Lintr : Commented code should be removed.

workflow4metabolomics · Oct 23, 2024 · bc6be48 · bc6be48
1 parent 0f42d95
commit bc6be48
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Showing 2 changed files with 18 additions and 18 deletions.
diff --git a/tools/metams/metaMS_runGC/metaMS_runGC.r b/tools/metams/metaMS_runGC/metaMS_runGC.r
@@ -28,7 +28,7 @@ cat("\nStart of the '", modNamC, "' Galaxy module call: ", format(Sys.time(), "%
 # ----- PROCESSING INFILE -----
 cat("\n\n\tARGUMENTS PROCESSING INFO\n\n")
 args <- parseCommandArgs(evaluate = FALSE) # interpretation of arguments given in command line as an R list of objects
-# write.table(as.matrix(args), col.names=F, quote=F, sep='\t\t')
+
 print(cbind(value = unlist(args)))
 
 # ----- PROCESSING INFILE -----
@@ -208,7 +208,7 @@ if (!is.null(args$singlefile_galaxyPath)) {
     if (length(xset@rt$raw) > 1) {
       # create an exceptable list of xset for metaMS
       xset.l <- vector("list", length(xset@rt$raw))
-      for (i in 1:length(xset@rt$raw)) {
+      for (i in seq_along(xset@rt$raw)) {
         xset.l[[i]] <- new("xcmsSet")
         xset.l[[i]]@peaks <- xset@peaks[which(xset@peaks[, "sample"] == i), ]
         df <- data.frame(class = xset@phenoData[i, ])

diff --git a/tools/metams/scripts/lib_metams.r b/tools/metams/scripts/lib_metams.r
@@ -224,12 +224,12 @@ getBPC2s <- function(files, xset = NULL, pdfname = "BPCs.pdf", rt = c("raw", "co
         colvect <- NULL
         for (j in seq_along(classnames[[k]])) {
           bpc <- BPC[[classnames[[k]][j]]]
-          # points(bpc[,1]/60, bpc[,2], col = cols[i], pch = pch[i], type="l")
+
           points(bpc[, 1] / 60, bpc[, 2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type = "l")
           colvect <- append(colvect, cols[classnames[[k]][j]])
         }
         for (j in seq_along(classnames[[l]])) {
-          # i=class2names[j]
+
           bpc <- BPC[[classnames[[l]][j]]]
           points(bpc[, 1] / 60, -bpc[, 2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type = "l")
           colvect <- append(colvect, cols[classnames[[l]][j]])
@@ -247,12 +247,12 @@ getBPC2s <- function(files, xset = NULL, pdfname = "BPCs.pdf", rt = c("raw", "co
 
     for (j in seq_along(classnames[[k]])) {
       bpc <- BPC[[classnames[[k]][j]]]
-      # points(bpc[,1]/60, bpc[,2], col = cols[i], pch = pch[i], type="l")
+
       points(bpc[, 1] / 60, bpc[, 2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type = "l")
       colvect <- append(colvect, cols[classnames[[k]][j]])
     }
     for (j in seq_along(classnames[[l]])) {
-      # i=class2names[j]
+
       bpc <- BPC[[classnames[[l]][j]]]
       points(bpc[, 1] / 60, -bpc[, 2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type = "l")
       colvect <- append(colvect, cols[classnames[[l]][j]])
@@ -270,7 +270,7 @@ getBPC2s <- function(files, xset = NULL, pdfname = "BPCs.pdf", rt = c("raw", "co
 
     for (j in seq_along(classnames[[k]])) {
       bpc <- BPC[[classnames[[k]][j]]]
-      # points(bpc[,1]/60, bpc[,2], col = cols[i], pch = pch[i], type="l")
+
       points(bpc[, 1] / 60, bpc[, 2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type = "l")
       colvect <- append(colvect, cols[classnames[[k]][j]])
     }
@@ -332,12 +332,12 @@ getTIC2s <- function(files, xset = NULL, pdfname = "TICs.pdf", rt = c("raw", "co
         colvect <- NULL
         for (j in seq_along(classnames[[k]])) {
           tic <- TIC[[classnames[[k]][j]]]
-          # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+
           points(tic[, 1] / 60, tic[, 2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type = "l")
           colvect <- append(colvect, cols[classnames[[k]][j]])
         }
         for (j in seq_along(classnames[[l]])) {
-          # i=class2names[j]
+
           tic <- TIC[[classnames[[l]][j]]]
           points(tic[, 1] / 60, -tic[, 2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type = "l")
           colvect <- append(colvect, cols[classnames[[l]][j]])
@@ -354,12 +354,12 @@ getTIC2s <- function(files, xset = NULL, pdfname = "TICs.pdf", rt = c("raw", "co
     colvect <- NULL
     for (j in seq_along(classnames[[k]])) {
       tic <- TIC[[classnames[[k]][j]]]
-      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+
       points(tic[, 1] / 60, tic[, 2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type = "l")
       colvect <- append(colvect, cols[classnames[[k]][j]])
     }
     for (j in seq_along(classnames[[l]])) {
-      # i=class2names[j]
+
       tic <- TIC[[classnames[[l]][j]]]
       points(tic[, 1] / 60, -tic[, 2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type = "l")
       colvect <- append(colvect, cols[classnames[[l]][j]])
@@ -374,7 +374,7 @@ getTIC2s <- function(files, xset = NULL, pdfname = "TICs.pdf", rt = c("raw", "co
     colvect <- NULL
     for (j in seq_along(classnames[[k]])) {
       tic <- TIC[[classnames[[k]][j]]]
-      # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
+
       points(tic[, 1] / 60, tic[, 2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type = "l")
       colvect <- append(colvect, cols[classnames[[k]][j]])
     }
@@ -445,9 +445,9 @@ plotUnknowns <- function(resGC, unkn = "", DB = NULL, fileFrom = NULL) {
     # recordPlot
     perpage <- 3 # if change change layout also!
     dev.new(width = 21 / 2.54, height = 29.7 / 2.54, file = paste("Unknown_", unkn[l], ".pdf", sep = "")) # A4 pdf
-    # par(mfrow=c(perpage,2))
+
     layout(matrix(c(1, 1, 2, 3, 4, 4, 5, 6, 7, 7, 8, 9), 6, 2, byrow = TRUE), widths = rep(c(1, 1), perpage), heights = rep(c(1, 5), perpage))
-    # layout.show(6)
+
     oma.saved <- par("oma")
     par(oma = rep.int(0, 4))
     par(oma = oma.saved)
@@ -468,10 +468,10 @@ plotUnknowns <- function(resGC, unkn = "", DB = NULL, fileFrom = NULL) {
       an <- resGC$xset[[c]]
       if (fileFrom == "zipfile") {
         an@xcmsSet@filepaths <- paste0("./", an@xcmsSet@phenoData[, "class"], "/", basename(an@xcmsSet@filepaths))
-      } # else {
-      # print(an@xcmsSet@filepaths)
-      # an@xcmsSet@filepaths <- paste0("./",basename(an@xcmsSet@filepaths))
-      # }
+      }
+
+
+
       # Find the good annotation for this sample
       for (a in seq_len(length(helpannotation))) {
         if (gsub(filepattern, "", names(helpannotation)[a]) == paste0("./", sampname)) {