diff nmr_alignement/NmrAlignment_wrapper.R @ 4:265ee538e120 draft default tip

Uploaded

--- a/nmr_alignement/NmrAlignment_wrapper.R	Wed Apr 12 04:32:23 2017 -0400
+++ b/nmr_alignement/NmrAlignment_wrapper.R	Wed Aug 09 06:28:10 2017 -0400
@@ -71,7 +71,7 @@
 leftBorder <- argLs[["left_border"]]
 rightBorder <- argLs[["right_border"]]
 
-		##Exclusion zone(s)
+		## Exclusion zone(s)
 exclusionZones <- argLs[["zone_exclusion_choices.choice"]]
 exclusionZonesBorders <- NULL
 if (!is.null(argLs$zone_exclusion_left))
@@ -91,6 +91,17 @@
 		## Intensity threshold for peak removal
 baselineThresh <- argLs[["baselineThresh"]]
 
+  ## Graphical zone(s)
+graphicalZones <- argLs[["zone_graphical_choices.choice"]]
+graphicalZonesBorders <- NULL
+if (!is.null(argLs$zone_exclusion_left))
+{
+  for(i in which(names(argLs)=="zone_graphical_left"))
+  {
+    graphicalZonesBorders <- c(graphicalZonesBorders,list(c(argLs[[i]],argLs[[i+1]])))
+  }
+}
+
 
 	# Outputs
 logOut <- argLs[["logOut"]]
@@ -98,6 +109,17 @@
 graphOut <- argLs[["graphOut"]]
 
 
+## Checking R packages
+##--------------------
+sink(logOut)
+cat("\tPACKAGE INFO\n")
+#pkgs=c("xcms","batch")
+pkgs=c("batch","speaq")
+for(pkg in pkgs) {
+    suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE)))
+    cat(pkg,"\t",as.character(packageVersion(pkg)),"\n",sep="")
+}
+
 ## Checking arguments
 ##-------------------
 error.stock <- "\n"
@@ -122,15 +144,10 @@
 write.table(t.directory.aligned,file=alignedSpectra,row.names=TRUE,quote=FALSE,sep="\t")
 
 
-excludedZone <- NULL
-for (c in 1:length(exclusionZonesBorders))
-{
-  excludedZone <- c(excludedZone,exclusionZonesBorders[[c]])
-  excludedZone <- sort(excludedZone)
-}
-
 ## Graphical output: overlay of raw and estimated spectra
 pdf(graphOut,onefile=TRUE)
+
+graphical.zone.length <- length(graphicalZonesBorders)
 par(mfrow=c(2,1))
 
 raw.spectra <- data.frame(directory.raw)
@@ -142,32 +159,22 @@
 drawSpec(raw.spectra,xlab="", ylab="Raw spectra", main="")
 drawSpec(aligned.spectra,xlab="", ylab="Aligned spectra", main="")
 
-nbZones <- length(excludedZone)/2
-if (nbZones != 0)
+if (graphical.zone.length != 0)
 {
-  n <- length(excludedZone)
-  drawSpec(raw.spectra[,1:which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n])[1]],xlab="", ylab="Raw spectra", main="")
-  drawSpec(aligned.spectra[,1:which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]],xlab="", ylab="Aligned spectra", main="")
-
-  n <- n - 1
-  while (n >= nbZones & nbZones > 1)
+  #   par(mfrow=c(2,1))
+  for (g in 1:graphical.zone.length)
   {
-    drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Raw spectra", main="")
-    drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n])[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[n-1])[1])],xlab="", ylab="Aligned spectra", main="")
-    n <- n - 2
+    print(paste(g, graphicalZonesBorders[[g]][1], graphicalZonesBorders[[g]][2]))
+    drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == graphicalZonesBorders[[g]][2])[1])],xlab="", main="")
+    drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == graphicalZonesBorders[[g]][1])[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == graphicalZonesBorders[[g]][2])[1])],xlab="", main="")
   }
-
-  drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == excludedZone[1])[1]):ncol(raw.spectra)],xlab="", ylab="Raw spectra", main="")
-  drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == excludedZone[1])[1]):ncol(aligned.spectra)],xlab="", ylab="Aligned spectra", main="")
 }
-drawSpec(raw.spectra[,(which(round(as.numeric(colnames(raw.spectra)),2) == 2.4)[1]):(which(round(as.numeric(colnames(raw.spectra)),2) == 2.8)[1])],xlab="", ylab="Raw spectra", main="")
-drawSpec(aligned.spectra[,(which(round(as.numeric(colnames(aligned.spectra)),2) == 2.4)[1]):(which(round(as.numeric(colnames(aligned.spectra)),2) == 2.8)[1])],xlab="", ylab="Aligned spectra", main="")
-
 dev.off()
 
 
 ## Ending
 ##---------------------
 cat("\nEnd of 'NMR alignment' Galaxy module call: ", as.character(Sys.time()), sep = "")
+sink()
 options(stringsAsFactors = strAsFacL)
 rm(list = ls())