R/f.plot.spec.R

In TESTgroup-BNL/PLSR_for_plant_trait_prediction: A simple add-on package to aid in the fitting of leaf or canopy scale spectra-trait PLSR models

##' @title f.plot.spec
##' 
##' @param Z Spectra matrix with each row corresponding to a spectra and wavelength in columns
##' @param wv vector of wavelengths corresponding to the column of the spectra matrix Z
##' @param xlim vector to change the default xlim of the plots (ex xlim = c(500, 2400))
##' @param position Position of the legend (see base function legend for help)
##' @param type Name of the y axis and of the legend. E.g. Reflectance, Transmittance
##' @param plot_label optional plot label to include with the figure
##' 
##' @importFrom stats quantile
##' @importFrom graphics polygon lines legend box
##' 
##' @author Julien Lamour, Shawn P. Serbin
##' @export
f.plot.spec <- function(
  Z,                  ## Spectra matrix with each row corresponding to a spectra and wavelength in columns
  wv,                 ## vector of wavelengths corresponding to the column of the spectra matrix Z
  xlim=NULL,          ## vector to change the default xlim of the plots (ex xlim = c(500, 2400))
  position='topright',## Position of the legend (see base function legend for help)
  type='Reflectance', ## Name of the y axis and of the legend
  plot_label=NULL     ## optional label for plot
){
  if(mean(as.matrix(Z),na.rm=TRUE)>1){Z=Z/100} ## Check if the spectra are in pc [0,100] or in [0,1]
  if(is.null(xlim)){xlim=c(min(wv),max(wv))}
  mean_spec <- colMeans(Z,na.rm=TRUE)
  spectra_quantiles <- apply(Z,2,quantile,na.rm=T,probs=c(0,0.025,0.05,0.5,0.95,0.975,1))
  
  plot(x=NULL,y=NULL,ylim=c(0,100),xlim=xlim,xlab="Wavelength (nm)",
       ylab=paste0(type," (%)"),main=plot_label)
  polygon(c(wv ,rev(wv)),c(spectra_quantiles[5,]*100, rev(spectra_quantiles[3,]*100)),
          col="#99CC99",border=NA)
  lines(wv,mean_spec*100,lwd=2, lty=1, col="black")
  lines(wv,spectra_quantiles[1,]*100, lty=3, col="grey40")
  lines(wv,spectra_quantiles[7,]*100, lty=3, col="grey40")
  legend(position,legend=c(paste("Mean",type),"Min/Max", "95% CI"),lty=c(1,3,1),
         lwd=c(2,1,10),col=c("black","grey40","#99CC99"),bty="n")
  box(lwd=2.2)
}