annotate multivariate_wrapper.R @ 0:fafba524dca6 draft

planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
author ethevenot
date Wed, 27 Jul 2016 11:22:56 -0400
parents
children da272496b32d
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fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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1 #!/usr/bin/env Rscript
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3 library(batch) ## parseCommandArgs
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5 ########
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6 # MAIN #
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7 ########
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9 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
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12 #### Start_of_tested_code <- function() {}
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15 ##------------------------------
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16 ## Initializing
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17 ##------------------------------
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19 ## options
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20 ##--------
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22 strAsFacL <- options()$stringsAsFactors
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23 options(stringsAsFactors = FALSE)
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25 ## libraries
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26 ##----------
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28 suppressMessages(library(ropls))
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30 if(packageVersion("ropls") < "1.4.0")
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31 cat("\nWarning: new version of the 'ropls' package is available\n", sep="")
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33 ## constants
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34 ##----------
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36 modNamC <- "Multivariate" ## module name
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38 topEnvC <- environment()
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39 flgC <- "\n"
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41 ## functions
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42 ##----------
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44 flgF <- function(tesC,
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45 envC = topEnvC,
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46 txtC = NA) { ## management of warning and error messages
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48 tesL <- eval(parse(text = tesC), envir = envC)
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50 if(!tesL) {
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52 sink(NULL)
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53 stpTxtC <- ifelse(is.na(txtC),
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54 paste0(tesC, " is FALSE"),
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55 txtC)
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57 stop(stpTxtC,
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58 call. = FALSE)
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60 }
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62 } ## flgF
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65 ## log file
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66 ##---------
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67
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68 sink(argVc["information"])
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70 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
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71 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
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74 ## arguments
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75 ##----------
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76
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77 xMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
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78 check.names = FALSE,
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79 header = TRUE,
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80 row.names = 1,
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81 sep = "\t")))
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82
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83 samDF <- read.table(argVc["sampleMetadata_in"],
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84 check.names = FALSE,
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85 header = TRUE,
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86 row.names = 1,
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87 sep = "\t")
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88 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")
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89
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90 varDF <- read.table(argVc["variableMetadata_in"],
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91 check.names = FALSE,
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92 header = TRUE,
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93 row.names = 1,
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94 sep = "\t")
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95 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")
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96
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97 flgF("argVc['respC'] == 'none' || (argVc['respC'] %in% colnames(samDF))",
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98 txtC = paste0("Y Response argument (", argVc['respC'], ") must be either none or one of the column names (first row) of your sample metadata"))
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99 if(argVc["respC"] != "none") {
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100 yMCN <- matrix(samDF[, argVc['respC']], ncol = 1, dimnames = list(rownames(xMN), argVc['respC']))
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101 } else
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102 yMCN <- NULL
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103
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104 if(argVc["testL"] == "TRUE") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
105 flgF("!is.null(yMCN)",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
106 txtC = "Predictions cannot be peformed with PCA models")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
107 flgF("'test.' %in% colnames(samDF)",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
108 txtC = "No 'test.' column found in the sample metadata")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
109 flgF("identical(sort(unique(samDF[, 'test.'])), c('no', 'yes'))",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
110 txtC = "'test.' column of sample metadata must contain both 'yes' (tested samples) and 'no' (samples to be used for model training) values, and nothing else")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
111 flgF("identical(sort(unique(samDF[, 'test.'])), c('no', 'yes'))",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
112 txtC = "'test.' column of sample metadata must contain both 'yes' (tested samples) and 'no' (samples to be used for model training) values, and nothing else")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
113 flgF("!any(is.na(yMCN[samDF[, 'test.'] == 'no', ]))",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
114 txtC = "samples for model training (i.e. 'no' value in the 'test.' column) should not contain NA in the response")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
115 tesVl <- samDF[, "test."] == "yes"
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
116 xTesMN <- xMN[tesVl, , drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
117 xMN <- xMN[!tesVl, , drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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118 yMCN <- yMCN[!tesVl, , drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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119 } else
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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120 tesVl <- NULL
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parents:
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121
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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122 if(!('parAsColC' %in% names(argVc)))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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123 argVc["parAsColC"] <- "none"
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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124 flgF("argVc['parAsColC'] == 'none' || argVc['parAsColC'] %in% colnames(samDF)", txtC = paste0("Sample color argument (", argVc['parAsColC'], ") must be either none or one of the column names (first row) of your sample metadata"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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125 if(argVc["parAsColC"] != "none") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
126 parAsColFcVn <- samDF[, argVc['parAsColC']]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
127 if(is.character(parAsColFcVn))
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parents:
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128 parAsColFcVn <- factor(parAsColFcVn)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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129 } else
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parents:
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130 parAsColFcVn <- NA
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parents:
diff changeset
131
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parents:
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132 if(!('parMahalC' %in% names(argVc)) || argVc["parMahalC"] == "NA") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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133 if(!is.null(yMCN) && ncol(yMCN) == 1 && mode(yMCN) == "character")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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134 argVc["parMahalC"] <- argVc["respC"]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
135 else
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
136 argVc["parMahalC"] <- "none"
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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137 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
138 flgF("argVc['parMahalC'] == 'none' || (argVc['parMahalC'] %in% colnames(samDF))",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
139 txtC = paste0("Mahalanobis argument (", argVc['parMahalC'], ") must be either 'NA', 'none' or one of the column names (first row) of your sample metadata"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
140 if(argVc["parMahalC"] == "none") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
141 parEllipsesL <- FALSE
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
142 } else {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
143 if(is.null(yMCN)) { ## PCA case
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
144 flgF("mode(samDF[, argVc['parMahalC']]) == 'character'",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
145 txtC = paste0("Mahalanobis argument (", argVc['parMahalC'], ") must correspond to a column of characters in your sampleMetadata"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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146 parAsColFcVn <- factor(samDF[, argVc["parMahalC"]])
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
147 parEllipsesL <- TRUE
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parents:
diff changeset
148 } else { ## (O)PLS-DA case
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
149 flgF("identical(as.character(argVc['respC']), as.character(argVc['parMahalC']))",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
150 txtC = paste0("The Mahalanobis argument (", argVc['parMahalC'], ") must be identical to the Y response argument (", argVc['respC'], ")"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
151 parEllipsesL <- TRUE
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parents:
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152 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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153 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
154
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parents:
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155 if(!('parLabVc' %in% names(argVc)))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
156 argVc["parLabVc"] <- "none"
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
157 flgF("argVc['parLabVc'] == 'none' || (argVc['parLabVc'] %in% colnames(samDF))",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
158 txtC = paste0("Sample labels argument (", argVc['parLabVc'], ") must be either none or one of the column names (first row) of your sample metadata"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
159 if('parLabVc' %in% names(argVc))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
160 if(argVc["parLabVc"] != "none") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
161 flgF("mode(samDF[, argVc['parLabVc']]) == 'character'",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
162 txtC = paste0("The sample label argument (", argVc['parLabVc'], ") must correspond to a sample metadata column of characters (not numerics)"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
163 parLabVc <- samDF[, argVc['parLabVc']]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
164 } else
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
165 parLabVc <- NA
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
166
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
167 if('parPc1I' %in% names(argVc)) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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168 parCompVi <- as.numeric(c(argVc["parPc1I"], argVc["parPc2I"]))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
169 } else
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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170 parCompVi <- c(1, 2)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
171
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parents:
diff changeset
172
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parents:
diff changeset
173 ## checking
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
174 ##---------
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
175
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parents:
diff changeset
176
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
177 flgF("argVc['predI'] == 'NA' || argVc['orthoI'] == 'NA' || as.numeric(argVc['orthoI']) > 0 || parCompVi[2] <= as.numeric(argVc['predI'])",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
178 txtC = paste0("The highest component to display (", parCompVi[2], ") must not exceed the number of predictive components of the model (", argVc['predI'], ")"))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
179
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parents:
diff changeset
180
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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181 if(argVc["orthoI"] == "NA" || argVc["orthoI"] != "0")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
182 if(argVc["predI"] == "NA" || argVc["predI"] != "0") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
183 argVc["predI"] <- "1"
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
184 cat("\nWarning: OPLS: number of predictive components ('predI' argument) set to 1\n", sep = "")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
185 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
186
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
187 if(argVc["predI"] != "NA")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
188 if(as.numeric(argVc["predI"]) > min(nrow(xMN), ncol(xMN))) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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189 argVc["predI"] <- as.character(min(nrow(xMN), ncol(xMN)))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
190 cat("\nWarning: 'predI' set to the minimum of the dataMatrix dimensions: ", as.numeric(argVc["predI"]), "\n", sep = "")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
191 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
192
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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193 if("algoC" %in% names(argVc) && argVc["algoC"] == "svd" && length(which(is.na(c(xMN)))) > 0) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
194 minN <- min(c(xMN[!is.na(xMN)])) / 2
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
195 cat("\nWarning: Missing values set to ", round(minN, 1), " (half minimum value) for 'svd' algorithm to be used\n", sep = "")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
196 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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197
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198
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199 ##------------------------------
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200 ## Computation and plot
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201 ##------------------------------
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202
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203
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204 sink()
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205
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206 optWrnN <- options()$warn
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207 options(warn = -1)
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208
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209 ropLs <- opls(x = xMN,
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210 y = yMCN,
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211 predI = ifelse(argVc["predI"] == "NA", NA, as.numeric(argVc["predI"])),
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212 orthoI = ifelse(argVc["orthoI"] == "NA", NA, as.numeric(argVc["orthoI"])),
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213 algoC = ifelse('algoC' %in% names(argVc), argVc["algoC"], "default"),
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214 crossvalI = ifelse('crossvalI' %in% names(argVc), as.numeric(argVc["crossvalI"]), 7),
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215 log10L = ifelse('log10L' %in% names(argVc), as.logical(argVc["log10L"]), FALSE),
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216 permI = ifelse('permI' %in% names(argVc), as.numeric(argVc["permI"]), 20),
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217 scaleC = ifelse('scaleC' %in% names(argVc), argVc["scaleC"], "standard"),
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218 subset = NULL,
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219 printL = FALSE,
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220 plotL = FALSE,
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221 .sinkC = argVc['information'])
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222
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223 modC <- ropLs@typeC
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224 sumDF <- getSummaryDF(ropLs)
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225 desMC <- ropLs@descriptionMC
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226 scoreMN <- getScoreMN(ropLs)
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227 loadingMN <- getLoadingMN(ropLs)
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228
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229 vipVn <- coeMN <- orthoScoreMN <- orthoLoadingMN <- orthoVipVn <- NULL
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230
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231 if(grepl("PLS", modC)) {
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232
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233 vipVn <- getVipVn(ropLs)
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234 coeMN <- coef(ropLs)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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235
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236 if(grepl("OPLS", modC)) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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237 orthoScoreMN <- getScoreMN(ropLs, orthoL = TRUE)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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238 orthoLoadingMN <- getLoadingMN(ropLs, orthoL = TRUE)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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239 orthoVipVn <- getVipVn(ropLs, orthoL = TRUE)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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240 }
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241
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242 }
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243
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244 ploC <- ifelse('typeC' %in% names(argVc), argVc["typeC"], "summary")
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245
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246 if(sumDF[, "pre"] + sumDF[, "ort"] < 2) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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247 if(!(ploC %in% c("permutation", "overview"))) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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248 ploC <- "summary"
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249 plotWarnL <- TRUE
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250 }
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251 } else
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252 plotWarnL <- FALSE
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253
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254 plot(ropLs,
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255 typeVc = ploC,
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256 parAsColFcVn = parAsColFcVn,
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257 parCexN = ifelse('parCexN' %in% names(argVc), as.numeric(argVc["parCexN"]), 0.8),
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258 parCompVi = parCompVi,
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259 parEllipsesL = parEllipsesL,
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260 parLabVc = parLabVc,
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261 file.pdfC = argVc['figure'],
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262 .sinkC = argVc['information'])
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263
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264 options(warn = optWrnN)
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265
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266
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267 ##------------------------------
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268 ## Print
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269 ##------------------------------
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270
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271
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272 sink(argVc["information"], append = TRUE)
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273
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274 if(plotWarnL)
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275 cat("\nWarning: For single component models, only 'overview' (and 'permutation' in case of single response (O)PLS(-DA)) plot(s) are available\n", sep = "")
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276
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277
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ethevenot
parents:
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278 cat("\n", modC, "\n", sep = "")
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279
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parents:
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280 cat("\n", desMC["samples", ],
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
281 " samples x ",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
282 desMC["X_variables", ],
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
283 " variables",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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284 ifelse(modC != "PCA",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
285 " and 1 response",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
286 ""),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
diff changeset
287 "\n", sep = "")
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288
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289 cat("\n", ropLs@suppLs[["scaleC"]], " scaling of dataMatrix",
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diff changeset
290 ifelse(modC == "PCA",
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ethevenot
parents:
diff changeset
291 "",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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292 paste0(" and ",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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293 ifelse(mode(ropLs@suppLs[["yMCN"]]) == "character" && ropLs@suppLs[["scaleC"]] != "standard",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
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parents:
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294 "standard scaling of ",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
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diff changeset
295 ""),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
296 "response\n")), sep = "")
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parents:
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297
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298 if(substr(desMC["missing_values", ], 1, 1) != "0")
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ethevenot
parents:
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299 cat("\n", desMC["missing_values", ], " NAs\n", sep = "")
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ethevenot
parents:
diff changeset
300
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
301 if(substr(desMC["near_zero_excluded_X_variables", ], 1, 1) != "0")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
302 cat("\n", desMC["near_zero_excluded_X_variables", ],
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
303 " excluded variables during model building (because of near zero variance)\n", sep = "")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
304
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
305 cat("\n")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
306
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
307 optDigN <- options()[["digits"]]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
308 options(digits = 3)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
309 print(ropLs@modelDF)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
310 options(digits = optDigN)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
311
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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312
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
313 ##------------------------------
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
314 ## Ending
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
315 ##------------------------------
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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316
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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317
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
318 ## Saving
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
319 ##-------
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
320
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
321
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
322 rspModC <- gsub("-", "", modC)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
323 if(rspModC != "PCA")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
324 rspModC <- paste0(make.names(argVc['respC']), "_", rspModC)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
325
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
326 if(sumDF[, "pre"] + sumDF[, "ort"] < 2) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
327
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
328 tCompMN <- scoreMN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
329 pCompMN <- loadingMN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
330
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
331 } else {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
332
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
333 if(sumDF[, "ort"] > 0) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
334 if(parCompVi[2] > sumDF[, "ort"] + 1)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
335 stop("Selected orthogonal component for plotting (ordinate) exceeds the total number of orthogonal components of the model", call. = FALSE)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
336 tCompMN <- cbind(scoreMN[, 1], orthoScoreMN[, parCompVi[2] - 1])
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
337 pCompMN <- cbind(loadingMN[, 1], orthoLoadingMN[, parCompVi[2] - 1])
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
338 colnames(pCompMN) <- colnames(tCompMN) <- c("h1", paste("o", parCompVi[2] - 1, sep = ""))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
339 } else {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
340 if(max(parCompVi) > sumDF[, "pre"])
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
341 stop("Selected component for plotting as ordinate exceeds the total number of predictive components of the model", call. = FALSE)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
342 tCompMN <- scoreMN[, parCompVi, drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
343 pCompMN <- loadingMN[, parCompVi, drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
344 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
345
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
346 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
347
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
348 ## x-scores and prediction
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
349
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
350 colnames(tCompMN) <- paste0(rspModC, "_XSCOR-", colnames(tCompMN))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
351 tCompDF <- as.data.frame(tCompMN)[rownames(samDF), , drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
352
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
353 if(modC != "PCA") {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
354
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
355 if(!is.null(tesVl)) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
356 tCompFulMN <- matrix(NA,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
357 nrow = nrow(samDF),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
358 ncol = ncol(tCompMN),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
359 dimnames = list(rownames(samDF), colnames(tCompMN)))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
360 mode(tCompFulMN) <- "numeric"
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
361 tCompFulMN[rownames(tCompMN), ] <- tCompMN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
362 tCompMN <- tCompFulMN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
363
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
364 fitMCN <- fitted(ropLs)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
365 fitFulMCN <- matrix(NA,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
366 nrow = nrow(samDF),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
367 ncol = 1,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
368 dimnames = list(rownames(samDF), NULL))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
369 mode(fitFulMCN) <- mode(fitMCN)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
370 fitFulMCN[rownames(fitMCN), ] <- fitMCN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
371 yPreMCN <- predict(ropLs, newdata = as.data.frame(xTesMN))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
372 fitFulMCN[rownames(yPreMCN), ] <- yPreMCN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
373 fitMCN <- fitFulMCN
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
374
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
375 } else
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
376 fitMCN <- fitted(ropLs)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
377
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
378 colnames(fitMCN) <- paste0(rspModC,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
379 "_predictions")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
380 fitDF <- as.data.frame(fitMCN)[rownames(samDF), , drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
381
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
382 tCompDF <- cbind.data.frame(tCompDF, fitDF)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
383 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
384
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
385 samDF <- cbind.data.frame(samDF, tCompDF)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
386
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
387 ## x-loadings and VIP
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
388
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
389 colnames(pCompMN) <- paste0(rspModC, "_XLOAD-", colnames(pCompMN))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
390 if(!is.null(vipVn)) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
391 pCompMN <- cbind(pCompMN, vipVn)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
392 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
393 "_VIP",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
394 ifelse(!is.null(orthoVipVn),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
395 "_pred",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
396 ""))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
397 if(!is.null(orthoVipVn)) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
398 pCompMN <- cbind(pCompMN, orthoVipVn)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
399 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
400 "_VIP_ortho")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
401 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
402 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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403 if(!is.null(coeMN)) {
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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404 pCompMN <- cbind(pCompMN, coeMN)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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405 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC, "_COEFF")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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406 }
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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407 pCompDF <- as.data.frame(pCompMN)[rownames(varDF), , drop = FALSE]
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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408 varDF <- cbind.data.frame(varDF, pCompDF)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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409
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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410 ## sampleMetadata
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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411
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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412 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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413 samDF)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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414 write.table(samDF,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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415 file = argVc["sampleMetadata_out"],
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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416 quote = FALSE,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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417 row.names = FALSE,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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418 sep = "\t")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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419
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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420 ## variableMetadata
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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421
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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422 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
423 varDF)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
424 write.table(varDF,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
425 file = argVc["variableMetadata_out"],
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
426 quote = FALSE,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
427 row.names = FALSE,
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
428 sep = "\t")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
429
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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430 # Output ropLs
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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431 if ( ! is.null(argVc['ropls_out']))
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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432 save(ropLs, file = argVc['ropls_out'])
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
433
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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434 ## Closing
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
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435 ##--------
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
436
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
437 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
438 as.character(Sys.time()), "\n", sep = "")
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
439
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
440 sink()
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
441
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
442 options(stringsAsFactors = strAsFacL)
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
443
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
444
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
445 #### End_of_tested_code <- function() {}
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
446
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
447
fafba524dca6 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 6596dbd39d20ee1962d9ebdd87eec04821239760
ethevenot
parents:
diff changeset
448 rm(list = ls())