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1 ## read args:
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2 args <- commandArgs(TRUE)
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3 #cat("args <- \"\"\n")
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4 ## a xcms xset saved as .RData
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5 args.xsetData <- args[1]
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6 #cat(paste("args.xsetData <- \"", args[1], "\"\n", sep=""))
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7
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8 args.class1 <- args[2]
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9 args.class2 <- args[3]
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10 #cat(paste("args.class1 <- \"", args[2], "\"\n", sep=""))
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11 #cat(paste("args.class2 <- \"", args[3], "\"\n", sep=""))
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12
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13 args.topcount <- strtoi(args[4])
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14 #cat(paste("args.topcount <- ", args[4], "\n", sep=""))
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15
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16 args.outTable <- args[5]
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17
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18 ## report files
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19 args.htmlReportFile <- args[6]
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20 args.htmlReportFile.files_path <- args[7]
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21 #cat(paste("args.htmlReportFile <- \"", args[6], "\"\n", sep=""))
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22 #cat(paste("args.htmlReportFile.files_path <- \"", args[7], "\"\n", sep=""))
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23
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24
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25 if (length(args) == 8)
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26 {
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27 args.outLogFile <- args[8]
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28 # suppress messages:
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29 # Send all STDERR to STDOUT using sink() see http://mazamascience.com/WorkingWithData/?p=888
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30 msg <- file(args.outLogFile, open="wt")
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31 sink(msg, type="message")
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32 sink(msg, type="output")
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33 }
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34
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35 tryCatch(
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36 {
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37 library(metaMS)
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38 library(xcms)
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39 #library("R2HTML")
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40
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41 # load the xset data :
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42 xsetData <- readRDS(args.xsetData)
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43 # if here to support both scenarios:
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44 if ("xcmsSet" %in% slotNames(xsetData) )
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45 {
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46 xsetData <- xsetData@xcmsSet
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47 }
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48
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49
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50 # info: levels(xcmsSet@phenoData$class) also gives access to the class names
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51 dir.create(file.path(args.htmlReportFile.files_path), showWarnings = FALSE, recursive = TRUE)
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52 # set cairo as default for png plots:
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53 png = function (...) grDevices::png(...,type='cairo')
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54 # run diffreport
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55 reporttab <- diffreport(xsetData, args.class1, args.class2, paste(args.htmlReportFile.files_path,"/fig", sep=""), args.topcount, metlin = 0.15, h=480, w=640)
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56
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57 # write out tsv table:
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58 write.table(reporttab, args.outTable, sep="\t", row.names=FALSE)
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59
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60 message("\nGenerating report.........")
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61
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62 cat("<html><body><h1>Differential analysis report</h1>", file= args.htmlReportFile)
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63 #HTML(reporttab[1:args.topcount,], file= args.htmlReportFile)
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64 figuresPath <- paste(args.htmlReportFile.files_path, "/fig_eic", sep="")
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65 message(figuresPath)
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66 listOfFiles <- list.files(path = figuresPath)
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67 for (i in 1:length(listOfFiles))
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68 {
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69 figureName <- listOfFiles[i]
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70 # maybe we still need to copy the figures to the args.htmlReportFile.files_path
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71 cat(paste("<img src='fig_eic/", figureName,"' />", sep=""), file= args.htmlReportFile, append=TRUE)
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72 cat(paste("<img src='fig_box/", figureName,"' />", sep=""), file= args.htmlReportFile, append=TRUE)
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73 }
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74
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75 message("finished generating report")
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76 cat("\nWarnings================:\n")
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77 str( warnings() )
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78 },
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79 error=function(cond) {
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80 sink(NULL, type="message") # default setting
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81 sink(stderr(), type="output")
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82 message("\nERROR: ===========\n")
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83 print(cond)
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84 }
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85 ) |
