annotate flagRemove.R @ 10:13034c3886f2 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f10386dee95f3b1fbc8d1eeec52d450381ba89c5

library(msPurity)
library(xcms)
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)

# This R function can handle both XCMS object versions (so following code
# no longer required - kept here for reference)
# 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"))
#     if (!is.null(xset@phenoData$sample_group)){
#       xcms::sampclass(xset) <- xset@phenoData$sample_group
#     }else{
#       xcms::sampclass(xset) <- "."
#     }
#     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 <- loadRData(opt$xset_path, c("xset", "xdata"))


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 - potential for multilist analysis (e)
    # nolint end
}