--- a/averageFragSpectra.R	Fri Nov 13 10:16:03 2020 +0000
+++ b/averageFragSpectra.R	Thu Mar 04 12:28:18 2021 +0000
@@ -4,33 +4,33 @@
 print(sessionInfo())
 
 
-get_av_spectra <- function(x){
+get_av_spectra <- function(x) {
 
-  if (length(x$av_intra)>0){
+  if (length(x$av_intra) > 0) {
     av_intra_df <- plyr::ldply(x$av_intra)
 
-    if (nrow(av_intra_df)==0){
+    if (nrow(av_intra_df) == 0) {
       av_intra_df <- NULL
     }else{
-      av_intra_df$method <- 'intra'
+      av_intra_df$method <- "intra"
     }
 
   }else{
     av_intra_df <- NULL
   }
 
-  if ((is.null(x$av_inter)) || (nrow(x$av_inter)==0)){
+  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'
+    av_inter_df$method <- "inter"
   }
 
-  if ((is.null(x$av_all)) || (nrow(x$av_all)==0)){
+  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'
+    av_all_df$method <- "all"
   }
 
   combined <- plyr::rbind.fill(av_intra_df, av_inter_df, av_all_df)
@@ -40,126 +40,116 @@
 
 
 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)
+  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))
+opt <- parse_args(OptionParser(option_list = option_list))
 print(opt)
 
 
-loadRData <- function(rdata_path, name){
-#loads an RData file, and returns the named xset object if it is there
+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 <- loadRData(opt$pa, 'pa')
+pa <- load_r_data(opt$pa, "pa")
 
 pa@cores <- opt$cores
 
-if(is.null(opt$rmp)){
-  rmp = FALSE
+if (is.null(opt$rmp)) {
+  rmp <- FALSE
 }else{
-  rmp = TRUE
+  rmp <- TRUE
 }
 
-if(is.null(opt$sumi)){
-
-  sumi = FALSE
+if (is.null(opt$sumi)) {
+  sumi <- FALSE
 }else{
-  sumi = TRUE
-
+  sumi <- TRUE
 }
 
-
-if(opt$av_level=="intra"){
-
+if (opt$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$cores)
+                                          minfrac = opt$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$av_level=="inter"){
+} else if (opt$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"){
+                                          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$cores)
-
+                                        minfrac = opt$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$out_rdata)
+save(pa, file = opt$out_rdata)
 
-
-if (length(pa)>0){
+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'
+  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$avid <- 1:nrow(av_spectra)
-        
-        filenames <- sapply(av_spectra$fileid, function(x) names(pa@fileList)[as.integer(x)])
-        # filenames_galaxy <- sapply(av_spectra$fileid, function(x) basename(pa@fileList[as.integer(x)]))
-        
-        av_spectra = as.data.frame(append(av_spectra, list(filename = filenames), after=2))
+
+    if ((length(pa@av_intra_params) > 0) || (length(pa@av_inter_params) > 0)) {
+      # Add some extra info (only required if av_intra or av_inter performed)
+      colnames(av_spectra)[2] <- "fileid"
+      av_spectra$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$out_peaklist, row.names=FALSE, sep='\t')
+    write.table(av_spectra, opt$out_peaklist, row.names = FALSE, sep = "\t")
 
   }
 }
-