Mercurial > repos > workflow4metabolomics > camera_combinexsannos

comparison lib.r @ 4:4c4945bce185 draft

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"planemo upload commit c1e276cf53b3c54d4702ab26d4f40a525a720998"
author workflow4metabolomics
date Thu, 22 Apr 2021 10:27:58 +0000
parents c4c13745e797
children 2443150161b4
comparison
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3:3bf04fc404d9 4:4c4945bce185
3 #@author G. Le Corguille 3 #@author G. Le Corguille
4 # solve an issue with batch if arguments are logical TRUE/FALSE 4 # solve an issue with batch if arguments are logical TRUE/FALSE
5 parseCommandArgs <- function(...) { 5 parseCommandArgs <- function(...) {
6 args <- batch::parseCommandArgs(...) 6 args <- batch::parseCommandArgs(...)
7 for (key in names(args)) { 7 for (key in names(args)) {
8 if (args[key] %in% c("TRUE","FALSE")) 8 if (args[key] %in% c("TRUE", "FALSE"))
9 args[key] = as.logical(args[key]) 9 args[key] <- as.logical(args[key])
10 } 10 }
11 return(args) 11 return(args)
12 } 12 }
13 13
14 #@author G. Le Corguille 14 #@author G. Le Corguille
15 # This function will 15 # This function will
16 # - load the packages 16 # - load the packages
17 # - display the sessionInfo 17 # - display the sessionInfo
18 loadAndDisplayPackages <- function(pkgs) { 18 loadAndDisplayPackages <- function(pkgs) {
19 for(pkg in pkgs) suppressPackageStartupMessages( stopifnot( library(pkg, quietly=TRUE, logical.return=TRUE, character.only=TRUE))) 19 for (pkg in pkgs) suppressPackageStartupMessages(stopifnot(library(pkg, quietly = TRUE, logical.return = TRUE, character.only = TRUE)))
20 20
21 sessioninfo = sessionInfo() 21 sessioninfo <- sessionInfo()
22 cat(sessioninfo$R.version$version.string,"\n") 22 cat(sessioninfo$R.version$version.string, "\n")
23 cat("Main packages:\n") 23 cat("Main packages:\n")
24 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") 24 for (pkg in names(sessioninfo$otherPkgs)) {
25 cat(paste(pkg, packageVersion(pkg)), "\t")
26 }
27 cat("\n")
25 cat("Other loaded packages:\n") 28 cat("Other loaded packages:\n")
26 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n") 29 for (pkg in names(sessioninfo$loadedOnly)) {
30 cat(paste(pkg, packageVersion(pkg)), "\t")
31 }
32 cat("\n")
27 } 33 }
28 34
29 # This function retrieve a xset like object 35 # This function retrieve a xset like object
30 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr 36 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
31 getxcmsSetObject <- function(xobject) { 37 getxcmsSetObject <- function(xobject) {
32 # XCMS 1.x 38 # XCMS 1.x
33 if (class(xobject) == "xcmsSet") 39 if (class(xobject) == "xcmsSet")
34 return (xobject) 40 return(xobject)
35 # XCMS 3.x 41 # XCMS 3.x
36 if (class(xobject) == "XCMSnExp") { 42 if (class(xobject) == "XCMSnExp") {
37 # Get the legacy xcmsSet object 43 # Get the legacy xcmsSet object
38 suppressWarnings(xset <- as(xobject, 'xcmsSet')) 44 suppressWarnings(xset <- as(xobject, "xcmsSet"))
39 if (is.null(xset@phenoData$sample_group)) 45 if (is.null(xset@phenoData$sample_group))
40 sampclass(xset) = "." 46 sampclass(xset) <- "."
41 else 47 else
42 sampclass(xset) <- xset@phenoData$sample_group 48 sampclass(xset) <- xset@phenoData$sample_group
43 if (!is.null(xset@phenoData$sample_name)) 49 if (!is.null(xset@phenoData$sample_name))
44 rownames(xset@phenoData) = xset@phenoData$sample_name 50 rownames(xset@phenoData) <- xset@phenoData$sample_name
45 return (xset) 51 return(xset)
46 } 52 }
47 } 53 }
48 54
49 #@author G. Le Corguille 55 #@author G. Le Corguille
50 #The function create a pdf from the different png generated by diffreport 56 #The function create a pdf from the different png generated by diffreport
51 diffreport_png2pdf <- function(filebase) { 57 diffreport_png2pdf <- function(filebase) {
52 dir.create("pdf") 58 dir.create("pdf")
53 59
54 pdfEicOutput = paste0("pdf/",filebase,"-eic_pdf.pdf") 60 pdfEicOutput <- paste0("pdf/", filebase, "-eic_pdf.pdf")
55 pdfBoxOutput = paste0("pdf/",filebase,"-box_pdf.pdf") 61 pdfBoxOutput <- paste0("pdf/", filebase, "-box_pdf.pdf")
56 62
57 system(paste0("gm convert ",filebase,"_eic/*.png ",pdfEicOutput)) 63 system(paste0("gm convert ", filebase, "_eic/*.png ", pdfEicOutput))
58 system(paste0("gm convert ",filebase,"_box/*.png ",pdfBoxOutput)) 64 system(paste0("gm convert ", filebase, "_box/*.png ", pdfBoxOutput))
59 65
60 } 66 }
61 67
62 #@author G. Le Corguille 68 #@author G. Le Corguille
63 #The function create a zip archive from the different png generated by diffreport 69 #The function create a zip archive from the different png generated by diffreport
64 diffreport_png2zip <- function() { 70 diffreport_png2zip <- function() {
65 zip("eic.zip", dir(pattern="_eic"), zip=Sys.which("zip")) 71 zip("eic.zip", dir(pattern = "_eic"), zip = Sys.which("zip"))
66 zip("box.zip", dir(pattern="_box"), zip=Sys.which("zip")) 72 zip("box.zip", dir(pattern = "_box"), zip = Sys.which("zip"))
67 } 73 }
68 74
69 #The function create a zip archive from the different tabular generated by diffreport 75 #The function create a zip archive from the different tabular generated by diffreport
70 diffreport_tabular2zip <- function() { 76 diffreport_tabular2zip <- function() {
71 zip("tabular.zip", dir(pattern="tabular/*"), zip=Sys.which("zip")) 77 zip("tabular.zip", dir(pattern = "tabular/*"), zip = Sys.which("zip"))
72 } 78 }
73 79
74 #@author G. Le Corguille 80 #@author G. Le Corguille
75 #This function convert if it is required the Retention Time in minutes 81 #This function convert if it is required the Retention Time in minutes
76 RTSecondToMinute <- function(variableMetadata, convertRTMinute) { 82 RTSecondToMinute <- function(variableMetadata, convertRTMinute) {
77 if (convertRTMinute){ 83 if (convertRTMinute) {
78 #converting the retention times (seconds) into minutes 84 #converting the retention times (seconds) into minutes
79 print("converting the retention times into minutes in the variableMetadata") 85 print("converting the retention times into minutes in the variableMetadata")
80 variableMetadata[,"rt"]=variableMetadata[,"rt"]/60 86 variableMetadata[, "rt"] <- variableMetadata[, "rt"] / 60
81 variableMetadata[,"rtmin"]=variableMetadata[,"rtmin"]/60 87 variableMetadata[, "rtmin"] <- variableMetadata[, "rtmin"] / 60
82 variableMetadata[,"rtmax"]=variableMetadata[,"rtmax"]/60 88 variableMetadata[, "rtmax"] <- variableMetadata[, "rtmax"] / 60
83 } 89 }
84 return (variableMetadata) 90 return(variableMetadata)
85 } 91 }
86 92
87 #@author G. Le Corguille 93 #@author G. Le Corguille
88 #This function format ions identifiers 94 #This function format ions identifiers
89 formatIonIdentifiers <- function(variableMetadata, numDigitsRT=0, numDigitsMZ=0) { 95 formatIonIdentifiers <- function(variableMetadata, numDigitsRT = 0, numDigitsMZ = 0) {
90 splitDeco = strsplit(as.character(variableMetadata$name),"_") 96 splitDeco <- strsplit(as.character(variableMetadata$name), "_")
91 idsDeco = sapply(splitDeco, function(x) { deco=unlist(x)[2]; if (is.na(deco)) return ("") else return(paste0("_",deco)) }) 97 idsDeco <- sapply(splitDeco, function(x) {
92 namecustom = make.unique(paste0("M",round(variableMetadata[,"mz"],numDigitsMZ),"T",round(variableMetadata[,"rt"],numDigitsRT),idsDeco)) 98 deco <- unlist(x)[2]; if (is.na(deco)) return("") else return(paste0("_", deco))
93 variableMetadata=cbind(name=variableMetadata$name, namecustom=namecustom, variableMetadata[,!(colnames(variableMetadata) %in% c("name"))]) 99 })
100 namecustom <- make.unique(paste0("M", round(variableMetadata[, "mz"], numDigitsMZ), "T", round(variableMetadata[, "rt"], numDigitsRT), idsDeco))
101 variableMetadata <- cbind(name = variableMetadata$name, namecustom = namecustom, variableMetadata[, !(colnames(variableMetadata) %in% c("name"))])
94 return(variableMetadata) 102 return(variableMetadata)
95 } 103 }
96 104
97 #The function annotateDiffreport without the corr function which bugs 105 #The function annotateDiffreport without the corr function which bugs
98 annotatediff <- function(xset=xset, args=args, variableMetadataOutput="variableMetadata.tsv") { 106 annotatediff <- function(xset = xset, args = args, variableMetadataOutput = "variableMetadata.tsv") {
99 # Resolve the bug with x11, with the function png 107 # Resolve the bug with x11, with the function png
100 options(bitmapType='cairo') 108 options(bitmapType = "cairo")
101 109
102 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. 110 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
103 res=try(is.null(xset@filled)) 111 res <- try(is.null(xset@filled))
104 112
105 # ------ annot ------- 113 # ------ annot -------
106 args$calcCiS=as.logical(args$calcCiS) 114 args$calcCiS <- as.logical(args$calcCiS)
107 args$calcIso=as.logical(args$calcIso) 115 args$calcIso <- as.logical(args$calcIso)
108 args$calcCaS=as.logical(args$calcCaS) 116 args$calcCaS <- as.logical(args$calcCaS)
109 117
110 # common parameters 118 # common parameters
111 args4annotate = list(object=xset, 119 args4annotate <- list(object = xset,
112 nSlaves=args$nSlaves,sigma=args$sigma,perfwhm=args$perfwhm, 120 nSlaves = args$nSlaves, sigma = args$sigma, perfwhm = args$perfwhm,
113 maxcharge=args$maxcharge,maxiso=args$maxiso,minfrac=args$minfrac, 121 maxcharge = args$maxcharge, maxiso = args$maxiso, minfrac = args$minfrac,
114 ppm=args$ppm,mzabs=args$mzabs,quick=args$quick, 122 ppm = args$ppm, mzabs = args$mzabs, quick = args$quick,
115 polarity=args$polarity,max_peaks=args$max_peaks,intval=args$intval) 123 polarity = args$polarity, max_peaks = args$max_peaks, intval = args$intval)
116 124
117 # quick == FALSE 125 if (args$quick == FALSE) {
118 if(args$quick==FALSE) { 126 args4annotate <- append(args4annotate,
119 args4annotate = append(args4annotate, 127 list(graphMethod = args$graphMethod, cor_eic_th = args$cor_eic_th, pval = args$pval,
120 list(graphMethod=args$graphMethod,cor_eic_th=args$cor_eic_th,pval=args$pval, 128 calcCiS = args$calcCiS, calcIso = args$calcIso, calcCaS = args$calcCaS))
121 calcCiS=args$calcCiS,calcIso=args$calcIso,calcCaS=args$calcCaS))
122 # no ruleset 129 # no ruleset
123 if (!is.null(args$multiplier)) { 130 if (!is.null(args$multiplier)) {
124 args4annotate = append(args4annotate, 131 args4annotate <- append(args4annotate,
125 list(multiplier=args$multiplier)) 132 list(multiplier = args$multiplier))
126 } 133 }
127 # ruleset 134 # ruleset
128 else { 135 else {
129 rulset=read.table(args$rules, h=T, sep=";") 136 rulset <- read.table(args$rules, h = T, sep = ";")
130 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep="\t") 137 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = T, sep = "\t")
131 if (ncol(rulset) < 4) rulset=read.table(args$rules, h=T, sep=",") 138 if (ncol(rulset) < 4) rulset <- read.table(args$rules, h = T, sep = ",")
132 if (ncol(rulset) < 4) { 139 if (ncol(rulset) < 4) {
133 error_message="Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation" 140 error_message <- "Your ruleset file seems not well formatted. The column separators accepted are ; , and tabulation"
134 print(error_message) 141 print(error_message)
135 stop(error_message) 142 stop(error_message)
136 } 143 }
137 144
138 args4annotate = append(args4annotate, 145 args4annotate <- append(args4annotate,
139 list(rules=rulset)) 146 list(rules = rulset))
140 } 147 }
141 } 148 }
142 149
143 150
144 # launch annotate 151 # launch annotate
145 xa = do.call("annotate", args4annotate) 152 xa <- do.call("annotate", args4annotate)
146 peakList=getPeaklist(xa,intval=args$intval) 153 peakList <- getPeaklist(xa, intval = args$intval)
147 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); 154 peakList <- cbind(groupnames(xa@xcmsSet), peakList); colnames(peakList)[1] <- c("name");
148 155
149 # --- Multi condition : diffreport --- 156 # --- Multi condition : diffreport ---
150 diffrepOri=NULL 157 diffrepOri <- NULL
151 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))>=2) { 158 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset)) >= 2) {
152 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped. 159 #Check if the fillpeaks step has been done previously, if it hasn't, there is an error message and the execution is stopped.
153 res=try(is.null(xset@filled)) 160 res <- try(is.null(xset@filled))
154 classes=levels(sampclass(xset)) 161 classes <- levels(sampclass(xset))
155 x=1:(length(classes)-1) 162 x <- 1:(length(classes) - 1)
156 for (i in seq(along=x) ) { 163 for (i in seq(along = x)) {
157 y=1:(length(classes)) 164 y <- 1:(length(classes))
158 for (n in seq(along=y)){ 165 for (n in seq(along = y)) {
159 if(i+n <= length(classes)){ 166 if (i + n <= length(classes)) {
160 filebase=paste(classes[i],class2=classes[i+n],sep="-vs-") 167 filebase <- paste(classes[i], class2 = classes[i + n], sep = "-vs-")
161 168
162 diffrep=diffreport( 169 diffrep <- diffreport(
163 object=xset,class1=classes[i],class2=classes[i+n], 170 object = xset, class1 = classes[i], class2 = classes[i + n],
164 filebase=filebase,eicmax=args$eicmax,eicwidth=args$eicwidth, 171 filebase = filebase, eicmax = args$eicmax, eicwidth = args$eicwidth,
165 sortpval=TRUE,value=args$value,h=args$h,w=args$w,mzdec=args$mzdec,missing=0) 172 sortpval = TRUE, value = args$value, h = args$h, w = args$w, mzdec = args$mzdec, missing = 0)
166 173
167 diffrepOri = diffrep 174 diffrepOri <- diffrep
168 175
169 # renamming of the column rtmed to rt to fit with camera peaklist function output 176 # renamming of the column rtmed to rt to fit with camera peaklist function output
170 colnames(diffrep)[colnames(diffrep)=="rtmed"] <- "rt" 177 colnames(diffrep)[colnames(diffrep) == "rtmed"] <- "rt"
171 colnames(diffrep)[colnames(diffrep)=="mzmed"] <- "mz" 178 colnames(diffrep)[colnames(diffrep) == "mzmed"] <- "mz"
172 179
173 # combines results and reorder columns 180 # combines results and reorder columns
174 diffrep = merge(peakList, diffrep[,c("name","fold","tstat","pvalue")], by.x="name", by.y="name", sort=F) 181 diffrep <- merge(peakList, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = F)
175 diffrep = cbind(diffrep[,!(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))],diffrep[,(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))]) 182 diffrep <- cbind(diffrep[, !(colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))], diffrep[, (colnames(diffrep) %in% c(sampnames(xa@xcmsSet)))])
176 183
177 diffrep = RTSecondToMinute(diffrep, args$convertRTMinute) 184 diffrep <- RTSecondToMinute(diffrep, args$convertRTMinute)
178 diffrep = formatIonIdentifiers(diffrep, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ) 185 diffrep <- formatIonIdentifiers(diffrep, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
179 186
180 if(args$sortpval){ 187 if (args$sortpval) {
181 diffrep=diffrep[order(diffrep$pvalue), ] 188 diffrep <- diffrep[order(diffrep$pvalue), ]
182 } 189 }
183 190
184 dir.create("tabular", showWarnings = FALSE) 191 dir.create("tabular", showWarnings = FALSE)
185 write.table(diffrep, sep="\t", quote=FALSE, row.names=FALSE, file=paste("tabular/",filebase,"_tsv.tabular",sep="")) 192 write.table(diffrep, sep = "\t", quote = FALSE, row.names = FALSE, file = paste("tabular/", filebase, "_tsv.tabular", sep = ""))
186 193
187 if (args$eicmax != 0) { 194 if (args$eicmax != 0) {
188 if (args$png2 == "pdf") 195 if (args$png2 == "pdf")
189 diffreport_png2pdf(filebase) 196 diffreport_png2pdf(filebase)
190 if (args$png2 == "zip") 197 if (args$png2 == "zip")
196 if (args$tabular2 == "zip") 203 if (args$tabular2 == "zip")
197 diffreport_tabular2zip() 204 diffreport_tabular2zip()
198 } 205 }
199 206
200 # --- variableMetadata --- 207 # --- variableMetadata ---
201 variableMetadata=peakList[,!(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))] 208 variableMetadata <- peakList[, !(make.names(colnames(peakList)) %in% c(make.names(sampnames(xa@xcmsSet))))]
202 variableMetadata = RTSecondToMinute(variableMetadata, args$convertRTMinute) 209 variableMetadata <- RTSecondToMinute(variableMetadata, args$convertRTMinute)
203 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=args$numDigitsRT, numDigitsMZ=args$numDigitsMZ) 210 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = args$numDigitsRT, numDigitsMZ = args$numDigitsMZ)
204 # if we have 2 conditions, we keep stat of diffrep 211 # if we have 2 conditions, we keep stat of diffrep
205 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset))==2) { 212 if (!is.null(args$runDiffreport) & nlevels(sampclass(xset)) == 2) {
206 variableMetadata = merge(variableMetadata, diffrep[,c("name","fold","tstat","pvalue")],by.x="name", by.y="name", sort=F) 213 variableMetadata <- merge(variableMetadata, diffrep[, c("name", "fold", "tstat", "pvalue")], by.x = "name", by.y = "name", sort = F)
207 if(exists("args[[\"sortpval\"]]")){ 214 if (exists("args[[\"sortpval\"]]")) {
208 variableMetadata=variableMetadata[order(variableMetadata$pvalue), ] 215 variableMetadata <- variableMetadata[order(variableMetadata$pvalue), ]
209 } 216 }
210 } 217 }
211 218
212 variableMetadataOri=variableMetadata 219 variableMetadataOri <- variableMetadata
213 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) 220 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
214 221
215 return(list("xa"=xa,"diffrep"=diffrepOri,"variableMetadata"=variableMetadataOri)); 222 return(list("xa" = xa, "diffrep" = diffrepOri, "variableMetadata" = variableMetadataOri));
216 223
217 } 224 }
218 225
219 226
220 combinexsAnnos_function <- function(xaP, xaN, diffrepP=NULL,diffrepN=NULL, 227 combinexsAnnos_function <- function(xaP, xaN, diffrepP = NULL, diffrepN = NULL,
221 pos=TRUE,tol=2,ruleset=NULL,keep_meta=TRUE, convertRTMinute=F, numDigitsMZ=0, 228 pos = TRUE, tol = 2, ruleset = NULL, keep_meta = TRUE, convertRTMinute = F, numDigitsMZ = 0,
222 numDigitsRT=0, variableMetadataOutput="variableMetadata.tsv"){ 229 numDigitsRT = 0, variableMetadataOutput = "variableMetadata.tsv") {
223 230
224 #Load the two Rdata to extract the xset objects from positive and negative mode 231 #Load the two Rdata to extract the xset objects from positive and negative mode
225 cat("\tObject xset from positive mode\n") 232 cat("\tObject xset from positive mode\n")
226 print(xaP) 233 print(xaP)
227 cat("\n") 234 cat("\n")
231 cat("\n") 238 cat("\n")
232 239
233 cat("\n") 240 cat("\n")
234 cat("\tCombining...\n") 241 cat("\tCombining...\n")
235 #Convert the string to numeric for creating matrix 242 #Convert the string to numeric for creating matrix
236 row=as.numeric(strsplit(ruleset,",")[[1]][1]) 243 row <- as.numeric(strsplit(ruleset, ",")[[1]][1])
237 column=as.numeric(strsplit(ruleset,",")[[1]][2]) 244 column <- as.numeric(strsplit(ruleset, ",")[[1]][2])
238 ruleset=cbind(row,column) 245 ruleset <- cbind(row, column)
239 #Test if the file comes from an older version tool 246 #Test if the file comes from an older version tool
240 if ((!is.null(xaP)) & (!is.null(xaN))) { 247 if ((!is.null(xaP)) & (!is.null(xaN))) {
241 #Launch the combinexsannos function from CAMERA 248 #Launch the combinexsannos function from CAMERA
242 cAnnot=combinexsAnnos(xaP, xaN,pos=pos,tol=tol,ruleset=ruleset) 249 cAnnot <- combinexsAnnos(xaP, xaN, pos = pos, tol = tol, ruleset = ruleset)
243 } else { 250 } else {
244 stop("You must relauch the CAMERA.annotate step with the lastest version.") 251 stop("You must relauch the CAMERA.annotate step with the lastest version.")
245 } 252 }
246 253
247 if(pos){ 254 if (pos) {
248 xa=xaP 255 xa <- xaP
249 mode="neg. Mode" 256 mode <- "neg. Mode"
250 } else { 257 } else {
251 xa=xaN 258 xa <- xaN
252 mode="pos. Mode" 259 mode <- "pos. Mode"
253 } 260 }
254 261
255 peakList=getPeaklist(xa) 262 peakList <- getPeaklist(xa)
256 peakList=cbind(groupnames(xa@xcmsSet),peakList); colnames(peakList)[1] = c("name"); 263 peakList <- cbind(groupnames(xa@xcmsSet), peakList); colnames(peakList)[1] <- c("name");
257 variableMetadata=cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup",mode)]); 264 variableMetadata <- cbind(peakList, cAnnot[, c("isotopes", "adduct", "pcgroup", mode)]);
258 variableMetadata=variableMetadata[,!(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))] 265 variableMetadata <- variableMetadata[, !(colnames(variableMetadata) %in% c(sampnames(xa@xcmsSet)))]
259 266
260 #Test if there are more than two classes (conditions) 267 #Test if there are more than two classes (conditions)
261 if ( nlevels(sampclass(xaP@xcmsSet))==2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) { 268 if (nlevels(sampclass(xaP@xcmsSet)) == 2 & (!is.null(diffrepN)) & (!is.null(diffrepP))) {
262 diffrepP = diffrepP[,c("name","fold","tstat","pvalue")]; colnames(diffrepP) = paste("P.",colnames(diffrepP),sep="") 269 diffrepP <- diffrepP[, c("name", "fold", "tstat", "pvalue")]; colnames(diffrepP) <- paste("P.", colnames(diffrepP), sep = "")
263 diffrepN = diffrepN[,c("name","fold","tstat","pvalue")]; colnames(diffrepN) = paste("N.",colnames(diffrepN),sep="") 270 diffrepN <- diffrepN[, c("name", "fold", "tstat", "pvalue")]; colnames(diffrepN) <- paste("N.", colnames(diffrepN), sep = "")
264 271
265 variableMetadata = merge(variableMetadata, diffrepP, by.x="name", by.y="P.name") 272 variableMetadata <- merge(variableMetadata, diffrepP, by.x = "name", by.y = "P.name")
266 variableMetadata = merge(variableMetadata, diffrepN, by.x="name", by.y="N.name") 273 variableMetadata <- merge(variableMetadata, diffrepN, by.x = "name", by.y = "N.name")
267 } 274 }
268 275
269 rownames(variableMetadata) = NULL 276 rownames(variableMetadata) <- NULL
270 #TODO: checker 277 #TODO: checker colnames(variableMetadata)[1:2] = c("name", "mz/rt");
271 #colnames(variableMetadata)[1:2] = c("name","mz/rt"); 278
272 279 variableMetadata <- RTSecondToMinute(variableMetadata, convertRTMinute)
273 variableMetadata = RTSecondToMinute(variableMetadata, convertRTMinute) 280 variableMetadata <- formatIonIdentifiers(variableMetadata, numDigitsRT = numDigitsRT, numDigitsMZ = numDigitsMZ)
274 variableMetadata = formatIonIdentifiers(variableMetadata, numDigitsRT=numDigitsRT, numDigitsMZ=numDigitsMZ)
275 281
276 #If the user want to keep only the metabolites which match a difference 282 #If the user want to keep only the metabolites which match a difference
277 if(keep_meta){ 283 if (keep_meta) {
278 variableMetadata=variableMetadata[variableMetadata[,c(mode)]!="",] 284 variableMetadata <- variableMetadata[variableMetadata[, c(mode)] != "", ]
279 } 285 }
280 286
281 #Write the output into a tsv file 287 #Write the output into a tsv file
282 write.table(variableMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=variableMetadataOutput) 288 write.table(variableMetadata, sep = "\t", quote = FALSE, row.names = FALSE, file = variableMetadataOutput)
283 return(variableMetadata); 289 return(variableMetadata);
284 290
285 } 291 }
286 292
287 # This function get the raw file path from the arguments 293 # This function get the raw file path from the arguments
288 getRawfilePathFromArguments <- function(singlefile, zipfile, args) { 294 getRawfilePathFromArguments <- function(singlefile, zipfile, args) {
289 if (!is.null(args$zipfile)) zipfile = args$zipfile 295 if (!is.null(args$zipfile)) zipfile <- args$zipfile
290 if (!is.null(args$zipfilePositive)) zipfile = args$zipfilePositive 296 if (!is.null(args$zipfilePositive)) zipfile <- args$zipfilePositive
291 if (!is.null(args$zipfileNegative)) zipfile = args$zipfileNegative 297 if (!is.null(args$zipfileNegative)) zipfile <- args$zipfileNegative
292 298
293 if (!is.null(args$singlefile_galaxyPath)) { 299 if (!is.null(args$singlefile_galaxyPath)) {
294 singlefile_galaxyPaths = args$singlefile_galaxyPath; 300 singlefile_galaxyPaths <- args$singlefile_galaxyPath;
295 singlefile_sampleNames = args$singlefile_sampleName 301 singlefile_sampleNames <- args$singlefile_sampleName
296 } 302 }
297 if (!is.null(args$singlefile_galaxyPathPositive)) { 303 if (!is.null(args$singlefile_galaxyPathPositive)) {
298 singlefile_galaxyPaths = args$singlefile_galaxyPathPositive; 304 singlefile_galaxyPaths <- args$singlefile_galaxyPathPositive;
299 singlefile_sampleNames = args$singlefile_sampleNamePositive 305 singlefile_sampleNames <- args$singlefile_sampleNamePositive
300 } 306 }
301 if (!is.null(args$singlefile_galaxyPathNegative)) { 307 if (!is.null(args$singlefile_galaxyPathNegative)) {
302 singlefile_galaxyPaths = args$singlefile_galaxyPathNegative; 308 singlefile_galaxyPaths <- args$singlefile_galaxyPathNegative;
303 singlefile_sampleNames = args$singlefile_sampleNameNegative 309 singlefile_sampleNames <- args$singlefile_sampleNameNegative
304 } 310 }
305 if (exists("singlefile_galaxyPaths")){ 311 if (exists("singlefile_galaxyPaths")) {
306 singlefile_galaxyPaths = unlist(strsplit(singlefile_galaxyPaths,",")) 312 singlefile_galaxyPaths <- unlist(strsplit(singlefile_galaxyPaths, ","))
307 singlefile_sampleNames = unlist(strsplit(singlefile_sampleNames,",")) 313 singlefile_sampleNames <- unlist(strsplit(singlefile_sampleNames, ","))
308 314
309 singlefile=NULL 315 singlefile <- NULL
310 for (singlefile_galaxyPath_i in seq(1:length(singlefile_galaxyPaths))) { 316 for (singlefile_galaxyPath_i in seq_len(length(singlefile_galaxyPaths))) {
311 singlefile_galaxyPath=singlefile_galaxyPaths[singlefile_galaxyPath_i] 317 singlefile_galaxyPath <- singlefile_galaxyPaths[singlefile_galaxyPath_i]
312 singlefile_sampleName=singlefile_sampleNames[singlefile_galaxyPath_i] 318 singlefile_sampleName <- singlefile_sampleNames[singlefile_galaxyPath_i]
313 singlefile[[singlefile_sampleName]] = singlefile_galaxyPath 319 singlefile[[singlefile_sampleName]] <- singlefile_galaxyPath
314 } 320 }
315 } 321 }
316 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative", 322 for (argument in c("zipfile", "zipfilePositive", "zipfileNegative",
317 "singlefile_galaxyPath", "singlefile_sampleName", 323 "singlefile_galaxyPath", "singlefile_sampleName",
318 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive", 324 "singlefile_galaxyPathPositive", "singlefile_sampleNamePositive",
319 "singlefile_galaxyPathNegative","singlefile_sampleNameNegative")) { 325 "singlefile_galaxyPathNegative", "singlefile_sampleNameNegative")) {
320 args[[argument]]=NULL 326 args[[argument]] <- NULL
321 } 327 }
322 return(list(zipfile=zipfile, singlefile=singlefile, args=args)) 328 return(list(zipfile = zipfile, singlefile = singlefile, args = args))
323 } 329 }
324 330
325 331
326 # This function retrieve the raw file in the working directory 332 # This function retrieve the raw file in the working directory
327 # - if zipfile: unzip the file with its directory tree 333 # - if zipfile: unzip the file with its directory tree
328 # - if singlefiles: set symlink with the good filename 334 # - if singlefiles: set symlink with the good filename
329 retrieveRawfileInTheWorkingDirectory <- function(singlefile, zipfile) { 335 retrieveRawfileInTheWorkingDir <- function(singlefile, zipfile) {
330 if(!is.null(singlefile) && (length("singlefile")>0)) { 336 if (!is.null(singlefile) && (length("singlefile") > 0)) {
331 for (singlefile_sampleName in names(singlefile)) { 337 for (singlefile_sampleName in names(singlefile)) {
332 singlefile_galaxyPath = singlefile[[singlefile_sampleName]] 338 singlefile_galaxyPath <- singlefile[[singlefile_sampleName]]
333 if(!file.exists(singlefile_galaxyPath)){ 339 if (!file.exists(singlefile_galaxyPath)) {
334 error_message=paste("Cannot access the sample:",singlefile_sampleName,"located:",singlefile_galaxyPath,". Please, contact your administrator ... if you have one!") 340 error_message <- paste("Cannot access the sample:", singlefile_sampleName, "located:", singlefile_galaxyPath, ". Please, contact your administrator ... if you have one!")
335 print(error_message); stop(error_message) 341 print(error_message); stop(error_message)
336 } 342 }
337 343
338 file.symlink(singlefile_galaxyPath,singlefile_sampleName) 344 file.symlink(singlefile_galaxyPath, singlefile_sampleName)
339 } 345 }
340 directory = "." 346 directory <- "."
341 347
342 } 348 }
343 if(!is.null(zipfile) && (zipfile!="")) { 349 if (!is.null(zipfile) && (zipfile != "")) {
344 if(!file.exists(zipfile)){ 350 if (!file.exists(zipfile)) {
345 error_message=paste("Cannot access the Zip file:",zipfile,". Please, contact your administrator ... if you have one!") 351 error_message <- paste("Cannot access the Zip file:", zipfile, ". Please, contact your administrator ... if you have one!")
346 print(error_message) 352 print(error_message)
347 stop(error_message) 353 stop(error_message)
348 } 354 }
349 355
350 #list all file in the zip file
351 #zip_files=unzip(zipfile,list=T)[,"Name"]
352
353 #unzip 356 #unzip
354 suppressWarnings(unzip(zipfile, unzip="unzip")) 357 suppressWarnings(unzip(zipfile, unzip = "unzip"))
355 358
356 #get the directory name 359 #get the directory name
357 filesInZip=unzip(zipfile, list=T); 360 filesInZip <- unzip(zipfile, list = T);
358 directories=unique(unlist(lapply(strsplit(filesInZip$Name,"/"), function(x) x[1]))); 361 directories <- unique(unlist(lapply(strsplit(filesInZip$Name, "/"), function(x) x[1])));
359 directories=directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir] 362 directories <- directories[!(directories %in% c("__MACOSX")) & file.info(directories)$isdir]
360 directory = "." 363 directory <- "."
361 if (length(directories) == 1) directory = directories 364 if (length(directories) == 1) directory <- directories
362 365
363 cat("files_root_directory\t",directory,"\n") 366 cat("files_root_directory\t", directory, "\n")
364 367
365 } 368 }
366 return (directory) 369 return(directory)
367 } 370 }
368