R/plot.integrate.RAMAN.go.R

In RichardLaBrie/paRafac_correction: Corrects EEM all at once before using Matlab for PARAFAC

plot.integrate.RAMAN.go <- function(EEM, maxf, graph=T)
{
  
  ex350  <- which(EEM$wlex == 350)
  em370  <- which(EEM$wlem == 370)
  em380  <- which(EEM$wlem == 380)
  em414  <- which(EEM$wlem == 414)
  em428  <- which(EEM$wlem == 428)
  
  # Substract baseline
  Df = data.frame(x = c(EEM$wlem[em370:em380], EEM$wlem[em414:em428]), y = c(EEM$EEM.list$eem[ex350,em370:em380], EEM$EEM.list$eem[ex350,em414:em428]))
  mod = lm(y~x, data=Df)
  offset = predict(mod, newdata = data.frame(x = EEM$wlem[em370:em428]))
  raman = EEM$EEM.list$eem[ex350,em370:em428] - offset
  
  # integration of the Raman peak folowwing LAWAETZ and STEDMON (2009)
  fx.linear <- approxfun(EEM$wlem[em370:em428], raman)
  res <- integrate(fx.linear, 371, 428)[1]
  RamanInt <- as.numeric(res)
  
  # Graph production
  
  if(graph)
  {
    plot(EEM$wlem[em370:em428], EEM$EEM.list$eem[ex350,em370:em428],
         type="l", lwd=3,
         xlab="Emission wavelenght", ylab="Fluorescence")
    abline(mod, lwd = 3, col = "blue")
    text(380,20, paste("Raman integration:", as.character(signif(RamanInt,5))))
    # dev.off()
  }
  return(RamanInt)
}