comparison lib_metams.r @ 8:d1ce2634135f draft

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

7:89af36e05548

    peaktable <- resGC$PeakTable
		
	par (mar=c(5, 4, 4, 2) + 0.1)
	#For each unknown
	for (l in 1:length(unkn)){
		#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)

		par(oma = oma.saved)
		o.par <- par(mar = rep.int(0, 4))
		on.exit(par(o.par))
		#For each sample
		for (c in 1:length(resGC$xset)) {	
			#get sample name
			sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
			#remove .cdf, .mzXML filepattern
			filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", 
									"[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
			filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")

                        if(helpannotation[[a]][r,"annotation"] == peaktable[unkn[l],1]){
                            findunkn <- TRUE
                            pcgrp <- helpannotation[[a]][r,"pspvector"]
							par (mar=c(0, 0, 0, 0) + 0.1)
							#Write title
							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
							plotEICs(an, pspec=pcgrp, maxlabel=2)
							#Window for pseudospectra
							plotPsSpectrum(an, pspec=pcgrp, maxlabel=2)
						}
					}
					if(!findunkn) {
						par (mar=c(0, 0, 0, 0) + 0.1)

					break
				}
    		}
		}
		graphics.off()
	}#end  for unkn[l]
}#end function

8:d1ce2634135f

    peaktable <- resGC$PeakTable
		
	par (mar=c(5, 4, 4, 2) + 0.1)
	#For each unknown
	for (l in 1:length(unkn)){
		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))
		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)

		par(oma = oma.saved)
		o.par <- par(mar = rep.int(0, 4))
		on.exit(par(o.par))
		#For each sample
		for (c in 1:length(resGC$xset)) {	
            #get sample name
			sampname<-basename(resGC$xset[[c]]@xcmsSet@filepaths)
			#remove .cdf, .mzXML filepattern
			filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", 
									"[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
			filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")

                        if(helpannotation[[a]][r,"annotation"] == peaktable[unkn[l],1]){
                            findunkn <- TRUE
                            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)
						}
					}
					if(!findunkn) {
						par (mar=c(0, 0, 0, 0) + 0.1)

					break
				}
    		}
		}
		graphics.off()
        print("graph off")
	}#end  for unkn[l]
    print("fin unkn")
}#end function