R/CreateScreePlot.R

In fdapace: Functional Data Analysis and Empirical Dynamics

#' Create the scree plot for the fitted eigenvalues
#'
#' This function will open a new device if not instructed otherwise.
#'
#' @param fpcaObj A object of class FPCA returned by the function FPCA().
#' @param ... Additional arguments for the 'plot' function.
#'
#' @examples
#' set.seed(1)
#' n <- 20
#' pts <- seq(0, 1, by=0.05)
#' sampWiener <- Wiener(n, pts)
#' sampWiener <- Sparsify(sampWiener, pts, 10)
#' res <- FPCA(sampWiener$Ly, sampWiener$Lt, 
#'             list(dataType='Sparse', error=FALSE, kernel='epan', verbose=TRUE))
#' CreateScreePlot(res)
#' @export

CreateScreePlot <-function(fpcaObj, ...){ 
 
  args1 <- list( main="Scree plot", ylab='Fraction of variance explained', xlab='Number of components')  
  inargs <- list(...)
  args1[names(inargs)] <- inargs
 
  ys <- fpcaObj$cumFVE ;
  
  
  if( !is.vector(ys) ){ 
    stop('Please use a vector as input.')   
  }
  if(max(ys) > 1){
    warning('The maximum number in the input vector is larger than 1; are you sure it is right?');
  }
  if(any(ys < 0) || any(diff(ys) <0) ){
    stop('This is not a valid cumulative FVE vector.')
  }

  dfbar <- do.call( barplot, c( args1, list( ylim=c(0,1.05)), list(axes=FALSE), list(height =  rep(NA,length(ys))) ) )
    
  abline(h=(seq(0,1,.05)), col="lightgray", lty="dotted")
  barplot(c(ys[1], diff(ys)), add = TRUE , names.arg = as.character(1:fpcaObj$selectK))
  lines(dfbar, y= ys, col='red')
  points(dfbar, y= ys, col='red')
  legend("right", "Cumul. FVE", col='red', lty=1, pch=1, bty='n') 
   
}