diff lib_metams.r @ 8:d1ce2634135f draft

planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit 88163f9ba0e3e95f00e18247c67b95cf7791fa98-dirty

--- a/lib_metams.r	Thu May 07 06:24:39 2020 -0400
+++ b/lib_metams.r	Mon Jul 06 03:04:16 2020 -0400
@@ -433,7 +433,8 @@
 	par (mar=c(5, 4, 4, 2) + 0.1)
 	#For each unknown
 	for (l in 1:length(unkn)){
-		#recordPlot
+		print("la")
+        #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))
@@ -446,7 +447,7 @@
 		on.exit(par(o.par))
 		#For each sample
 		for (c in 1:length(resGC$xset)) {	
-			#get sample name
+            #get sample name
 			sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
 			#remove .cdf, .mzXML filepattern
 			filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", 
@@ -472,13 +473,18 @@
                             pcgrp <- helpannotation[[a]][r,"pspvector"]
 							par (mar=c(0, 0, 0, 0) + 0.1)
 							#Write title
+                            print("on plot le new")
 							plot.new()
 							box()
 							text(0.5, 0.5, title1, cex=2)						
 							par (mar=c(3, 2.5, 3, 1.5) + 0.1)
 							#Window for EIC
+                            print("plot eic")
+                            print(an)
+                            print(pcgrp)
 							plotEICs(an, pspec=pcgrp, maxlabel=2)
 							#Window for pseudospectra
+                            print("plotPsSpectrum")
 							plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
 						}
 					}
@@ -502,5 +508,7 @@
     		}
 		}
 		graphics.off()
+        print("graph off")
 	}#end  for unkn[l]
+    print("fin unkn")
 }#end function