R/loadSpectra.R

In CeMOS-Mannheim/MALDIcellassay: Automated MALDI Cell Assays Using Dose-Response Curve Fitting

#' load bruker MALDI target plate spectra
#'
#' @param Dir         Character, parent directory of spectra.
#' @param filter      Character vector, filter out spectra which match the given vector.
#' @param nameSpectra Logical, if TRUE the spectra in the resulting list will be named according to the dirname.
#' @param verbose     Logical, print logs to the console. 
#'
#' @return List of MALDIquant::MassSpectra 
#' @export
#'
#' @importFrom svMisc progress
#' @importFrom MALDIquantForeign importBrukerFlex
#' 
#' @examples
#' dataDir <- system.file("extdata", package="MALDIcellassay")
#' unzip(file.path(dataDir, "example-raw-spectra.zip"))
#'
#' loadSpectra("example-raw-spectra/")
#'
#' unlink("example-raw-spectra/", recursive = TRUE)
loadSpectra <- function(Dir, filter = NA, nameSpectra = TRUE, verbose = TRUE) {
  # get names of all anaylses
  analyses <- basename(list.dirs(Dir, recursive = F))

  # filter Calibration spectra
  analyses <- analyses[which(!analyses %in% filter)]



  # determine number of measured spots
  total_n <- vector("numeric", 1)
  for (i in 1:length(analyses)) {
    n <- length(list.dirs(file.path(Dir, analyses[i]), recursive = F))
    total_n <- total_n + n
  }

  spectra <- vector("list", length = total_n)
  counter <- 0
  if(verbose) {
    cat(timeNow(), "Loading spectra...\n\n")
  }
  
  for (i in analyses) {
    path <- file.path(Dir, i)
    spots <- list.files(path, recursive = T)[grepl(pattern = "fid", x = list.files(path, recursive = T))]
    for (spot in spots) {
      counter <- counter + 1
      suppressWarnings(
        spec <- MALDIquantForeign::importBrukerFlex(path = file.path(path, spot), verbose = F)
        )
      # metaData(spec[[1]]) <- list(name = i)
      spectra[[counter]] <- spec[[1]]

      if (nameSpectra) {
        names(spectra)[counter] <- i
      }
      if(verbose) {
        svMisc::progress(counter / total_n * 100)
      }
    }
  }
  if(verbose) {
    cat("\n")
  }
  

  return(spectra)
}

#' load mzML spectra
#'
#' @param Dir         Character, parent directory of spectra.
#' @param filter      Character vector, filter out spectra which match the given vector.
#' @param nameSpectra Logical, if TRUE the spectra in the resulting list will be named according to the dirname.
#' @param verbose     Logical, print logs to console
#' @param centroided  Logical, if FALSE (default) a list of MALDIquant::MassSpectrum is returned, otherwise a list of MALDIquant::MassPeaks are returned.
#' @return            List of MALDIquant::MassSpectra
#' @export
#'
#' @importFrom svMisc progress
#' @importFrom MALDIquantForeign importMzMl
#' 
#' @examples
#' dataDir <- system.file("extdata", package="MALDIcellassay")
#' 
#' loadSpectraMzML(file.path(dataDir, "Koch2024mzML"))
loadSpectraMzML <- function(Dir, filter = NA, nameSpectra = TRUE, verbose = TRUE, centroided = FALSE) {
  # get names of all anaylses
  analyses <- list.files(Dir, recursive = F)

  # filter Calibration spectra
  analyses <- analyses[which(!analyses %in% filter)]

  spectra <- vector("list", length = length(analyses))
  
  if(verbose) {
    cat(timeNow(), "Loading spectra...\n\n")  
  }
  
  counter <- 0
  for (i in analyses) {
    counter <- counter + 1
    path <- file.path(Dir, i)

    spec <- MALDIquantForeign::importMzMl(path = file.path(path), verbose = F, centroided = centroided)


    if (nameSpectra) {
      names(spec) <- rep(tools::file_path_sans_ext(i), length(spec))
    }

    spectra[[counter]] <- spec
    if(verbose) {
      svMisc::progress(counter / length(analyses) * 100)  
    }
    
  }
  if(verbose) {
    cat("\n")  
  }

  return(unlist(spectra))
}