c(1,1))

  }



  if (Deviance==TRUE){
  par(mfrow=c(1,2))
  boxplot(Object$dev_S0, main = expression(S[0]), ylab = "deviance", ylim = NULL)
  boxplot(Object$dev_S1, main = expression(S[1]), ylab = "deviance", ylim = NULL)
  par(mfrow=c(1,2))
  }


  }