Mercurial > repos > ethevenot > biosigner

annotate biosigner_wrapper.R @ 2:b2414be87d4b draft

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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
author ethevenot
date Sat, 06 Aug 2016 12:17:12 -0400
parents 48e4be935243
children fa80bd02055f
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48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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1 #!/usr/bin/env Rscript
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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3 library(batch) ## parseCommandArgs
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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5 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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8 ##------------------------------
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9 ## Initializing
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10 ##------------------------------
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12 ## options
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13 ##--------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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15 strAsFacL <- options()$stringsAsFactors
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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16 options(stringsAsFactors = FALSE)
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18 ## libraries
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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19 ##----------
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21 suppressMessages(library(biosigner))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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23 if(packageVersion("biosigner") < "1.0.0")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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24 stop("Please use 'biosigner' versions of 1.0.0 and above")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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25 if(packageVersion("ropls") < "1.4.0")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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26 stop("Please use 'ropls' versions of 1.4.0 and above")
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28 ## constants
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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29 ##----------
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31 modNamC <- "Biosigner" ## module name
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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33 topEnvC <- environment()
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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34 flgC <- "\n"
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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36 ## functions
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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37 ##----------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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39 flgF <- function(tesC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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40 envC = topEnvC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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41 txtC = NA) { ## management of warning and error messages
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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43 tesL <- eval(parse(text = tesC), envir = envC)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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45 if(!tesL) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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47 sink(NULL)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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48 stpTxtC <- ifelse(is.na(txtC),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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49 paste0(tesC, " is FALSE"),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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50 txtC)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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52 stop(stpTxtC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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53 call. = FALSE)
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54
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55 }
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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56
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57 } ## flgF
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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58
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59
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60 ## log file
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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61 ##---------
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62
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63 sink(argVc["information"])
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64
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65 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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66 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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67
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68
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69 ## arguments
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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70 ##----------
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71
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72 xMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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73 check.names = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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74 header = TRUE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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75 row.names = 1,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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76 sep = "\t")))
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77
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78 samDF <- read.table(argVc["sampleMetadata_in"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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79 check.names = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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80 header = TRUE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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81 row.names = 1,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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82 sep = "\t")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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83 flgF("identical(rownames(xMN), rownames(samDF))", txtC = "Sample names (or number) in the data matrix (first row) and sample metadata (first column) are not identical; use the 'Check Format' module in the 'Quality Control' section")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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84
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85 varDF <- read.table(argVc["variableMetadata_in"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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86 check.names = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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87 header = TRUE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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88 row.names = 1,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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89 sep = "\t")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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90 flgF("identical(colnames(xMN), rownames(varDF))", txtC = "Variable names (or number) in the data matrix (first column) and sample metadata (first column) are not identical; use the 'Check Format' module in the 'Quality Control' section")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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91
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92 flgF("argVc['respC'] %in% colnames(samDF)",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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93 txtC = paste0("Class argument (", argVc['respC'], ") must be either none or one of the column names (first row) of your sample metadata"))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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94 respVc <- samDF[, argVc["respC"]]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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95 flgF("mode(respVc) == 'character'",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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96 txtC = paste0("'", argVc['respC'], "' column of sampleMetadata does not contain only characters"))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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97 respFc <- factor(respVc)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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98 flgF("length(levels(respFc)) == 2",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
99 txtC = paste0("'", argVc['respC'], "' column of sampleMetadata does not contain only 2 types of characters (e.g., 'case' and 'control')"))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
100 tierMaxC <- ifelse("tierC" %in% names(argVc), argVc["tierC"], "S")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
101 pvalN <- ifelse("pvalN" %in% names(argVc), as.numeric(argVc["pvalN"]), 0.05)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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102
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103
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parents:
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104 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
105 ## Computation and plot
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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106 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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107
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108
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parents:
diff changeset
109 sink()
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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110
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parents:
diff changeset
111 optWrnN <- options()$warn
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
diff changeset
112 options(warn = -1)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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113
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parents:
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114 if("seedI" %in% names(argVc) && argVc["seedI"] != "0")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
115 set.seed(as.integer(argVc["seedI"]))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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116
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ethevenot
parents:
diff changeset
117 bsnLs <- biosign(x = xMN,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
118 y = respFc,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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119 methodVc = ifelse("methodC" %in% names(argVc), argVc["methodC"], "all"),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
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120 bootI = ifelse("bootI" %in% names(argVc), as.numeric(argVc["bootI"]), 50),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
121 pvalN = pvalN,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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122 printL = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
123 plotL = FALSE,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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124 .sinkC = argVc["information"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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125
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parents:
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126 if("seedI" %in% names(argVc) && argVc["seedI"] != "0")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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127 set.seed(NULL)
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128
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parents:
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129 tierMC <- bsnLs@tierMC
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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130
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parents:
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131 if(!is.null(tierMC)) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
132 plot(bsnLs,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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133 tierMaxC = tierMaxC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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134 file.pdfC = argVc["figure_tier"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
135 .sinkC = argVc["information"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
136 plot(bsnLs,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
137 tierMaxC = tierMaxC,
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
138 typeC = "boxplot",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
139 file.pdfC = argVc["figure_boxplot"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
140 .sinkC = argVc["information"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
141 } else {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
142 pdf(argVc["figure_tier"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
143 plot(1, bty = "n", type = "n",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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144 xaxt = "n", yaxt = "n", xlab = "", ylab = "")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
145 text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
146 labels = "No significant variable to display")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
147 dev.off()
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
148 pdf(argVc["figure_boxplot"])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
149 plot(1, bty = "n", type = "n",
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
150 xaxt = "n", yaxt = "n", xlab = "", ylab = "")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
151 text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
152 labels = "No significant variable to display")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
153 dev.off()
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parents:
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154 }
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parents:
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155
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parents:
diff changeset
156
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ethevenot
parents:
diff changeset
157 options(warn = optWrnN)
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parents:
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158
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parents:
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159
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ethevenot
parents:
diff changeset
160 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
161 ## Print
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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162 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
163
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ethevenot
parents:
diff changeset
164 sink(argVc["information"], append = TRUE)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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165
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ethevenot
parents:
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166 tierFullVc <- c("S", LETTERS[1:5])
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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167 tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
diff changeset
168
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ethevenot
parents:
diff changeset
169 if(sum(tierMC %in% tierVc)) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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170 cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
171 print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), ,
2
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 0
diff changeset
172 drop = FALSE])
b2414be87d4b planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit d85321a93588817e9e8884b90dde6331292bbe79
ethevenot
parents: 0
diff changeset
173
0
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
174 cat("\nAccuracy:\n")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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175 print(round(getAccuracyMN(bsnLs), 3))
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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176 } else
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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177 cat("\nNo significant variable found for any classifier\n")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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178
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179
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parents:
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180 ##------------------------------
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parents:
diff changeset
181 ## Ending
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ethevenot
parents:
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182 ##------------------------------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
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parents:
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183
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parents:
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184 ## Saving
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
185 ##-------
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
186
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ethevenot
parents:
diff changeset
187 if(!is.null(tierMC)) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
188 tierDF <- data.frame(tier = sapply(rownames(varDF),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
189 function(varC) {
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
190 varTirVc <- tierMC[varC, ]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
191 varTirVc <- names(varTirVc)[varTirVc %in% tierVc]
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
192 paste(varTirVc, collapse = "|")
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
193 }),
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
diff changeset
194 stringsAsFactors = FALSE)
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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195 colnames(tierDF) <- paste(argVc["respC"],
48e4be935243 planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit b8af709c9fd6ed283fc4e4249dcf692556927b2d
ethevenot
parents:
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196 colnames(tierDF),
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197 paste(tierVc, collapse = ""),
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198 sep = "_")
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199 varDF <- cbind.data.frame(varDF, tierDF)
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200 }
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201
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202 ## variableMetadata
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203
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204 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
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205 varDF)
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206 write.table(varDF,
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207 file = argVc["variableMetadata_out"],
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208 quote = FALSE,
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209 row.names = FALSE,
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210 sep = "\t")
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211
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212
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213 ## Closing
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214 ##--------
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215
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216 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
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217 as.character(Sys.time()), "\n", sep = "")
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218
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219 sink()
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220
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221 options(stringsAsFactors = strAsFacL)
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222
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223 rm(list = ls())
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224