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annotate multivariate_wrapper.R @ 1:60c360e466a8 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit 0f382a5296aae9bfc77df06b0a5ad493eb3c01f3
author ethevenot
date Wed, 28 Feb 2018 10:04:14 -0500
parents 4b9488602d57
children
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4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
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1 #!/usr/bin/env Rscript
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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2
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3 library(batch) ## parseCommandArgs
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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4
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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5 # Constants
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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6 argv <- commandArgs(trailingOnly = FALSE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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7 script.path <- sub("--file=","",argv[grep("--file=",argv)])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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8 prog.name <- basename(script.path)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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9
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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10 # Print help
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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11 if (length(grep('-h', argv)) >0) {
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12 cat("Usage:", prog.name,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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13 "dataMatrix_in myDataMatrix.tsv",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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14 "sampleMetadata_in mySampleData.tsv",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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15 "variableMetadata_in myVariableMetadata.tsv",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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16 "respC ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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17 "predI ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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18 "orthoI ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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19 "testL ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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20 "typeC ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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21 "parAsColC ...",
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22 "parCexN ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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23 "parPc1I ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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24 "parPc2I ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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25 "parMahalC ...",
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26 "parLabVc ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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27 "algoC ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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28 "crossvalI ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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29 "log10L ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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30 "permI ...",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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31 "scaleC ...",
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32 "sampleMetadata_out mySampleMetadata_out.tsv",
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33 "variableMetadata_out myVariableMetadata_out.tsv",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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34 "figure figure.pdf",
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35 "information information.txt",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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36 "\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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37 quit(status = 0)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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38 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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39
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40 ########
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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41 # MAIN #
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42 ########
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43
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44 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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45
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46 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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47 ## Initializing
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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48 ##------------------------------
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49
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50 ## options
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
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51 ##--------
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52
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53 strAsFacL <- options()$stringsAsFactors
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54 options(stringsAsFactors = FALSE)
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55
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56 ## libraries
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57 ##----------
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58
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59 suppressMessages(library(ropls))
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60
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61 if(packageVersion("ropls") < "1.4.0")
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62 stop("Please use 'ropls' versions of 1.4.0 and above")
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63
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64 ## constants
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65 ##----------
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66
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67 modNamC <- "Multivariate" ## module name
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68
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69 topEnvC <- environment()
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70 flgC <- "\n"
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71
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72 ## functions
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73 ##----------
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74
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75 flgF <- function(tesC,
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76 envC = topEnvC,
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77 txtC = NA) { ## management of warning and error messages
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79 tesL <- eval(parse(text = tesC), envir = envC)
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80
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81 if(!tesL) {
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82
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83 sink()
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84 stpTxtC <- ifelse(is.na(txtC),
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85 paste0(tesC, " is FALSE"),
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86 txtC)
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87
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88 stop(stpTxtC,
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89 call. = FALSE)
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90
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91 }
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93 } ## flgF
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94
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95
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96 ## log file
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97 ##---------
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99 sink(argVc["information"])
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100
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101 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
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parents:
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102 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
103
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
104
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
105 ## arguments
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
106 ##----------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
107
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
108 xMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
109 check.names = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
110 header = TRUE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
111 row.names = 1,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
112 sep = "\t",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
113 comment.char = "")))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
114
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
115 samDF <- read.table(argVc["sampleMetadata_in"],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
116 check.names = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
117 header = TRUE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
118 row.names = 1,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
119 sep = "\t",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
120 comment.char = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
121 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")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
122
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
123 varDF <- read.table(argVc["variableMetadata_in"],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
124 check.names = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
125 header = TRUE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
126 row.names = 1,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
127 sep = "\t",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
128 comment.char = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
129 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")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
130
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
131 flgF("argVc['respC'] == 'none' || (argVc['respC'] %in% colnames(samDF))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
132 txtC = paste0("Y Response argument (", argVc['respC'], ") must be either none or one of the column names (first row) of your sample metadata"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
133 if(argVc["respC"] != "none") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
134 yMCN <- matrix(samDF[, argVc['respC']], ncol = 1, dimnames = list(rownames(xMN), argVc['respC']))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
135 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
136 yMCN <- NULL
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
137
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
138 if(argVc["testL"] == "TRUE") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
139 flgF("!is.null(yMCN)",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
140 txtC = "Predictions cannot be peformed with PCA models")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
141 flgF("'test.' %in% colnames(samDF)",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
142 txtC = "No 'test.' column found in the sample metadata")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
143 flgF("identical(sort(unique(samDF[, 'test.'])), c('no', 'yes'))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
144 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")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
145 flgF("identical(sort(unique(samDF[, 'test.'])), c('no', 'yes'))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
146 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")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
147 flgF("!any(is.na(yMCN[samDF[, 'test.'] == 'no', ]))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
148 txtC = "samples for model training (i.e. 'no' value in the 'test.' column) should not contain NA in the response")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
149 tesVl <- samDF[, "test."] == "yes"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
150 xTesMN <- xMN[tesVl, , drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
151 xMN <- xMN[!tesVl, , drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
152 yMCN <- yMCN[!tesVl, , drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
153 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
154 tesVl <- NULL
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
155
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
156 if(!('parAsColC' %in% names(argVc)))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
157 argVc["parAsColC"] <- "none"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
158 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"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
159 if(argVc["parAsColC"] != "none") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
160 parAsColFcVn <- samDF[, argVc['parAsColC']]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
161 if(is.character(parAsColFcVn))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
162 parAsColFcVn <- factor(parAsColFcVn)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
163 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
164 parAsColFcVn <- NA
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
165
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
166 if(!('parMahalC' %in% names(argVc)) || argVc["parMahalC"] == "NA") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
167 if(!is.null(yMCN) && ncol(yMCN) == 1 && mode(yMCN) == "character")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
168 argVc["parMahalC"] <- argVc["respC"]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
169 else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
170 argVc["parMahalC"] <- "none"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
171 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
172 flgF("argVc['parMahalC'] == 'none' || (argVc['parMahalC'] %in% colnames(samDF))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
173 txtC = paste0("Mahalanobis argument (", argVc['parMahalC'], ") must be either 'NA', 'none' or one of the column names (first row) of your sample metadata"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
174 if(argVc["parMahalC"] == "none") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
175 parEllipsesL <- FALSE
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
176 } else {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
177 if(is.null(yMCN)) { ## PCA case
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
178 flgF("mode(samDF[, argVc['parMahalC']]) == 'character'",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
179 txtC = paste0("Mahalanobis argument (", argVc['parMahalC'], ") must correspond to a column of characters in your sampleMetadata"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
180 parAsColFcVn <- factor(samDF[, argVc["parMahalC"]])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
181 parEllipsesL <- TRUE
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
182 } else { ## (O)PLS-DA case
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
183 flgF("identical(as.character(argVc['respC']), as.character(argVc['parMahalC']))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
184 txtC = paste0("The Mahalanobis argument (", argVc['parMahalC'], ") must be identical to the Y response argument (", argVc['respC'], ")"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
185 parEllipsesL <- TRUE
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
186 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
187 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
188
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
189 if(!('parLabVc' %in% names(argVc)))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
190 argVc["parLabVc"] <- "none"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
191 flgF("argVc['parLabVc'] == 'none' || (argVc['parLabVc'] %in% colnames(samDF))",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
192 txtC = paste0("Sample labels argument (", argVc['parLabVc'], ") must be either none or one of the column names (first row) of your sample metadata"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
193 if('parLabVc' %in% names(argVc))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
194 if(argVc["parLabVc"] != "none") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
195 flgF("mode(samDF[, argVc['parLabVc']]) == 'character'",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
196 txtC = paste0("The sample label argument (", argVc['parLabVc'], ") must correspond to a sample metadata column of characters (not numerics)"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
197 parLabVc <- samDF[, argVc['parLabVc']]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
198 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
199 parLabVc <- NA
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
200
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
201 if('parPc1I' %in% names(argVc)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
202 parCompVi <- as.numeric(c(argVc["parPc1I"], argVc["parPc2I"]))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
203 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
204 parCompVi <- c(1, 2)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
205
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
206
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
207 ## checking
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
208 ##---------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
209
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
210
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
211 flgF("argVc['predI'] == 'NA' || argVc['orthoI'] == 'NA' || as.numeric(argVc['orthoI']) > 0 || parCompVi[2] <= as.numeric(argVc['predI'])",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
212 txtC = paste0("The highest component to display (", parCompVi[2], ") must not exceed the number of predictive components of the model (", argVc['predI'], ")"))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
213
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
214
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
215 if(argVc["orthoI"] == "NA" || argVc["orthoI"] != "0")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
216 if(argVc["predI"] == "NA" || argVc["predI"] != "0") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
217 argVc["predI"] <- "1"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
218 cat("\nWarning: OPLS: number of predictive components ('predI' argument) set to 1\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
219 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
220
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
221 if(argVc["predI"] != "NA")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
222 if(as.numeric(argVc["predI"]) > min(nrow(xMN), ncol(xMN))) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
223 argVc["predI"] <- as.character(min(nrow(xMN), ncol(xMN)))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
224 cat("\nWarning: 'predI' set to the minimum of the dataMatrix dimensions: ", as.numeric(argVc["predI"]), "\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
225 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
226
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
227 if("algoC" %in% names(argVc) && argVc["algoC"] == "svd" && length(which(is.na(c(xMN)))) > 0) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
228 minN <- min(c(xMN[!is.na(xMN)])) / 2
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
229 cat("\nWarning: Missing values set to ", round(minN, 1), " (half minimum value) for 'svd' algorithm to be used\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
230 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
231
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
232
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
233 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
234 ## Computation and plot
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
235 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
236
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
237
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
238 sink()
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
239
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
240 optWrnN <- options()$warn
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
241 options(warn = -1)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
242
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
243 ropLs <- opls(x = xMN,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
244 y = yMCN,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
245 predI = ifelse(argVc["predI"] == "NA", NA, as.numeric(argVc["predI"])),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
246 orthoI = ifelse(argVc["orthoI"] == "NA", NA, as.numeric(argVc["orthoI"])),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
247 algoC = ifelse('algoC' %in% names(argVc), argVc["algoC"], "default"),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
248 crossvalI = ifelse('crossvalI' %in% names(argVc), as.numeric(argVc["crossvalI"]), 7),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
249 log10L = ifelse('log10L' %in% names(argVc), as.logical(argVc["log10L"]), FALSE),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
250 permI = ifelse('permI' %in% names(argVc), as.numeric(argVc["permI"]), 20),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
251 scaleC = ifelse('scaleC' %in% names(argVc), argVc["scaleC"], "standard"),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
252 subset = NULL,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
253 printL = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
254 plotL = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
255 .sinkC = argVc['information'])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
256
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
257 modC <- ropLs@typeC
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
258 sumDF <- getSummaryDF(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
259 desMC <- ropLs@descriptionMC
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
260 scoreMN <- getScoreMN(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
261 loadingMN <- getLoadingMN(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
262
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
263 vipVn <- coeMN <- orthoScoreMN <- orthoLoadingMN <- orthoVipVn <- NULL
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
264
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
265 if(grepl("PLS", modC)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
266
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
267 vipVn <- getVipVn(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
268 coeMN <- coef(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
269
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
270 if(grepl("OPLS", modC)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
271 orthoScoreMN <- getScoreMN(ropLs, orthoL = TRUE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
272 orthoLoadingMN <- getLoadingMN(ropLs, orthoL = TRUE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
273 orthoVipVn <- getVipVn(ropLs, orthoL = TRUE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
274 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
275
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
276 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
277
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
278 ploC <- ifelse('typeC' %in% names(argVc), argVc["typeC"], "summary")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
279
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
280 if(sumDF[, "pre"] + sumDF[, "ort"] < 2) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
281 if(!(ploC %in% c("permutation", "overview"))) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
282 ploC <- "summary"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
283 plotWarnL <- TRUE
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
284 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
285 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
286 plotWarnL <- FALSE
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
287
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
288 plot(ropLs,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
289 typeVc = ploC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
290 parAsColFcVn = parAsColFcVn,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
291 parCexN = ifelse('parCexN' %in% names(argVc), as.numeric(argVc["parCexN"]), 0.8),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
292 parCompVi = parCompVi,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
293 parEllipsesL = parEllipsesL,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
294 parLabVc = parLabVc,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
295 file.pdfC = argVc['figure'],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
296 .sinkC = argVc['information'])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
297
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
298 options(warn = optWrnN)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
299
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ethevenot
parents:
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300
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
301 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
302 ## Print
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
303 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
304
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
305
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
306 sink(argVc["information"], append = TRUE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
307
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
308 if(plotWarnL)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
309 cat("\nWarning: For single component models, only 'overview' (and 'permutation' in case of single response (O)PLS(-DA)) plot(s) are available\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
310
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
311
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
312 cat("\n", modC, "\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
313
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
314 cat("\n", desMC["samples", ],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
315 " samples x ",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
316 desMC["X_variables", ],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
317 " variables",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
318 ifelse(modC != "PCA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
319 " and 1 response",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
320 ""),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
321 "\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
322
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
323 cat("\n", ropLs@suppLs[["scaleC"]], " scaling of dataMatrix",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
324 ifelse(modC == "PCA",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
325 "",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
326 paste0(" and ",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
327 ifelse(mode(ropLs@suppLs[["yMCN"]]) == "character" && ropLs@suppLs[["scaleC"]] != "standard",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
328 "standard scaling of ",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
329 ""),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
330 "response\n")), sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
331
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
332 if(substr(desMC["missing_values", ], 1, 1) != "0")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
333 cat("\n", desMC["missing_values", ], " NAs\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
334
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
335 if(substr(desMC["near_zero_excluded_X_variables", ], 1, 1) != "0")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
336 cat("\n", desMC["near_zero_excluded_X_variables", ],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
337 " excluded variables during model building (because of near zero variance)\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
338
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
339 cat("\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
340
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
341 optDigN <- options()[["digits"]]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
342 options(digits = 3)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
343 print(ropLs@modelDF)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
344 options(digits = optDigN)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
345
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
346
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
347 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
348 ## Ending
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
349 ##------------------------------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
350
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
351
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
352 ## Saving
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
353 ##-------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
354
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
355
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
356 rspModC <- gsub("-", "", modC)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
357 if(rspModC != "PCA")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
358 rspModC <- paste0(make.names(argVc['respC']), "_", rspModC)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
359
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
360 if(sumDF[, "pre"] + sumDF[, "ort"] < 2) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
361
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
362 tCompMN <- scoreMN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
363 pCompMN <- loadingMN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
364
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
365 } else {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
366
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
367 if(sumDF[, "ort"] > 0) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
368 if(parCompVi[2] > sumDF[, "ort"] + 1)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
369 stop("Selected orthogonal component for plotting (ordinate) exceeds the total number of orthogonal components of the model", call. = FALSE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
370 tCompMN <- cbind(scoreMN[, 1], orthoScoreMN[, parCompVi[2] - 1])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
371 pCompMN <- cbind(loadingMN[, 1], orthoLoadingMN[, parCompVi[2] - 1])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
372 colnames(pCompMN) <- colnames(tCompMN) <- c("h1", paste("o", parCompVi[2] - 1, sep = ""))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
373 } else {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
374 if(max(parCompVi) > sumDF[, "pre"])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
375 stop("Selected component for plotting as ordinate exceeds the total number of predictive components of the model", call. = FALSE)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
376 tCompMN <- scoreMN[, parCompVi, drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
377 pCompMN <- loadingMN[, parCompVi, drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
378 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
379
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
380 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
381
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
382 ## x-scores and prediction
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
383
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
384 colnames(tCompMN) <- paste0(rspModC, "_XSCOR-", colnames(tCompMN))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
385 tCompDF <- as.data.frame(tCompMN)[rownames(samDF), , drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
386
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
387 if(modC != "PCA") {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
388
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
389 if(!is.null(tesVl)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
390 tCompFulMN <- matrix(NA,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
391 nrow = nrow(samDF),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
392 ncol = ncol(tCompMN),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
393 dimnames = list(rownames(samDF), colnames(tCompMN)))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
394 mode(tCompFulMN) <- "numeric"
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
395 tCompFulMN[rownames(tCompMN), ] <- tCompMN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
396 tCompMN <- tCompFulMN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
397
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
398 fitMCN <- fitted(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
399 fitFulMCN <- matrix(NA,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
400 nrow = nrow(samDF),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
401 ncol = 1,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
402 dimnames = list(rownames(samDF), NULL))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
403 mode(fitFulMCN) <- mode(fitMCN)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
404 fitFulMCN[rownames(fitMCN), ] <- fitMCN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
405 yPreMCN <- predict(ropLs, newdata = as.data.frame(xTesMN))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
406 fitFulMCN[rownames(yPreMCN), ] <- yPreMCN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
407 fitMCN <- fitFulMCN
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
408
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
409 } else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
410 fitMCN <- fitted(ropLs)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
411
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
412 colnames(fitMCN) <- paste0(rspModC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
413 "_predictions")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
414 fitDF <- as.data.frame(fitMCN)[rownames(samDF), , drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
415
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
416 tCompDF <- cbind.data.frame(tCompDF, fitDF)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
417 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
418
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
419 samDF <- cbind.data.frame(samDF, tCompDF)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
420
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
421 ## x-loadings and VIP
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
422
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
423 colnames(pCompMN) <- paste0(rspModC, "_XLOAD-", colnames(pCompMN))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
424 if(!is.null(vipVn)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
425 pCompMN <- cbind(pCompMN, vipVn)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
426 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
427 "_VIP",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
428 ifelse(!is.null(orthoVipVn),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
429 "_pred",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
430 ""))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
431 if(!is.null(orthoVipVn)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
432 pCompMN <- cbind(pCompMN, orthoVipVn)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
433 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
434 "_VIP_ortho")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
435 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
436 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
437 if(!is.null(coeMN)) {
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
438 pCompMN <- cbind(pCompMN, coeMN)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
439 if(ncol(coeMN) == 1)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
440 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC, "_COEFF")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
441 else
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
442 colnames(pCompMN)[(ncol(pCompMN) - ncol(coeMN) + 1):ncol(pCompMN)] <- paste0(rspModC, "_", colnames(coeMN), "-COEFF")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
443 }
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
444 pCompDF <- as.data.frame(pCompMN)[rownames(varDF), , drop = FALSE]
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
445 varDF <- cbind.data.frame(varDF, pCompDF)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
446
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
447 ## sampleMetadata
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
448
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
449 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
450 samDF)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
451 write.table(samDF,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
452 file = argVc["sampleMetadata_out"],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
453 quote = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
454 row.names = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
455 sep = "\t")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
456
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
457 ## variableMetadata
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
458
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
459 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
460 varDF)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
461 write.table(varDF,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
462 file = argVc["variableMetadata_out"],
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
463 quote = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
464 row.names = FALSE,
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
465 sep = "\t")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
466
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
467 # Output ropLs
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
468 if (!is.null(argVc['ropls_out']) && !is.na(argVc['ropls_out']))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
469 save(ropLs, file = argVc['ropls_out'])
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
470
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
471 ## Closing
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
472 ##--------
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
473
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
474 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
475 as.character(Sys.time()), "\n", sep = "")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
476
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
477 cat("\n\n\n============================================================================")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
478 cat("\nAdditional information about the call:\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
479 cat("\n1) Parameters:\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
480 print(cbind(value = argVc))
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
481
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
482 cat("\n2) Session Info:\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
483 sessioninfo <- sessionInfo()
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
484 cat(sessioninfo$R.version$version.string,"\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
485 cat("Main packages:\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
486 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
487 cat("Other loaded packages:\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
488 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
489
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
490 cat("============================================================================\n")
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
491
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
492 sink()
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
493
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
494 options(stringsAsFactors = strAsFacL)
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
495
4b9488602d57 planemo upload for repository https://github.com/workflow4metabolomics/multivariate.git commit ebbe4eb415f9e153eec5015bbffcdf0a925f2fa4
ethevenot
parents:
diff changeset
496 rm(list = ls())