# HG changeset patch
# User pieter.lukasse@wur.nl
# Date 1415286884 -3600
# Node ID e67149fbff20871d3949c2dcc4ab78d035f674d5
# Parent a7b609941846ecd2a29cd462443797fcab4fa887
small changes/improvements;
new metams and xcms tools
diff -r a7b609941846 -r e67149fbff20 combine_output.xml
--- a/combine_output.xml Fri Sep 19 16:14:58 2014 +0200
+++ b/combine_output.xml Thu Nov 06 16:14:44 2014 +0100
@@ -4,10 +4,11 @@
combine_output.py $rankfilter_in $caslookup_in $out_single $out_multi
-
+
-
+
diff -r a7b609941846 -r e67149fbff20 library_lookup.xml
--- a/library_lookup.xml Fri Sep 19 16:14:58 2014 +0200
+++ b/library_lookup.xml Thu Nov 06 16:14:44 2014 +0100
@@ -13,16 +13,23 @@
$regression.model
+
+
+
-
+
/" + dir_name :
galaxy_output = [("Configuration error: expected file not found in /" + dir_name, "", False)]
diff -r a7b609941846 -r e67149fbff20 metaMS_cmd_interface.r
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metaMS_cmd_interface.r Thu Nov 06 16:14:44 2014 +0100
@@ -0,0 +1,99 @@
+## read args:
+args <- commandArgs(TRUE)
+## the constructed DB, e.g. "E:/Rworkspace/metaMS/data/LCDBtest.RData"
+args.constructedDB <- args[1]
+## data files, e.g. "E:/Rworkspace/metaMS/data/data.zip" (with e.g. .CDF files) and unzip output dir, e.g. "E:/"
+args.dataZip <- args[2]
+args.zipExtrDir <- paste(args[2],"dir/")
+## settings file, e.g. "E:/Rworkspace/metaMS/data/settings.r", should contain assignment to an object named "customMetaMSsettings"
+args.settings <- args[3]
+
+## output file names, e.g. "E:/Rworkspace/metaMS/data/out.txt"
+args.outAnnotationTable <- args[4]
+args.outLogFile <- args[5]
+args.xsetOut <- args[6]
+
+## report files
+args.htmlReportFile <- args[7]
+args.htmlReportFile.files_path <- args[8]
+
+# Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
+msg <- file(args.outLogFile, open="wt")
+sink(msg, type="message")
+sink(msg, type="output")
+
+cat("\nSettings used===============:\n")
+cat(readChar(args.settings, 1e5))
+
+
+tryCatch(
+ {
+ library(metaMS)
+
+ ## load the constructed DB :
+ tempEnv <- new.env()
+ testDB <- load(args.constructedDB, envir=tempEnv)
+
+ ## load the data files from a zip file
+ files <- unzip(args.dataZip, exdir=args.zipExtrDir)
+
+ ## load settings "script" into "customMetaMSsettings"
+ source(args.settings, local=tempEnv)
+ message(paste(" loaded : ", args.settings))
+
+ # Just to highlight: if you want to use more than one
+ # trigger runLC:
+ LC <- runLC(files, settings = tempEnv[["customMetaMSsettings"]], DB = tempEnv[[testDB[1]]]$DB, nSlaves=20, returnXset = TRUE)
+
+ # write out runLC annotation results:
+ write.table(LC$Annotation$annotation.table, args.outAnnotationTable, sep="\t", row.names=FALSE)
+
+ # the used constructed DB (write to log):
+ cat("\nConstructed DB info===============:\n")
+ str(tempEnv[[testDB[1]]]$Info)
+ cat("\nConstructed DB table===============:\n")
+ write.table(tempEnv[[testDB[1]]]$DB, args.outLogFile, append=TRUE, row.names=FALSE)
+ write.table(tempEnv[[testDB[1]]]$Reftable, args.outLogFile, sep="\t", append=TRUE, row.names=FALSE)
+ # save xset as rdata:
+ xsetData <- LC$xset@xcmsSet
+ saveRDS(xsetData, file=args.xsetOut)
+
+ message("\nGenerating report.........")
+ # report
+ dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE)
+ setwd(file.path(args.htmlReportFile.files_path))
+ html <- "Extracted Ion Chromatograms of groups with more than 3 peaks
"
+
+ LC$xset@xcmsSet
+ gt <- groups(LC$xset@xcmsSet)
+ colnames(gt)
+ groupidx1 <- which(gt[,"rtmed"] > 0 & gt[,"rtmed"] < 3000 & gt[,"npeaks"] > 3)
+ if (length(groupidx1) > 0)
+ {
+ eiccor <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1))
+ eicraw <- getEIC(LC$xset@xcmsSet, groupidx = c(groupidx1), rt = "raw")
+ for (i in 1:length(groupidx1))
+ {
+ figureName <- paste(args.htmlReportFile.files_path, "/figure", i,".png", sep="")
+ html <- paste(html,"![](", "figure", i,".png)
", sep="")
+ png( figureName )
+ plot(eiccor, LC$xset@xcmsSet, groupidx = i)
+ devname = dev.off()
+ }
+ }
+
+
+ html <- paste(html,"")
+ message("finished generating report")
+ write(html,file=args.htmlReportFile)
+ # unlink(args.htmlReportFile)
+ cat("\nWarnings================:\n")
+ str( warnings() )
+ },
+ error=function(cond) {
+ sink(NULL, type="message") # default setting
+ sink(stderr(), type="output")
+ message("\nERROR: ===========\n")
+ print(cond)
+ }
+ )
diff -r a7b609941846 -r e67149fbff20 metams_lcms_annotate.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/metams_lcms_annotate.xml Thu Nov 06 16:14:44 2014 +0100
@@ -0,0 +1,136 @@
+
+ Runs metaMS process for LC/MS feature grouping and annotation
+
+ R_bioc_metams
+
+
+ metaMS_cmd_interface.r
+ $constructed_db
+ $data_files
+ $customMetaMSsettings
+ $outputFile
+ $outputLog
+ $xsetOut
+ $htmlReportFile
+ $htmlReportFile.files_path
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+## start comment
+ ## metaMS process settings
+ customMetaMSsettings <- metaMSsettings(protocolName = "${protocolName}",
+ chrom = "LC",
+ PeakPicking = list(
+ method = "${method}",
+ step = ${step},
+ fwhm = ${fwhm},
+ snthresh = ${snthresh},
+ max = ${max}),
+ Alignment = list(
+ min.class.fraction = ${min_class_fraction},
+ min.class.size = ${min_class_size},
+ mzwid = ${mzwid},
+ bws = c(${bws}),
+ missingratio = ${missingratio},
+ extraratio = ${extraratio},
+ retcormethod = "${retcormethod}",
+ retcorfamily = "${retcorfamily}",
+ fillPeaks = ${fillPeaks}),
+ CAMERA = list(
+ perfwhm = ${perfwhm},
+ cor_eic_th = ${cor_eic_th},
+ ppm= ${ppm}))
+metaSetting(customMetaMSsettings, "match2DB") <- list(
+ rtdiff = ${rtdiff},
+ rtval = ${rtval},
+ mzdiff = ${mzdiff},
+ ppm = ${match2DB_ppm},
+ minfeat = ${minfeat})
+
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+Differential analysis report
", file= args.htmlReportFile)
+ #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile)
+ figuresPath <- paste(args.htmlReportFile.files_path, "/fig_eic", sep="")
+ message(figuresPath)
+ listOfFiles <- list.files(path = figuresPath)
+ for (i in 1:length(listOfFiles))
+ {
+ figureName <- listOfFiles[i]
+ # maybe we still need to copy the figures to the args.htmlReportFile.files_path
+ cat(paste("![](fig_eic/", figureName,")
", sep=""), file= args.htmlReportFile, append=TRUE)
+ cat(paste("![](fig_box/", figureName,")
", sep=""), file= args.htmlReportFile, append=TRUE)
+ }
+
+ message("finished generating report")
+ cat("\nWarnings================:\n")
+ str( warnings() )
+ },
+ error=function(cond) {
+ sink(NULL, type="message") # default setting
+ sink(stderr(), type="output")
+ message("\nERROR: ===========\n")
+ print(cond)
+ }
+ )
\ No newline at end of file
diff -r a7b609941846 -r e67149fbff20 xcms_differential_analysis.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/xcms_differential_analysis.xml Thu Nov 06 16:14:44 2014 +0100
@@ -0,0 +1,55 @@
+
+ Runs xcms diffreport function for differential Analsysis
+
+ R_bioc_metams
+
+
+ xcms_differential_analysis.r
+ $xsetData
+ $class1
+ $class2
+ $topcount
+ $outTable
+ $outLogFile
+ $htmlReportFile
+ $htmlReportFile.files_path
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+.. class:: infomark
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+Runs xcms diffreport for showing the most significant differences between two sets/classes of samples. This tool also creates extracted ion chromatograms (EICs) for
+the most significant differences. The figure below shows an example of such an EIC.
+
+.. image:: $PATH_TO_IMAGES/diffreport.png
+
+
+
+
+
+
+ 10.1021/ac051437y
+
+
\ No newline at end of file