more R script linting

workflow4metabolomics · Jan 21, 2025 · 76af97e · 76af97e
1 parent 0b4d82a
commit 76af97e
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diff --git a/tools/ms2snoop/MS2snoop.R b/tools/ms2snoop/MS2snoop.R
diff --git a/tools/mzxmlshaper/mzXMLShaper.R b/tools/mzxmlshaper/mzXMLShaper.R
@@ -15,8 +15,10 @@ library("tools")
 
 args <- W4MRUtils::parse_args(args = commandArgs())
 
-cat("\n\n--------------------------------------------------------------------",
-    "\nParameters used by the 'mz(X)MLShaper' tool:\n\n")
+cat(
+    "\n\n--------------------------------------------------------------------",
+    "\nParameters used by the 'mz(X)MLShaper' tool:\n\n"
+)
 cat("--------------------------------------------------------------------\n\n")
 print(args)
 
@@ -32,15 +34,19 @@ pks <- mzR::spectra(spectrum)
 hdr <- mzR::header(spectrum)
 
 if (outputfileformat == "mzml") {
-  writeMSData(pks, file = outputfilename, outformat = "mzml", header = hdr)
+    writeMSData(pks, file = outputfilename, outformat = "mzml", header = hdr)
 }
 
 if (outputfileformat == "mzXml") {
-  writeMSData(pks, file = outputfilename, outformat = "mzxml", header = hdr)
+    writeMSData(pks, file = outputfilename, outformat = "mzxml", header = hdr)
 }
 
-cat("\n--------------------------------------------------------------------",
-    "\nInformation about R (version, Operating System, attached or loaded packages):\n\n")
+cat(
+    "\n--------------------------------------------------------------------",
+    "\nInformation about R (version, Operating System, attached or loaded packages):\n\n"
+)
 sessionInfo()
-cat("--------------------------------------------------------------------\n",
-    "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X"))
+cat(
+    "--------------------------------------------------------------------\n",
+    "\nJob ending time:\n", format(Sys.time(), "%a %d %b %Y %X")
+)
diff --git a/tools/nmr_annotation/DrawSpec.R b/tools/nmr_annotation/DrawSpec.R
@@ -1,74 +1,72 @@
-drawSpec <- function (X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1, 
-                      xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0) 
-{
-  groupLabel_name = groupLabel
-  X = as.data.frame(X)
-#  colnames(X) = c(1:ncol(X))
-  X = as.matrix(X)
-  if (highBound != -1) {
-    for (i in 1:nrow(X)) {
-      myIndex = which(X[i, ] > highBound)
-      X[i, myIndex] = highBound
+drawSpec <- function(X, startP = -1, endP = -1, groupLabel = NULL, useLog = -1, highBound = -1, lowBound = -1,
+                     xlab = NULL, ylab = NULL, main = NULL, nAxisPos = 4, offside = 0) {
+    groupLabel_name <- groupLabel
+    X <- as.data.frame(X)
+    #  colnames(X) = c(1:ncol(X))
+    X <- as.matrix(X)
+    if (highBound != -1) {
+        for (i in 1:nrow(X)) {
+            myIndex <- which(X[i, ] > highBound)
+            X[i, myIndex] <- highBound
+        }
     }
-  }
-  if (lowBound != -1) {
-    for (i in 1:nrow(X)) {
-      myIndex = which(X[i, ] < lowBound)
-      X[i, myIndex] = lowBound
+    if (lowBound != -1) {
+        for (i in 1:nrow(X)) {
+            myIndex <- which(X[i, ] < lowBound)
+            X[i, myIndex] <- lowBound
+        }
     }
-  }
-  if (is.null(groupLabel)) {
-    groupLabel = c(1:nrow(X))
-    groupLabel = as.factor(groupLabel)
-  }
-  else {
-    levels(groupLabel) = c(1:length(levels(groupLabel)))
-  }
-  if (startP == -1) 
-    startP = 1
-  if (endP == -1) 
-    endP = ncol(X)
-  if (is.null(xlab)) {
-    xlab = "index"
-  }
-  if (is.null(ylab)) {
-    ylab = "intensity"
-  }
-  if (is.null(main)) {
-    main = paste(" ", startP + offside, "-", endP + offside)
-  }
-  GraphRange <- c(startP:endP)
-  yn <- X[, GraphRange]
-  if (useLog != -1) 
-    yn = log(yn)
-  if (length(yn) > ncol(X))
-  {
-    plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
-    tempVal = trunc(length(GraphRange)/nAxisPos)
-    xPos = c(0:nAxisPos) * tempVal
-    axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
-    for (i in 1:length(levels(groupLabel))) 
-    {
-      groupLabelIdx = which(groupLabel == levels(groupLabel)[i])
-      color <- palette(rainbow(length(levels(groupLabel))))
-      for (j in 1:length(groupLabelIdx)) 
-      {
-        lines(yn[groupLabelIdx[j], ], col = color[i])
-      }
+    if (is.null(groupLabel)) {
+        groupLabel <- c(1:nrow(X))
+        groupLabel <- as.factor(groupLabel)
+    } else {
+        levels(groupLabel) <- c(1:length(levels(groupLabel)))
     }
-    if (!is.null(groupLabel_name)) 
-    {
-      legendPos = "topleft"
-      legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90")
+    if (startP == -1) {
+        startP <- 1
     }
-  }
-  if (length(yn) == ncol(X))
-  {
-    plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
-    tempVal = trunc(length(GraphRange)/nAxisPos)
-    xPos = c(0:nAxisPos) * tempVal
-#    axis(1, at = xPos, labels = xPos + startP + offside)
-    axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
-    lines(yn)
-  }
-}
+    if (endP == -1) {
+        endP <- ncol(X)
+    }
+    if (is.null(xlab)) {
+        xlab <- "index"
+    }
+    if (is.null(ylab)) {
+        ylab <- "intensity"
+    }
+    if (is.null(main)) {
+        main <- paste(" ", startP + offside, "-", endP + offside)
+    }
+    GraphRange <- c(startP:endP)
+    yn <- X[, GraphRange]
+    if (useLog != -1) {
+        yn <- log(yn)
+    }
+    if (length(yn) > ncol(X)) {
+        plot(yn[1, ], ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
+        tempVal <- trunc(length(GraphRange) / nAxisPos)
+        xPos <- c(0:nAxisPos) * tempVal
+        axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
+        for (i in 1:length(levels(groupLabel)))
+        {
+            groupLabelIdx <- which(groupLabel == levels(groupLabel)[i])
+            color <- palette(rainbow(length(levels(groupLabel))))
+            for (j in 1:length(groupLabelIdx))
+            {
+                lines(yn[groupLabelIdx[j], ], col = color[i])
+            }
+        }
+        if (!is.null(groupLabel_name)) {
+            legendPos <- "topleft"
+            legend(legendPos, levels(groupLabel_name), col = as.integer(levels(groupLabel)), text.col = "black", pch = c(19, 19), bg = "gray90")
+        }
+    }
+    if (length(yn) == ncol(X)) {
+        plot(yn, ylim = c(min(yn), max(yn)), type = "n", ylab = ylab, xlab = xlab, main = main, xaxt = "n")
+        tempVal <- trunc(length(GraphRange) / nAxisPos)
+        xPos <- c(0:nAxisPos) * tempVal
+        #    axis(1, at = xPos, labels = xPos + startP + offside)
+        axis(1, at = xPos, labels = colnames(X)[xPos + startP + offside])
+        lines(yn)
+    }
+}