annotate averageFragSpectra.R @ 7:942e676515fe draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit e3b17490a958d80ebe78ef1bebebef48948e1240"

library(optparse)
library(msPurity)
library(xcms)
print(sessionInfo())


get_av_spectra <- function(x) {

  if (length(x$av_intra) > 0) {
    av_intra_df <- plyr::ldply(x$av_intra)

    if (nrow(av_intra_df) == 0) {
      av_intra_df <- NULL
    }else{
      av_intra_df$method <- "intra"
    }

  }else{
    av_intra_df <- NULL
  }

  if ((is.null(x$av_inter)) || (nrow(x$av_inter) == 0)) {
    av_inter_df <- NULL
  }else{
    av_inter_df <- x$av_inter
    av_inter_df$method <- "inter"
  }

  if ((is.null(x$av_all)) || (nrow(x$av_all) == 0)) {
    av_all_df <- NULL
  }else{
    av_all_df <- x$av_all
    av_all_df$method <- "all"
  }

  combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)

  return(combined)
}


option_list <- list(
  make_option("--out_rdata", type = "character"),
  make_option("--out_peaklist", type = "character"),
  make_option("--pa", type = "character"),
  make_option("--av_level", type = "character"),
  make_option("--minfrac", default = 0.5),
  make_option("--minnum", default = 1),
  make_option("--ppm", default = 5.0),
  make_option("--snr", default = 0),
  make_option("--ra", default = 0),
  make_option("--av", default = "median", type = "character"),
  make_option("--sumi", action = "store_true"),
  make_option("--rmp", action = "store_true"),
  make_option("--cores", default = 1)
)

opt <- parse_args(OptionParser(option_list = option_list))
print(opt)


load_r_data <- function(rdata_path, name) {
    #loads an RData file, and returns the named xset object if it is there
    load(rdata_path)
    return(get(ls()[ls() %in% name]))
}

# Requires
pa <- load_r_data(opt$pa, "pa")

pa@cores <- opt$cores

if (is.null(opt$rmp)) {
  rmp <- FALSE
}else{
  rmp <- TRUE
}

if (is.null(opt$sumi)) {
  sumi <- FALSE
}else{
  sumi <- TRUE
}

if (opt$av_level == "intra") {
  pa <- msPurity::averageIntraFragSpectra(pa,
                                          minfrac = opt$minfrac,
                                          minnum = opt$minnum,
                                          ppm = opt$ppm,
                                          snr = opt$snr,
                                          ra = opt$ra,
                                          av = opt$av,
                                          sumi = sumi,
                                          rmp = rmp,
                                          cores = opt$cores)

} else if (opt$av_level == "inter") {

  pa <- msPurity::averageInterFragSpectra(pa,
                                          minfrac = opt$minfrac,
                                          minnum = opt$minnum,
                                          ppm = opt$ppm,
                                          snr = opt$snr,
                                          ra = opt$ra,
                                          av = opt$av,
                                          sumi = sumi,
                                          rmp = rmp,
                                          cores = opt$cores)
} else if (opt$av_level == "all") {

  pa <- msPurity::averageAllFragSpectra(pa,
                                        minfrac = opt$minfrac,
                                        minnum = opt$minnum,
                                        ppm = opt$ppm,
                                        snr = opt$snr,
                                        ra = opt$ra,
                                        av = opt$av,
                                        sumi = sumi,
                                        rmp = rmp,
                                        cores = opt$cores)
}

print(pa)
save(pa, file = opt$out_rdata)

if (length(pa) > 0) {

  av_spectra <- plyr::ldply(pa@av_spectra, get_av_spectra)

  if (nrow(av_spectra) == 0) {
    message("No average spectra available")
  } else {
    colnames(av_spectra)[1] <- "grpid"
    av_spectra$grpid <- names(pa@av_spectra)[av_spectra$grpid]

    if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
      # Add some extra info (only required if av_intra or av_inter performed)
      colnames(av_spectra)[2] <- "fileid"
      av_spectra$avid <- seq_len(nrow(av_spectra))

      filenames <- sapply(av_spectra$fileid,
                          function(x) names(pa@fileList)[as.integer(x)])
      # filenames_galaxy <- sapply(
      #    av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))

        av_spectra <- as.data.frame(
          append(av_spectra, list(filename = filenames), after = 2))
    }


    print(head(av_spectra))
    write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")

  }
}