Mercurial > repos > workflow4metabolomics > metams_plot

comparison metaMS_plot.r @ 2:96debae917e4 draft

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planemo upload for repository https://github.com/workflow4metabolomics/metaMS commit c7a518686137f6d62b7415715152e8d5a9953ed7
author workflow4metabolomics
date Fri, 06 Sep 2019 06:12:08 -0400
parents b60dc620bd14
children
comparison
equal deleted inserted replaced
1:708ab9928a70 2:96debae917e4
94 94
95 #Use getTIC2s and getBPC2s because getTICs and getBPCs can exists due to transfert of function in Rdata 95 #Use getTIC2s and getBPC2s because getTICs and getBPCs can exists due to transfert of function in Rdata
96 96
97 if(!is.null(singlefile)) { 97 if(!is.null(singlefile)) {
98 files <- paste("./",names(singlefile),sep="") 98 files <- paste("./",names(singlefile),sep="")
99 #WARNING if user has CDF files (not yet good for plotting)
100 if(MSnbase:::isCdfFile(files)){
101 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"
102 warning(warning_message)
103 cat(paste("\n","/!\\Warning/!\\",warning_message,sep="\n"))
104 }
99 if(!is.null(files)){ 105 if(!is.null(files)){
100 if(args$selectbpc){ 106 if(args$selectbpc){
101 cat("\n\tProcessing BPC(s) from XCMS files...\n") 107 cat("\n\tProcessing BPC(s) from XCMS files...\n")
102 c <- getBPC2s(files = files, xset = xset, rt="raw", pdfname="BPCs_raw.pdf") 108 c <- getBPC2s(files = files, xset = xset, rt="raw", pdfname="BPCs_raw.pdf")
103 cat("BPC(s) created...\n") 109 cat("BPC(s) created...\n")