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comparison lib.r @ 4:2db1d1d0f131 draft

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planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 83b80dcd96b379518c2e4ace992affc889d32ca6
author lecorguille
date Fri, 08 Apr 2016 10:39:09 -0400
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children 2c1d7df89cf6
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3:98e33cdf0eb1 4:2db1d1d0f131
1 # lib.r version="2.0.1"
2 #Authors ABiMS TEAM
3 #Lib.r for Galaxy Workflow4Metabo
4 #version 2.2
5 #Based on lib.r 2.1
6 #Modifications made by Guitton Yann
7 #correct bug in Base Peak Chromatogram (BPC) option, not only TIC when scanrange used in xcmsSet
8 #Note if scanrange is used a warning is prompted in R console but do not stop PDF generation
9
10
11
12
13 #@author Y. Guitton
14 getBPC <- function(file,rtcor=NULL, ...) {
15 object <- xcmsRaw(file)
16 sel <- profRange(object, ...)
17 cbind(if (is.null(rtcor)) object@scantime[sel$scanidx] else rtcor ,xcms:::colMax(object@env$profile[sel$massidx,sel$scanidx,drop=FALSE]))
18 #plotChrom(xcmsRaw(file), base=T)
19 }
20
21 #@author Y. Guitton
22 getBPCs <- function (xcmsSet=NULL, pdfname="BPCs.pdf",rt=c("raw","corrected"), scanrange=NULL) {
23 cat("Creating BIC pdf...\n")
24
25 if (is.null(xcmsSet)) {
26 cat("Enter an xcmsSet \n")
27 stop()
28 } else {
29 files <- filepaths(xcmsSet)
30 }
31
32 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
33
34 classnames<-vector("list",length(class))
35 for (i in 1:length(class)){
36 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
37 }
38
39 N <- dim(phenoData(xcmsSet))[1]
40
41 TIC <- vector("list",N)
42
43
44 for (j in 1:N) {
45
46 TIC[[j]] <- getBPC(files[j])
47 #good for raw
48 # seems strange for corrected
49 #errors if scanrange used in xcmsSetgeneration
50 if (!is.null(xcmsSet) && rt == "corrected")
51 rtcor <- xcmsSet@rt$corrected[[j]] else
52 rtcor <- NULL
53
54 TIC[[j]] <- getBPC(files[j],rtcor=rtcor)
55 # TIC[[j]][,1]<-rtcor
56 }
57
58
59
60 pdf(pdfname,w=16,h=10)
61 cols <- rainbow(N)
62 lty = 1:N
63 pch = 1:N
64 #search for max x and max y in BPCs
65 xlim = range(sapply(TIC, function(x) range(x[,1])))
66 ylim = range(sapply(TIC, function(x) range(x[,2])))
67 ylim = c(-ylim[2], ylim[2])
68
69
70 ##plot start
71
72 if (length(class)>2){
73 for (k in 1:(length(class)-1)){
74 for (l in (k+1):length(class)){
75 #print(paste(class[k],"vs",class[l],sep=" "))
76 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")
77 colvect<-NULL
78 for (j in 1:length(classnames[[k]])) {
79 tic <- TIC[[classnames[[k]][j]]]
80 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
81 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
82 colvect<-append(colvect,cols[classnames[[k]][j]])
83 }
84 for (j in 1:length(classnames[[l]])) {
85 # i=class2names[j]
86 tic <- TIC[[classnames[[l]][j]]]
87 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
88 colvect<-append(colvect,cols[classnames[[l]][j]])
89 }
90 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
91 }
92 }
93 }#end if length >2
94
95 if (length(class)==2){
96 k=1
97 l=2
98 colvect<-NULL
99 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")
100
101 for (j in 1:length(classnames[[k]])) {
102
103 tic <- TIC[[classnames[[k]][j]]]
104 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
105 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
106 colvect<-append(colvect,cols[classnames[[k]][j]])
107 }
108 for (j in 1:length(classnames[[l]])) {
109 # i=class2names[j]
110 tic <- TIC[[classnames[[l]][j]]]
111 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
112 colvect<-append(colvect,cols[classnames[[l]][j]])
113 }
114 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
115
116 }#end length ==2
117
118 dev.off() #pdf(pdfname,w=16,h=10)
119
120 invisible(TIC)
121 }
122
123
124
125 #@author Y. Guitton
126 getTIC <- function(file,rtcor=NULL) {
127 object <- xcmsRaw(file)
128 cbind(if (is.null(rtcor)) object@scantime else rtcor, rawEIC(object,mzrange=range(object@env$mz))$intensity)
129 }
130
131 ##
132 ## overlay TIC from all files in current folder or from xcmsSet, create pdf
133 ##
134 #@author Y. Guitton
135 getTICs <- function(xcmsSet=NULL,files=NULL, pdfname="TICs.pdf",rt=c("raw","corrected")) {
136 cat("Creating TIC pdf...\n")
137
138 if (is.null(xcmsSet)) {
139 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]", "[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
140 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""), collapse = "|")
141 if (is.null(files))
142 files <- getwd()
143 info <- file.info(files)
144 listed <- list.files(files[info$isdir], pattern = filepattern, recursive = TRUE, full.names = TRUE)
145 files <- c(files[!info$isdir], listed)
146 } else {
147 files <- filepaths(xcmsSet)
148 }
149
150 class<-as.vector(levels(xcmsSet@phenoData[,1])) #sometime phenoData have more than 1 column use first as class
151
152 classnames<-vector("list",length(class))
153 for (i in 1:length(class)){
154 classnames[[i]]<-which( xcmsSet@phenoData[,1]==class[i])
155 }
156
157 N <- length(files)
158 TIC <- vector("list",N)
159
160 for (i in 1:N) {
161 if (!is.null(xcmsSet) && rt == "corrected")
162 rtcor <- xcmsSet@rt$corrected[[i]] else
163 rtcor <- NULL
164 TIC[[i]] <- getTIC(files[i],rtcor=rtcor)
165 }
166
167 pdf(pdfname,w=16,h=10)
168 cols <- rainbow(N)
169 lty = 1:N
170 pch = 1:N
171 #search for max x and max y in TICs
172 xlim = range(sapply(TIC, function(x) range(x[,1])))
173 ylim = range(sapply(TIC, function(x) range(x[,2])))
174 ylim = c(-ylim[2], ylim[2])
175
176
177 ##plot start
178 if (length(class)>2){
179 for (k in 1:(length(class)-1)){
180 for (l in (k+1):length(class)){
181 #print(paste(class[k],"vs",class[l],sep=" "))
182 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")
183 colvect<-NULL
184 for (j in 1:length(classnames[[k]])) {
185
186 tic <- TIC[[classnames[[k]][j]]]
187 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
188 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
189 colvect<-append(colvect,cols[classnames[[k]][j]])
190 }
191 for (j in 1:length(classnames[[l]])) {
192 # i=class2names[j]
193 tic <- TIC[[classnames[[l]][j]]]
194 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
195 colvect<-append(colvect,cols[classnames[[l]][j]])
196 }
197 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
198 }
199 }
200 }#end if length >2
201 if (length(class)==2){
202 k=1
203 l=2
204
205 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")
206 colvect<-NULL
207 for (j in 1:length(classnames[[k]])) {
208 tic <- TIC[[classnames[[k]][j]]]
209 # points(tic[,1]/60, tic[,2], col = cols[i], pch = pch[i], type="l")
210 points(tic[,1]/60, tic[,2], col = cols[classnames[[k]][j]], pch = pch[classnames[[k]][j]], type="l")
211 colvect<-append(colvect,cols[classnames[[k]][j]])
212 }
213 for (j in 1:length(classnames[[l]])) {
214 # i=class2names[j]
215 tic <- TIC[[classnames[[l]][j]]]
216 points(tic[,1]/60, -tic[,2], col = cols[classnames[[l]][j]], pch = pch[classnames[[l]][j]], type="l")
217 colvect<-append(colvect,cols[classnames[[l]][j]])
218 }
219 legend("topright",paste(basename(files[c(classnames[[k]],classnames[[l]])])), col = colvect, lty = lty, pch = pch)
220
221 }#end length ==2
222 dev.off() #pdf(pdfname,w=16,h=10)
223
224 invisible(TIC)
225 }
226
227
228
229 ##
230 ## Get the polarities from all the samples of a condition
231 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
232 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
233 getSampleMetadata <- function(xcmsSet=NULL, sampleMetadataOutput="sampleMetadata.tsv") {
234 cat("Creating the sampleMetadata file...\n")
235
236 #Create the sampleMetada dataframe
237 sampleMetadata=xset@phenoData
238 sampleNamesOrigin=rownames(sampleMetadata)
239 sampleNamesMakeNames=make.names(sampleNamesOrigin)
240
241 if (any(duplicated(sampleNamesMakeNames))) {
242 write("\n\nERROR: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names().\nIn your case, at least two columns after the renaming obtain the same name, thus XCMS will collapse those columns per name.", stderr())
243 for (sampleName in sampleNamesOrigin) {
244 write(paste(sampleName,"\t->\t",make.names(sampleName)),stderr())
245 }
246 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
247 }
248
249 if (!all(sampleNamesOrigin == sampleNamesMakeNames)) {
250 cat("\n\nWARNING: Usually, R has trouble to deal with special characters in its column names, so it rename them using make.names()\nIn your case, one or more sample names will be renamed in the sampleMetadata and dataMatrix files:\n")
251 for (sampleName in sampleNamesOrigin) {
252 cat(paste(sampleName,"\t->\t",make.names(sampleName),"\n"))
253 }
254 }
255
256 sampleMetadata$sampleMetadata=sampleNamesMakeNames
257 sampleMetadata=cbind(sampleMetadata["sampleMetadata"],sampleMetadata["class"]) #Reorder columns
258 rownames(sampleMetadata)=NULL
259
260 #Create a list of files name in the current directory
261 list_files=xset@filepaths
262 #For each sample file, the following actions are done
263 for (file in list_files){
264 #Check if the file is in the CDF format
265 if (!mzR:::netCDFIsFile(file)){
266
267 # If the column isn't exist, with add one filled with NA
268 if (is.null(sampleMetadata$polarity)) sampleMetadata$polarity=NA
269
270 #Create a simple xcmsRaw object for each sample
271 xcmsRaw=xcmsRaw(file)
272 #Extract the polarity (a list of polarities)
273 polarity=xcmsRaw@polarity
274 #Verify if all the scans have the same polarity
275 uniq_list=unique(polarity)
276 if (length(uniq_list)>1){
277 polarity="mixed"
278 } else {
279 polarity=as.character(uniq_list)
280 }
281 #Transforms the character to obtain only the sample name
282 filename=basename(file)
283 library(tools)
284 samplename=file_path_sans_ext(filename)
285
286 #Set the polarity attribute
287 sampleMetadata$polarity[sampleMetadata$sampleMetadata==samplename]=polarity
288
289 #Delete xcmsRaw object because it creates a bug for the fillpeaks step
290 rm(xcmsRaw)
291 }
292
293 }
294
295 write.table(sampleMetadata, sep="\t", quote=FALSE, row.names=FALSE, file=sampleMetadataOutput)
296
297 return(list("sampleNamesOrigin"=sampleNamesOrigin,"sampleNamesMakeNames"=sampleNamesMakeNames))
298
299 }
300
301
302 ##
303 ## This function check if xcms will found all the files
304 ##
305 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr ABiMS TEAM
306 checkFilesCompatibilityWithXcms <- function(directory) {
307 cat("Checking files filenames compatibilities with xmcs...\n")
308 # WHAT XCMS WILL FIND
309 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
310 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
311 info <- file.info(directory)
312 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
313 files <- c(directory[!info$isdir], listed)
314 files_abs <- file.path(getwd(), files)
315 exists <- file.exists(files_abs)
316 files[exists] <- files_abs[exists]
317 files[exists] <- sub("//","/",files[exists])
318
319 # WHAT IS ON THE FILESYSTEM
320 filesystem_filepaths=system(paste("find $PWD/",directory," -not -name '\\.*' -not -path '*conda-env*' -type f -name \"*\"", sep=""), intern=T)
321 filesystem_filepaths=filesystem_filepaths[grep(filepattern, filesystem_filepaths, perl=T)]
322
323 # COMPARISON
324 if (!is.na(table(filesystem_filepaths %in% files)["FALSE"])) {
325 write("\n\nERROR: List of the files which will not be imported by xcmsSet",stderr())
326 write(filesystem_filepaths[!(filesystem_filepaths %in% files)],stderr())
327 stop("\n\nERROR: One or more of your files will not be import by xcmsSet. It may due to bad characters in their filenames.")
328
329 }
330 }
331
332
333
334 ##
335 ## This function check if XML contains special caracters. It also checks integrity and completness.
336 ##
337 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
338 checkXmlStructure <- function (directory) {
339 cat("Checking XML structure...\n")
340
341 cmd=paste("IFS=$'\n'; for xml in $(find",directory,"-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'); do if [ $(xmllint --nonet --noout \"$xml\" 2> /dev/null; echo $?) -gt 0 ]; then echo $xml;fi; done;")
342 capture=system(cmd,intern=TRUE)
343
344 if (length(capture)>0){
345 #message=paste("The following mzXML or mzML file is incorrect, please check these files first:",capture)
346 write("\n\nERROR: The following mzXML or mzML file(s) are incorrect, please check these files first:", stderr())
347 write(capture, stderr())
348 stop("ERROR: xcmsSet cannot continue with incorrect mzXML or mzML files")
349 }
350
351 }
352
353
354 ##
355 ## This function check if XML contain special characters
356 ##
357 #@author Misharl Monsoor misharl.monsoor@sb-roscoff.fr ABiMS TEAM
358 deleteXmlBadCharacters<- function (directory) {
359 cat("Checking Non ASCII characters in the XML...\n")
360
361 processed=F
362 l=system( paste("find",directory, "-not -name '\\.*' -not -path '*conda-env*' -type f -iname '*.*ml*'"),intern=TRUE)
363 for (i in l){
364 cmd=paste("LC_ALL=C grep '[^ -~]' \"",i,"\"",sep="")
365 capture=suppressWarnings(system(cmd,intern=TRUE))
366 if (length(capture)>0){
367 cmd=paste("perl -i -pe 's/[^[:ascii:]]//g;'",i)
368 print( paste("WARNING: Non ASCII characters have been removed from the ",i,"file") )
369 c=system(cmd,intern=TRUE)
370 capture=""
371 processed=T
372 }
373 }
374 if (processed) cat("\n\n")
375 return(processed)
376 }
377
378
379 ##
380 ## This function will compute MD5 checksum to check the data integrity
381 ##
382 #@author Gildas Le Corguille lecorguille@sb-roscoff.fr
383 getMd5sum <- function (directory) {
384 cat("Compute md5 checksum...\n")
385 # WHAT XCMS WILL FIND
386 filepattern <- c("[Cc][Dd][Ff]", "[Nn][Cc]", "([Mm][Zz])?[Xx][Mm][Ll]","[Mm][Zz][Dd][Aa][Tt][Aa]", "[Mm][Zz][Mm][Ll]")
387 filepattern <- paste(paste("\\.", filepattern, "$", sep = ""),collapse = "|")
388 info <- file.info(directory)
389 listed <- list.files(directory[info$isdir], pattern = filepattern,recursive = TRUE, full.names = TRUE)
390 files <- c(directory[!info$isdir], listed)
391 exists <- file.exists(files)
392 files <- files[exists]
393
394 library(tools)
395
396 #cat("\n\n")
397
398 return(as.matrix(md5sum(files)))
399 }
400