# The plotting functions for the AnalysisResults object

# (predict from parameters)

##' @import ggplot2

#' @include study.R results.R eventPrediction_package.R

NULL

##' @param text Text to display be in title, e.g. output

##' from the getSummaryText() function.

##' @param options Use this to customize the output.

##' @param show.separate.arms Logical, if TRUE (and if x is a two arm study) the expected event

##' curves for the separate arms are displayed on the graph, otherwise do not show the curves.

##' @rdname plot-methods

##' @name plot

##' @aliases plot,AnalysisResults,missing-method

##' @export

setMethod( "plot", 

  signature( x = "AnalysisResults",y="missing" ),

  function(x,text=getFromParameterText(x, options = options), 

        options = DisplayOptions(text.width=110), show.title=TRUE,show.separate.arms=!isSingleArm(x@study),

             ylim=NULL) {

    ####### draw plot ######

    daysinyear <- standarddaysinyear()

    study <- x@study

    if(isSingleArm(study)) show.separate.arms <- FALSE

    ts <- x@grid$time

    recruit.tot <- x@grid$recruit.tot

    events1 <- x@grid$events1

    events2 <- x@grid$events2

    events.tot <- x@grid$events.tot

    N <- study@N 

    Y <- study@study.duration

    oldmar <- par()$mar

    oldlas <- par()$las

    if(show.title){

      chr.pos <- which(unlist(strsplit(text,NULL)) == '\n') 

      chr.count <- length(chr.pos) 

      mar_val <- 1+chr.count

    }

    else{

      mar_val <- 0.4

    }

    par( mar= c(5,4,mar_val,2)+0.1, las=1 )

    plot(range(ts),range(x@grid$recruit.tot),type='n',xlab=" ",ylab=" ", axes=F, ylim=ylim)

    #Y axes

    if(is.null(ylim)){ 

      ylim <- c(0,N)

    }

    else{

      N <- ylim[2]-ylim[1]

    }  

    rounding <- -floor(log(N,10)-0.3)

    startpoint <- round(ylim[1],rounding)

    endpoint <- ylim[2]

    axis(side=2,at=(seq(startpoint,endpoint,10^(-rounding))), adj=1, cex.axis=1.00)

    mtext("N",side=2,at=((ylim[2]-ylim[1])/2),line=3) 

    #X Axis 

    if(options@StartDate=="0") {

      #Numbers

      axis(side=1,at=(0:Y), adj=1, cex.axis=0.85)

    }

    else{

      #Dates  

      startd <- as.Date( options@StartDate, format="%d/%m/%Y")

      date2  <- as.Date(startd+(0:ceiling(ts[length(ts)]))*daysinyear/12, format="%d/%m/%Y")

      date  <- format(date2, format="%b %Y")

      every <- floor(length(date)/50)

      ats <- seq(0,length(date)-1,every+1)

      date <- date[c(TRUE,rep(FALSE,every))]

      axis(side=1,at=ats, labels=as.character(date),adj=1,cex.axis=0.85, las=2)

    }

    #X Axes Labels

    if( options@StartDate=="0" ) {

      mtext('Time (Months)',side=1,at=(Y/2),line=2)

    } else{

      #Dates - not outputting  

      #mtext('Time',side=1,at=-1.5,line=2)

    }

    #Add Lines

    box()

    lines(ts,recruit.tot,lty=1,col="black",lwd=2)

    if(show.separate.arms ){  

      lines(ts,events2,lty=8,col="red",lwd=2)

      lines(ts,events1,lty=8,col="blue",lwd=2)

    }

    lines(ts,events.tot,lty=8,col="black",lwd=2)

    if( nrow(x@critical.data)>0 ) abline( v = x@critical.data$time )

    if( nrow(x@predict.data) > 0  )  {

      abline(v = x@predict.data$time, lty = 2)

      if(show.separate.arms){ 

        abline(h = x@predict.data$events2,lty=2,col="red")

        abline(h = x@predict.data$events1,lty=2, col="blue")

      }

    }

    if(show.separate.arms){ 

      legend( "topleft", c("Recruitment", "Events : Total", "Events : Control", "Events : Experimental" ),

              col=c( "black", "black", "blue", "red" ),

              lty=c(1,8,8,8),text.col=c("black","black","blue","red"), lwd=c(2,2,2,2), bty="n")

    }

    else{

      legend( "topleft", c("Recruitment", "Events : Total" ),

              col=c( "black", "black" ),

              lty=c(1,8),text.col=c("black","black"), lwd=c(2,2), bty="n")  

    }

    ####### Add in Summary Info and Results ######

    if( show.title==TRUE ) {

      mtext(text,side=3,cex=1,adj=0)

    } 

    par( mar=oldmar, las=oldlas )

})