R_MM_backup/matspec.R

In kimsche/MetaboMate: All you need for NMR-based metabolic profiling with R!

#' Simple plotting of multiple NMR spectra overlayed
#' @export
#' @param ppm ppm vector.
#' @param X NMR matrix with spectra represented in rows.
#' @param shift Chemical shift region to be plotted (in ppm).
#' @param add Logical indicating if spectra should be added to a current plot generated with \code{spec()} or \code{matspec()}.
#' @param ... Additional parameters to be passed on to the plot function.
#' @seealso \code{\link{spec}} \code{\link{plot}}
#' @aliases matspec
#' @details Low-level plotting function for NMR spectra.
#' @importFrom graphics matplot matpoints
#' @author Torben Kimhofer \email{tkimhofer@@gmail.com}
matspec=function(ppm, X, shift=c(0,9.5), add=F, ...){
  idx=get.idx(shift, ppm)

  if(add==T){
    matpoints(ppm[idx], t(X[,idx]), type='l', ...)

  } else{
    matplot(ppm[idx], t(X[,idx]), type='l', xlim=rev(range(ppm[idx])), xlab='ppm', ylab='Intensity (AU)', ...)}

}