From bc6be488ac0edab0ec56fc820964d1592ada2f3a Mon Sep 17 00:00:00 2001 From: Damien RAT Date: Wed, 23 Oct 2024 12:13:29 +0200 Subject: [PATCH] Lintr : Commented code should be removed. --- tools/metams/metaMS_runGC/metaMS_runGC.r | 4 +-- tools/metams/scripts/lib_metams.r | 32 ++++++++++++------------ 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/tools/metams/metaMS_runGC/metaMS_runGC.r b/tools/metams/metaMS_runGC/metaMS_runGC.r index a35801cd4..81b331507 100644 --- 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 index a94b1f9b3..6460f3ba0 100644 --- 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)) {