--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/flagRemove.R	Thu Mar 04 12:17:52 2021 +0000
@@ -0,0 +1,197 @@
+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
+
+
+}