R/hyperSpec2spectra.R

In Chathurga/HyperChemoBridge: Bridge Between hyperSpec & ChemoSpec

#'
#' Convert a hyperSpec object to a ChemoSpec object
#'
#' This function converts a \code{hyperSpec} object from the package of the same
#' name, to a \code{Spectra} object as used in the \code{ChemoSpec} package.
#'
#' @param hyperSpec A \href{https://cbeleites.github.io/hyperSpec/reference/hyperSpec-class.html}{hyperSpec} object.
#'
#' @param desc Character.  A description of the data set.
#'
#' @param names Character.  A vector of sample names.
#'
#' @param colors Character.  A vector of colors.
#'
#' @param groups Factor.  A vector of factors giving the sample membership.
#'
#' @return A \code{\link[ChemoSpec]{Spectra}} object.
#'
#' @keywords utilities
#' @author Conor McManus
#' @export
#' @importFrom ChemoSpec chkSpectra
#' 
#' @examples
#' require("hyperSpec")
#' require("RColorBrewer")
#' quinine <- hyperSpec2spectra(hyperSpec = flu,
#'   desc = "Quinine fluorescence calibration data from hyperSpec",
#'   names = paste("flu", 1:6, sep = ""),
#'   groups = rep("calib", 6),
#'   colors = brewer.pal(6, "Set1"))
#' sumSpectra(quinine)
#' str(quinine)
#' 
hyperSpec2spectra <- function(hyperSpec, desc = "no description provided",
	names = NULL, groups = NULL, colors = NULL) {

  spectra <- vector("list")
  freq <- data <- sym <- alt.sym <- .wavelength <- spc <- unit <- NA
  spectra$freq <- hyperSpec@wavelength
  spectra$data <- hyperSpec@data$spc
  x <- dim(spectra$data)[1]
  spectra$names <- if (!is.null(names)) as.character(names) else rep.int("Name?", x)
  spectra$groups <- if (!is.null(groups)) as.factor(groups) else as.factor(rep("Grp?", x))
  spectra$colors <- if (!is.null(colors)) colors else rep.int("black", x)
  spectra$sym <- rep.int(20L, x)
  spectra$alt.sym <- rep.int("a", x)
  
  if (!is.null(groups)) {
  	message("Spectra$sym & Spectra$alt.sym need to be manually assigned")
  	ng <- length(levels(groups))
  }

  # units are potentially a wee bit more complex, need to handle expressions
  ex1 <- ex2 <- FALSE
  ex1 <- is.expression(hyperSpec@label$.wavelength)
  ex2 <- is.expression(hyperSpec@label$spc)

  if (!ex1) unit1 <- hyperSpec@label$.wavelength
  if (!ex2) unit2 <- hyperSpec@label$spc
  if (ex1) {
  	unit1 <- toString(hyperSpec@label$.wavelength)
  	message("Expression was stripped from the x-axis units")
  	}
  if (ex2) {
  	unit2 <- toString(hyperSpec@label$spc)
  	message("Expression was stripped from the y-axis units")
  	}

  spectra$unit[1] <- unit1
  spectra$unit[2] <- unit2

  spectra$desc <- desc
  class(spectra) <- "Spectra"
  chkSpectra(spectra)
  spectra
}