R/delScattering.R

In EEM: Read and Preprocess Fluorescence Excitation-Emission Matrix (EEM) Data

#' Delete scattering rays
#'
#' This function deletes two regions that are not related to fluorescence emission: 
#' (1) regions where emission wavelength is shorten than excitation light, 
#' (2) scattering rays and their second, third and forth order lights. 
#'
#' @param EEM A list containing EEM data as created by \code{\link{readEEM}} function.
#' @param rep (optional) Regions to be deleted are to be replaced with \code{rep}: 0 or NA
#' @param first (optional) Width of region to be deleted for first order scattering rays [nm]
#' @param second (optional) Width of region to be deleted for second order scattering rays [nm]
#' @param third (optional) Width of region to be deleted for third order scattering rays [nm]
#' @param forth (optional) Width of region to be deleted for forth order scattering rays [nm]
#'
#' @return A list similar to input \code{EEM} is returned but with all scattering rays deleted. 
#'
#' @examples
#' data(applejuice)
#' drawEEM(delScattering(applejuice, NA), 1)
#' 
#' @references Fujita, K., Tsuta, M., Kokawa, M., and Sugiyama, J. (2010). Detection of deoxynivalenol using fluorescence excitation--emission matrix. Food and Bioprocess Technology, 3(6), 922--927.
#' @keywords scattering
#'
#' @export

delScattering <-
function(EEM, rep = 0, first = 30, second = 40, third = 40, forth = 40){
  # input: EEM (list), rep: 0 or NA
  
  # make sure that all EEMs has the same dimension
  dimMat <- sapply(EEM , dim)
  if (sum(!apply(dimMat, 2, function (x) identical(dimMat[,1], x))) > 0){
    stop("Dimensions do not match. Please check your data.")
  }
  
  # get Ex and Em value
  Ex <- as.numeric(colnames(EEM[[1]]))
  Em <- as.numeric(rownames(EEM[[1]]))
  numEx <- length(Ex)
  numEm <- length(Em)
  
  # expand Ex and Em to full grid
  Ex_grid <- t(matrix(rep(Ex, numEm), numEx, numEm))
  Em_grid <- matrix(rep(Em, numEx), numEm, numEx)
  
  # set index for regions to be deleted (Em<Ex)
  delIndex <- Ex_grid >= Em_grid
  
  # number of samples and variables
  numSamp <- length(EEM)
  
  # set index for regions that fell into 1st~4th scattering
  for (i in 1:4){
    increment <- switch(i, first, second, third, forth)
    plusInd <- i * Ex_grid + increment > Em_grid
    minusInd <- i * Ex_grid - increment < Em_grid
    tempInd <- plusInd & minusInd
    delIndex <- delIndex | tempInd
  }
  
  # replace targets with rep
  EEM_delS <- EEM
  for (i in 1:numSamp){
    EEM_delS[[i]][delIndex] <- rep
  }
  return(EEM_delS)
}