--- a/flagRemove.R	Fri Nov 13 09:57:42 2020 +0000
+++ b/flagRemove.R	Thu Mar 04 12:33:09 2021 +0000
@@ -2,105 +2,100 @@
 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("-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(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("--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("--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("--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("--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("--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.
+  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("--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
+  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("--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("--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("--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("--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)
+  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("--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("--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("--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("--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("--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")
-
-
-
-
+  make_option("--samplelist",  type = "character", help = "Sample list to determine the blank class")
 
 )
 
-  #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 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 <- parse_args(OptionParser(option_list = option_list))
 
 opt <- replace(opt, opt == "NA", NA)
 
-
-
-
-if (is.null(opt$temp_save)){
-    temp_save<-FALSE
+if (is.null(opt$temp_save)) {
+    temp_save <- FALSE
 }else{
-    temp_save<-TRUE
+    temp_save <- TRUE
 }
 
-if (is.null(opt$remove_spectra)){
-    remove_spectra<-FALSE
+if (is.null(opt$remove_spectra)) {
+    remove_spectra <- FALSE
 }else{
-    remove_spectra<-TRUE
+    remove_spectra <- TRUE
 }
 
 
@@ -109,35 +104,35 @@
 getxcmsSetObject <- function(xobject) {
     # XCMS 1.x
     if (class(xobject) == "xcmsSet")
-        return (xobject)
+        return(xobject)
     # XCMS 3.x
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
-        suppressWarnings(xset <- as(xobject, 'xcmsSet'))
-        sampclass(xset) <- xset@phenoData$sample_group
-        return (xset)
+        suppressWarnings(xset <- as(xobject, "xcmsSet"))
+        xcms::sampclass(xset) <- xset@phenoData$sample_group
+        return(xset)
     }
 }
 
 
-loadRData <- function(rdata_path, name){
+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$xset_path, c('xset','xdata')))
+xset <- getxcmsSetObject(loadRData(opt$xset_path, c("xset", "xdata")))
 
 print(xset)
-if (is.null(opt$samplelist)){
+if (is.null(opt$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'])
+    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')
+    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)
@@ -145,47 +140,47 @@
 }
 
 
-if (is.null(opt$multilist)){
+if (is.null(opt$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')
+                        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$out_dir, 'xset_filtered.RData'), version=2)
+    save.image(file = file.path(opt$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$out_dir, 'peaklist_filtered.tsv')
+    peak_pth <- file.path(opt$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')
+    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$out_dir, 'removed_peaks.tsv'), row.names=FALSE, sep='\t')
+    write.table(data.frame("ID" = rownames(removed_peaks), removed_peaks),
+        file.path(opt$out_dir, "removed_peaks.tsv"), row.names = FALSE, sep = "\t")
 
 }else{
 
-   
+   # nolint start
    # TODO
    #xsets <- split(xset, multilist_df$multlist)
    #
@@ -193,12 +188,10 @@
    #
    #for (mgrp in mult_grps){
    #   xset_i <- xsets[mgrp]
-   #   xcms::group(xset_i, 
+   #   xcms::group(xset_i,
    #
    # }
-
+   # nolint end
 
 
 }
-
-