# HG changeset patch
# User workflow4metabolomics
# Date 1567764728 14400
# Node ID 96debae917e469b9f4817e8cb4232ff986ebbcb6
# Parent  708ab9928a70c0ac44368f2f84633b6377413ce8
planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit c7a518686137f6d62b7415715152e8d5a9953ed7

diff -r 708ab9928a70 -r 96debae917e4 lib_metams.r
--- a/lib_metams.r	Tue Jul 16 09:57:10 2019 -0400
+++ b/lib_metams.r	Fri Sep 06 06:12:08 2019 -0400
@@ -162,27 +162,12 @@
 ##ADDITIONS FROM Y. Guitton
 getBPC <- function(file,rtcor=NULL, ...) {
     object <- xcmsRaw(file)
-	sel <- profRange(object, ...)
-	cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
+    sel <- profRange(object, ...)
+    cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
 }
 
 getBPC2s <- function (files, xset = NULL, pdfname="BPCs.pdf", rt = c("raw","corrected"), scanrange=NULL) {
     require(xcms)
-    
-    #Verification for cdf files
-    stop=FALSE
-    for(i in 1:length(files)){
-        extension <- unlist(strsplit(basename(files[i]),"\\."))[length(unlist(strsplit(basename(files[i]),"\\.")))]
-        if(extension == "CDF" || extension == "cdf"){
-            stop = TRUE
-            break
-        }
-    }
-    if(stop){
-        error_message <- "You have a CDF file and there is an issue to resolve on them for chromatograms.... !"
-        print(error_message)
-        stop(error_message)
-    }
 
     #create sampleMetadata, get sampleMetadata and class
     if(!is.null(xset)) {
@@ -199,10 +184,10 @@
     }
 
     N <- dim(sampleMetadata)[1]
-    TIC <- vector("list",N)
+    BPC <- vector("list",N)
 
     for (j in 1:N) {
-        TIC[[j]] <- getBPC(files[j])
+        BPC[[j]] <- getBPC(files[j])
         #good for raw 
         # seems strange for corrected
         #errors if scanrange used in xcmsSetgeneration
@@ -211,7 +196,7 @@
         }else{
             rtcor <- NULL
         }
-        TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
+        BPC[[j]] <- getBPC(files[j],rtcor=rtcor)
     }
 
     pdf(pdfname,w=16,h=10)
@@ -219,8 +204,10 @@
     lty = 1:N
     pch = 1:N
     #search for max x and max y in BPCs
-    xlim = range(sapply(TIC, function(x) range(x[,1])))
-    ylim = range(sapply(TIC, function(x) range(x[,2])))
+
+    xlim = range(sapply(BPC, function(x) range(x[,1])))
+    ylim = range(sapply(BPC, function(x) range(x[,2])))
+
     ylim = c(-ylim[2], ylim[2])
 
     ##plot start
@@ -231,15 +218,15 @@
                 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
                 colvect<-NULL
                 for (j in 1:length(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")
+                    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 1:length(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")
+                    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]])
                 }
                 legend("topright",paste(gsub("(^.+)\\..*$","\\1",basename(files[c(classnames[[k]],classnames[[l]])]))), col = colvect, lty = lty, pch = pch)
@@ -254,15 +241,15 @@
         plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k],"vs",class[l], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
 
         for (j in 1:length(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")
+            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 1:length(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")
+            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]])
         }
         legend("topright",paste(gsub("(^.+)\\..*$","\\1",basename(files[c(classnames[[k]],classnames[[l]])]))), col = colvect, lty = lty, pch = pch)
@@ -270,14 +257,16 @@
     
     if (length(class)==1){
         k=1
-		ylim = range(sapply(TIC, function(x) range(x[,2])))
+
+		ylim = range(sapply(BPC, function(x) range(x[,2])))
+
         colvect<-NULL
         plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Base Peak Chromatograms \n","BPCs_",class[k], sep=""), xlab = "Retention Time (min)", ylab = "BPC")
 
         for (j in 1:length(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")
+            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]])
         }
         legend("topright",paste(gsub("(^.+)\\..*$","\\1",basename(files[c(classnames[[k]])]))), col = colvect, lty = lty, pch = pch)
@@ -294,21 +283,6 @@
 getTIC2s <- function(files, xset=NULL, pdfname="TICs.pdf", rt=c("raw","corrected")) {
     require(xcms)
 
-    #Verification for cdf files
-    stop=FALSE
-    for(i in 1:length(files)){
-        extension <- unlist(strsplit(basename(files[i]),"\\."))[length(unlist(strsplit(basename(files[i]),"\\.")))]
-        if(extension == "CDF" || extension == "cdf"){
-            stop = TRUE
-            break
-        }
-    }
-    if(stop){
-        error_message <- "You have a CDF file and there is an issue to resolve on them for chromatograms.... !"
-        print(error_message)
-        stop(error_message)
-    }
-
     #create sampleMetadata, get sampleMetadata and class
     if(!is.null(xset)){
 		#When files come from XCMS3 before metaMS treatment
@@ -327,7 +301,6 @@
     TIC <- vector("list",N)
 
     for (i in 1:N) {
-        cat(files[i],"\n")
         if (!is.null(xcmsSet) && rt == "corrected")
             rtcor <- xcmsSet@rt$corrected[[i]]
         else
@@ -348,7 +321,7 @@
     if (length(class)>2){
         for (k in 1:(length(class)-1)){
             for (l in (k+1):length(class)){
-                print(paste(class[k],"vs",class[l],sep=" ")) 
+                cat(paste(class[k],"vs",class[l],"\n",sep=" ")) 
                 plot(0, 0, type="n", xlim = xlim/60, ylim = ylim, main = paste("Total Ion Chromatograms \n","TICs_",class[k]," vs ",class[l], sep=""), xlab = "Retention Time (min)", ylab = "TIC")
                 colvect<-NULL
                 for (j in 1:length(classnames[[k]])) {
@@ -412,21 +385,6 @@
 #only for Galaxy 
 plotUnknowns<-function(resGC, unkn="", DB=NULL, fileFrom=NULL){
 
-    #Verification for cdf files
-    stop=FALSE
-    for(i in 1:length(names(resGC$annotation))){
-        extension <- unlist(strsplit(basename(names(resGC$annotation)[i]),"\\."))[length(unlist(strsplit(basename(names(resGC$annotation)[i]),"\\.")))]
-        if(extension == "CDF" || extension == "cdf"){
-            stop = TRUE
-            break
-        }
-    }
-    if(stop){
-        error_message <- "You have a CDF file and there is an issue to resolve on them for chromatograms.... !"
-        print(error_message)
-        stop(error_message)
-    }
-
     ##Annotation table each value is a pcgrp associated to the unknown 
     ##NOTE pcgrp index are different between xcmsSet and resGC due to filtering steps in metaMS
     ##R. Wehrens give me some clues on that and we found a correction
@@ -545,4 +503,4 @@
 		}
 		graphics.off()
 	}#end  for unkn[l]
-}#end function
\ No newline at end of file
+}#end function
diff -r 708ab9928a70 -r 96debae917e4 metaMS_plot.r
--- a/metaMS_plot.r	Tue Jul 16 09:57:10 2019 -0400
+++ b/metaMS_plot.r	Fri Sep 06 06:12:08 2019 -0400
@@ -96,6 +96,12 @@
 
 if(!is.null(singlefile)) {
     files <- paste("./",names(singlefile),sep="")
+    #WARNING if user has CDF files (not yet good for plotting)
+    if(MSnbase:::isCdfFile(files)){
+        warning_message <- "You have CDF files, for the moment you can't obtain plot after runGC! A new update will follow with the good correction\n"
+        warning(warning_message)
+        cat(paste("\n","/!\\Warning/!\\",warning_message,sep="\n"))
+    }
     if(!is.null(files)){
         if(args$selectbpc){
             cat("\n\tProcessing BPC(s) from XCMS files...\n")