annotate flagRemove.R @ 6:2f71b3495221 draft

"planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2579c8746819670348c378f86116f83703c493eb"

library(msPurity)
library(optparse)
print(sessionInfo())
option_list <- list(
  make_option(c("-o", "--out_dir"), type = "character", default = getwd(),
              help = "Output folder for resulting files [default = %default]"
  ),
  make_option(c("-x", "--xset_path"), type = "character", default = file.path(getwd(), "xset.rds"),
              help = "The path to the xcmsSet object [default = %default]"
  ),
  make_option("--polarity", default = NA,
              help = "polarity (just used for naming purpose for files being saved) [positive, negative, NA] [default %default]"
  ),
  make_option("--rsd_i_blank", default = 100,
              help = "RSD threshold for the blank [default = %default]"
  ),
  make_option("--minfrac_blank", default = 0.5,
              help = "minimum fraction of files for features needed for the blank [default = %default]"
  ),
  make_option("--rsd_rt_blank", default = 100,
              help = "RSD threshold for the RT of the blank [default = %default]"
  ),

  make_option("--ithres_blank", default = 0,
              help = "Intensity threshold for the blank [default = %default]"
  ),
  make_option("--s2b", default = 10,
              help = "fold change (sample/blank) needed for sample peak to be allowed. e.g.
                    if s2b set to 10 and the recorded sample 'intensity' value was 100 and blank was 10.
                    1000/10 = 100, so sample has fold change higher than the threshold and the peak
                    is not considered a blank [default = %default]"
  ),
  make_option("--blank_class", default = "blank", type = "character",
              help = "A string representing the class that will be used for the blank.[default = %default]"
  ),
  make_option("--egauss_thr", default = NA,
              help = "Threshold for filtering out non gaussian shaped peaks. Note this only works
                            if the 'verbose columns' and 'fit gauss' was used with xcms
                            [default = %default]"
  ),
  make_option("--rsd_i_sample", default = 100,
              help = "RSD threshold for the samples [default = %default]"
  ),
  make_option("--minfrac_sample", default = 0.8,
              help = "minimum fraction of files for features needed for the samples [default = %default]"
  ),
  make_option("--rsd_rt_sample", default = 100,
              help = "RSD threshold for the RT of the samples [default = %default]"
  ),
  make_option("--ithres_sample", default = 5000,
              help = "Intensity threshold for the sample [default = %default]"
  ),
  make_option("--grp_rm_ids", default = NA,
              help = "vector of grouped_xcms peaks to remove (corresponds to the row from xcms::group output)
              [default = %default]"
  ),
  make_option("--remove_spectra",  action = "store_true",
              help = "TRUE if flagged spectra is to be removed [default = %default]"
  ),
  make_option("--minfrac_xcms", default = 0.5,
              help = "minfrac for xcms  grouping [default = %default]"
  ),
  make_option("--mzwid", default = 0.001,
              help = "mzwid for xcms  grouping [default = %default]"
  ),
  make_option("--bw", default = 5,
              help = "bw for xcms  grouping [default = %default]"
  ),

  make_option("--temp_save",  action = "store_true",
              help = "Assign True if files for each step saved (for testing purposes) [default = %default]"
  ),

  make_option("--samplelist",  type = "character", help = "Sample list to determine the blank class")

)

# nolint start
#  make_option("--multilist", action="store_true"
#            help="NOT CURRENTLY IMPLEMENTED: If paired blank removal is to be performed a - multilist -  sample list file has to be provided"
# ),
# nolint end

# store options
opt <- parse_args(OptionParser(option_list = option_list))

opt <- replace(opt, opt == "NA", NA)

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

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


print(opt)

getxcmsSetObject <- function(xobject) {
    # XCMS 1.x
    if (class(xobject) == "xcmsSet")
        return(xobject)
    # XCMS 3.x
    if (class(xobject) == "XCMSnExp") {
        # Get the legacy xcmsSet object
        suppressWarnings(xset <- as(xobject, "xcmsSet"))
        xcms::sampclass(xset) <- xset@phenoData$sample_group
        return(xset)
    }
}


loadRData <- 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]))
}

xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))

print(xset)
if (is.null(opt$samplelist)) {
    blank_class <- opt$blank_class
}else{
    samplelist <- read.table(opt$samplelist, sep = "\t", header = TRUE)
    samplelist_blank <- unique(samplelist$sample_class[samplelist$blank == "yes"])

    chosen_blank <- samplelist_blank[samplelist_blank %in% xset@phenoData$class]
    if (length(chosen_blank) > 1) {
        print("ERROR: only 1 blank is currently allowed to be used with this tool")
        quit()
    }
    blank_class <- as.character(chosen_blank)
    print(blank_class)
}


if (is.null(opt$multilist)) {
    ffrm_out <- flag_remove(xset,
                        pol = opt$polarity,
                        rsd_i_blank = opt$rsd_i_blank,
                        minfrac_blank = opt$minfrac_blank,
                        rsd_rt_blank = opt$rsd_rt_blank,
                        ithres_blank = opt$ithres_blank,
                        s2b = opt$s2b,
                        ref.class = blank_class,
                        egauss_thr = opt$egauss_thr,
                        rsd_i_sample = opt$rsd_i_sample,
                        minfrac_sample = opt$minfrac_sample,
                        rsd_rt_sample = opt$rsd_rt_sample,
                        ithres_sample = opt$ithres_sample,
                        minfrac_xcms = opt$minfrac_xcms,
                        mzwid = opt$mzwid,
                        bw = opt$bw,
                        out_dir = opt$out_dir,
                        temp_save = temp_save,
                        remove_spectra = remove_spectra,
                        grp_rm_ids = unlist(strsplit(as.character(opt$grp_rm_ids), split = ", "))[[1]])
    print("flag remove finished")
    xset <- ffrm_out[[1]]
    grp_peaklist <- ffrm_out[[2]]
    removed_peaks <- ffrm_out[[3]]

    save.image(file = file.path(opt$out_dir, "xset_filtered.RData"), version = 2)

    # grpid needed for mspurity ID needed for deconrank... (will clean up at some up)
    peak_pth <- file.path(opt$out_dir, "peaklist_filtered.tsv")
    print(peak_pth)
    write.table(data.frame("grpid" = rownames(grp_peaklist), "ID" = rownames(grp_peaklist), grp_peaklist),
                peak_pth, row.names = FALSE, sep = "\t")

    removed_peaks <- data.frame(removed_peaks)
    write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),
        file.path(opt$out_dir, "removed_peaks.tsv"), row.names = FALSE, sep = "\t")

}else{

   # nolint start
   # TODO
   #xsets <- split(xset, multilist_df$multlist)
   #
   #mult_grps <- unique(multilist_df$multlist)
   #
   #for (mgrp in mult_grps){
   #   xset_i <- xsets[mgrp]
   #   xcms::group(xset_i,
   #
   # }
   # nolint end


}