multivariate: multivariate_wrapper.R annotate

annotate multivariate_wrapper.R @ 0:b2b02fb81a0a draft default tip

planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty

author	eschen42
date	Mon, 14 Aug 2017 20:57:59 -0400
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children

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0 b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	1 #!/usr/bin/env Rscript
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	2
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	3 library(batch) ## parseCommandArgs
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	4
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	5 # Constants
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	6 argv <- commandArgs(trailingOnly = FALSE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	7 script.path <- sub("--file=","",argv[grep("--file=",argv)])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	8 prog.name <- basename(script.path)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	9
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	10 # Print help
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	11 if (length(grep('-h', argv)) >0) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	12 cat("Usage:", prog.name,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	13 "dataMatrix_in myDataMatrix.tsv",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	14 "sampleMetadata_in mySampleData.tsv",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	15 "variableMetadata_in myVariableMetadata.tsv",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	16 "respC ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	17 "predI ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	18 "orthoI ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	19 "testL ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	20 "typeC ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	21 "parAsColC ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	22 "parCexN ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	23 "parPc1I ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	24 "parPc2I ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	25 "parMahalC ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	26 "parLabVc ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	27 "algoC ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	28 "crossvalI ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	29 "log10L ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	30 "permI ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	31 "scaleC ...",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	32 "sampleMetadata_out mySampleMetadata_out.tsv",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	33 "variableMetadata_out myVariableMetadata_out.tsv",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	34 "figure figure.pdf",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	35 "information information.txt",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	36 "\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	37 quit(status = 0)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	38 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	39
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	40 ########
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	41 # MAIN #
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	42 ########
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	43
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	44 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	45
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	46 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	47 ## Initializing
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	48 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	49
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	50 ## options
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	51 ##--------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	52
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	53 strAsFacL <- options()$stringsAsFactors
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	54 options(stringsAsFactors = FALSE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	55
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	56 ## libraries
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	57 ##----------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	58
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	59 suppressMessages(library(ropls))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	60
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	61 if(packageVersion("ropls") < "1.4.0")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	62 stop("Please use 'ropls' versions of 1.4.0 and above")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	63
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	64 ## constants
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	65 ##----------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	66
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	67 modNamC <- "Multivariate" ## module name
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	68
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	69 topEnvC <- environment()
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	70 flgC <- "\n"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	71
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	72 ## functions
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	73 ##----------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	74
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	75 flgF <- function(tesC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	76 envC = topEnvC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	77 txtC = NA) { ## management of warning and error messages
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	78
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	79 tesL <- eval(parse(text = tesC), envir = envC)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	80
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	81 if(!tesL) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	82
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	83 sink()
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	84 stpTxtC <- ifelse(is.na(txtC),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	85 paste0(tesC, " is FALSE"),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	86 txtC)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	87
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	88 stop(stpTxtC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	89 call. = FALSE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	90
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	91 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	92
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	93 } ## flgF
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	94
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	95
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	96 ## log file
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	97 ##---------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	98
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	99 sink(argVc["information"])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	100
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	101 cat("\nStart of the '", modNamC, "' Galaxy module call: ",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	102 format(Sys.time(), "%a %d %b %Y %X"), "\n", sep="")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	103
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	104
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	105 ## arguments
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	106 ##----------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	107
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	108 xMN <- t(as.matrix(read.table(argVc["dataMatrix_in"],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	109 check.names = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	110 header = TRUE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	111 row.names = 1,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	112 sep = "\t",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	113 comment.char = "")))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	114
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	115 samDF <- read.table(argVc["sampleMetadata_in"],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	116 check.names = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	117 header = TRUE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	118 row.names = 1,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	119 sep = "\t",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	120 comment.char = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	122
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	123 varDF <- read.table(argVc["variableMetadata_in"],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	124 check.names = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	125 header = TRUE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	126 row.names = 1,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	127 sep = "\t",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	128 comment.char = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	130
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	131 flgF("argVc['respC'] == 'none' \|\| (argVc['respC'] %in% colnames(samDF))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	133 if(argVc["respC"] != "none") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	134 yMCN <- matrix(samDF[, argVc['respC']], ncol = 1, dimnames = list(rownames(xMN), argVc['respC']))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	135 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	136 yMCN <- NULL
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	137
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	138 if(argVc["testL"] == "TRUE") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	139 flgF("!is.null(yMCN)",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	140 txtC = "Predictions cannot be peformed with PCA models")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	141 flgF("'test.' %in% colnames(samDF)",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	142 txtC = "No 'test.' column found in the sample metadata")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	143 flgF("identical(sort(unique(samDF[, 'test.'])), c('no', 'yes'))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	145 flgF("identical(sort(unique(samDF[, 'test.'])), c('no', 'yes'))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	147 flgF("!any(is.na(yMCN[samDF[, 'test.'] == 'no', ]))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	148 txtC = "samples for model training (i.e. 'no' value in the 'test.' column) should not contain NA in the response")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	149 tesVl <- samDF[, "test."] == "yes"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	150 xTesMN <- xMN[tesVl, , drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	151 xMN <- xMN[!tesVl, , drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	152 yMCN <- yMCN[!tesVl, , drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	153 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	154 tesVl <- NULL
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	155
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	156 if(!('parAsColC' %in% names(argVc)))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	157 argVc["parAsColC"] <- "none"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	159 if(argVc["parAsColC"] != "none") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	160 parAsColFcVn <- samDF[, argVc['parAsColC']]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	161 if(is.character(parAsColFcVn))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	162 parAsColFcVn <- factor(parAsColFcVn)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	163 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	164 parAsColFcVn <- NA
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	165
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	166 if(!('parMahalC' %in% names(argVc)) \|\| argVc["parMahalC"] == "NA") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	167 if(!is.null(yMCN) && ncol(yMCN) == 1 && mode(yMCN) == "character")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	168 argVc["parMahalC"] <- argVc["respC"]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	169 else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	170 argVc["parMahalC"] <- "none"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	171 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	172 flgF("argVc['parMahalC'] == 'none' \|\| (argVc['parMahalC'] %in% colnames(samDF))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	174 if(argVc["parMahalC"] == "none") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	175 parEllipsesL <- FALSE
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	176 } else {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	177 if(is.null(yMCN)) { ## PCA case
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	178 flgF("mode(samDF[, argVc['parMahalC']]) == 'character'",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	179 txtC = paste0("Mahalanobis argument (", argVc['parMahalC'], ") must correspond to a column of characters in your sampleMetadata"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	180 parAsColFcVn <- factor(samDF[, argVc["parMahalC"]])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	181 parEllipsesL <- TRUE
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	182 } else { ## (O)PLS-DA case
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	183 flgF("identical(as.character(argVc['respC']), as.character(argVc['parMahalC']))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	184 txtC = paste0("The Mahalanobis argument (", argVc['parMahalC'], ") must be identical to the Y response argument (", argVc['respC'], ")"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	185 parEllipsesL <- TRUE
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	186 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	187 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	188
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	189 if(!('parLabVc' %in% names(argVc)))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	190 argVc["parLabVc"] <- "none"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	191 flgF("argVc['parLabVc'] == 'none' \|\| (argVc['parLabVc'] %in% colnames(samDF))",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	193 if('parLabVc' %in% names(argVc))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	194 if(argVc["parLabVc"] != "none") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	195 flgF("mode(samDF[, argVc['parLabVc']]) == 'character'",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	196 txtC = paste0("The sample label argument (", argVc['parLabVc'], ") must correspond to a sample metadata column of characters (not numerics)"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	197 parLabVc <- samDF[, argVc['parLabVc']]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	198 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	199 parLabVc <- NA
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	200
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	201 if('parPc1I' %in% names(argVc)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	202 parCompVi <- as.numeric(c(argVc["parPc1I"], argVc["parPc2I"]))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	203 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	204 parCompVi <- c(1, 2)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	205
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	206
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	207 ## checking
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	208 ##---------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	209
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	210
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	211 flgF("argVc['predI'] == 'NA' \|\| argVc['orthoI'] == 'NA' \|\| as.numeric(argVc['orthoI']) > 0 \|\| parCompVi[2] <= as.numeric(argVc['predI'])",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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'], ")"))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	213
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	214
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	215 if(argVc["orthoI"] == "NA" \|\| argVc["orthoI"] != "0")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	216 if(argVc["predI"] == "NA" \|\| argVc["predI"] != "0") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	217 argVc["predI"] <- "1"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	218 cat("\nWarning: OPLS: number of predictive components ('predI' argument) set to 1\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	219 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	220
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	221 if(argVc["predI"] != "NA")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	222 if(as.numeric(argVc["predI"]) > min(nrow(xMN), ncol(xMN))) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	223 argVc["predI"] <- as.character(min(nrow(xMN), ncol(xMN)))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	224 cat("\nWarning: 'predI' set to the minimum of the dataMatrix dimensions: ", as.numeric(argVc["predI"]), "\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	225 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	226
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	227 if("algoC" %in% names(argVc) && argVc["algoC"] == "svd" && length(which(is.na(c(xMN)))) > 0) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	228 minN <- min(c(xMN[!is.na(xMN)])) / 2
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	229 cat("\nWarning: Missing values set to ", round(minN, 1), " (half minimum value) for 'svd' algorithm to be used\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	230 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	231
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	232
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	233 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	234 ## Computation and plot
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	235 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	236
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	237
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	238 sink()
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	239
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	240 optWrnN <- options()$warn
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	241 options(warn = -1)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	242
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	243 ropLs <- opls(x = xMN,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	244 y = yMCN,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	245 predI = ifelse(argVc["predI"] == "NA", NA, as.numeric(argVc["predI"])),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	246 orthoI = ifelse(argVc["orthoI"] == "NA", NA, as.numeric(argVc["orthoI"])),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	247 algoC = ifelse('algoC' %in% names(argVc), argVc["algoC"], "default"),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	248 crossvalI = ifelse('crossvalI' %in% names(argVc), as.numeric(argVc["crossvalI"]), 7),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	249 log10L = ifelse('log10L' %in% names(argVc), as.logical(argVc["log10L"]), FALSE),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	250 permI = ifelse('permI' %in% names(argVc), as.numeric(argVc["permI"]), 20),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	251 scaleC = ifelse('scaleC' %in% names(argVc), argVc["scaleC"], "standard"),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	252 subset = NULL,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	253 printL = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	254 plotL = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	255 .sinkC = argVc['information'])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	256
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	257 modC <- ropLs@typeC
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	258 sumDF <- getSummaryDF(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	259 desMC <- ropLs@descriptionMC
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	260 scoreMN <- getScoreMN(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	261 loadingMN <- getLoadingMN(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	262
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	263 vipVn <- coeMN <- orthoScoreMN <- orthoLoadingMN <- orthoVipVn <- NULL
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	264
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	265 if(grepl("PLS", modC)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	266
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	267 vipVn <- getVipVn(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	268 coeMN <- coef(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	269
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	270 if(grepl("OPLS", modC)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	271 orthoScoreMN <- getScoreMN(ropLs, orthoL = TRUE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	272 orthoLoadingMN <- getLoadingMN(ropLs, orthoL = TRUE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	273 orthoVipVn <- getVipVn(ropLs, orthoL = TRUE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	274 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	275
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	276 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	277
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	278 ploC <- ifelse('typeC' %in% names(argVc), argVc["typeC"], "summary")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	279
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	280 if(sumDF[, "pre"] + sumDF[, "ort"] < 2) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	281 if(!(ploC %in% c("permutation", "overview"))) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	282 ploC <- "summary"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	283 plotWarnL <- TRUE
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	284 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	285 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	286 plotWarnL <- FALSE
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	287
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	288 plot(ropLs,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	289 typeVc = ploC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	290 parAsColFcVn = parAsColFcVn,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	291 parCexN = ifelse('parCexN' %in% names(argVc), as.numeric(argVc["parCexN"]), 0.8),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	292 parCompVi = parCompVi,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	293 parEllipsesL = parEllipsesL,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	294 parLabVc = parLabVc,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	295 file.pdfC = argVc['figure'],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	296 .sinkC = argVc['information'])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	297
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	298 options(warn = optWrnN)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	299
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	300
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	301 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	302 ## Print
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	303 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	304
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	305
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	306 sink(argVc["information"], append = TRUE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	307
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	308 if(plotWarnL)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 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 = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	310
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	311
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	312 cat("\n", modC, "\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	313
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	314 cat("\n", desMC["samples", ],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	315 " samples x ",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	316 desMC["X_variables", ],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	317 " variables",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	318 ifelse(modC != "PCA",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	319 " and 1 response",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	320 ""),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	321 "\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	322
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	323 cat("\n", ropLs@suppLs[["scaleC"]], " scaling of dataMatrix",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	324 ifelse(modC == "PCA",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	325 "",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	326 paste0(" and ",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	327 ifelse(mode(ropLs@suppLs[["yMCN"]]) == "character" && ropLs@suppLs[["scaleC"]] != "standard",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	328 "standard scaling of ",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	329 ""),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	330 "response\n")), sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	331
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	332 if(substr(desMC["missing_values", ], 1, 1) != "0")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	333 cat("\n", desMC["missing_values", ], " NAs\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	334
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	335 if(substr(desMC["near_zero_excluded_X_variables", ], 1, 1) != "0")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	336 cat("\n", desMC["near_zero_excluded_X_variables", ],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	337 " excluded variables during model building (because of near zero variance)\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	338
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	339 cat("\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	340
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	341 optDigN <- options()[["digits"]]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	342 options(digits = 3)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	343 print(ropLs@modelDF)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	344 options(digits = optDigN)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	345
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	346
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	347 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	348 ## Ending
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	349 ##------------------------------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	350
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	351
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	352 ## Saving
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	353 ##-------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	354
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	355
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	356 rspModC <- gsub("-", "", modC)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	357 if(rspModC != "PCA")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	358 rspModC <- paste0(make.names(argVc['respC']), "_", rspModC)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	359
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	360 if(sumDF[, "pre"] + sumDF[, "ort"] < 2) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	361
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	362 tCompMN <- scoreMN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	363 pCompMN <- loadingMN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	364
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	365 } else {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	366
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	367 if(sumDF[, "ort"] > 0) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	368 if(parCompVi[2] > sumDF[, "ort"] + 1)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	369 stop("Selected orthogonal component for plotting (ordinate) exceeds the total number of orthogonal components of the model", call. = FALSE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	370 tCompMN <- cbind(scoreMN[, 1], orthoScoreMN[, parCompVi[2] - 1])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	371 pCompMN <- cbind(loadingMN[, 1], orthoLoadingMN[, parCompVi[2] - 1])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	372 colnames(pCompMN) <- colnames(tCompMN) <- c("h1", paste("o", parCompVi[2] - 1, sep = ""))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	373 } else {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	374 if(max(parCompVi) > sumDF[, "pre"])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	375 stop("Selected component for plotting as ordinate exceeds the total number of predictive components of the model", call. = FALSE)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	376 tCompMN <- scoreMN[, parCompVi, drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	377 pCompMN <- loadingMN[, parCompVi, drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	378 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	379
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	380 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	381
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	382 ## x-scores and prediction
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	383
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	384 colnames(tCompMN) <- paste0(rspModC, "_XSCOR-", colnames(tCompMN))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	385 tCompDF <- as.data.frame(tCompMN)[rownames(samDF), , drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	386
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	387 if(modC != "PCA") {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	388
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	389 if(!is.null(tesVl)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	390 tCompFulMN <- matrix(NA,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	391 nrow = nrow(samDF),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	392 ncol = ncol(tCompMN),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	393 dimnames = list(rownames(samDF), colnames(tCompMN)))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	394 mode(tCompFulMN) <- "numeric"
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	395 tCompFulMN[rownames(tCompMN), ] <- tCompMN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	396 tCompMN <- tCompFulMN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	397
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	398 fitMCN <- fitted(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	399 fitFulMCN <- matrix(NA,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	400 nrow = nrow(samDF),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	401 ncol = 1,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	402 dimnames = list(rownames(samDF), NULL))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	403 mode(fitFulMCN) <- mode(fitMCN)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	404 fitFulMCN[rownames(fitMCN), ] <- fitMCN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	405 yPreMCN <- predict(ropLs, newdata = as.data.frame(xTesMN))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	406 fitFulMCN[rownames(yPreMCN), ] <- yPreMCN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	407 fitMCN <- fitFulMCN
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	408
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	409 } else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	410 fitMCN <- fitted(ropLs)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	411
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	412 colnames(fitMCN) <- paste0(rspModC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	413 "_predictions")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	414 fitDF <- as.data.frame(fitMCN)[rownames(samDF), , drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	415
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	416 tCompDF <- cbind.data.frame(tCompDF, fitDF)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	417 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	418
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	419 samDF <- cbind.data.frame(samDF, tCompDF)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	420
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	421 ## x-loadings and VIP
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	422
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	423 colnames(pCompMN) <- paste0(rspModC, "_XLOAD-", colnames(pCompMN))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	424 if(!is.null(vipVn)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	425 pCompMN <- cbind(pCompMN, vipVn)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	426 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	427 "_VIP",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	428 ifelse(!is.null(orthoVipVn),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	429 "_pred",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	430 ""))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	431 if(!is.null(orthoVipVn)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	432 pCompMN <- cbind(pCompMN, orthoVipVn)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	433 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	434 "_VIP_ortho")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	435 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	436 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	437 if(!is.null(coeMN)) {
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	438 pCompMN <- cbind(pCompMN, coeMN)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	439 if(ncol(coeMN) == 1)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	440 colnames(pCompMN)[ncol(pCompMN)] <- paste0(rspModC, "_COEFF")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	441 else
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	442 colnames(pCompMN)[(ncol(pCompMN) - ncol(coeMN) + 1):ncol(pCompMN)] <- paste0(rspModC, "_", colnames(coeMN), "-COEFF")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	443 }
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	444 pCompDF <- as.data.frame(pCompMN)[rownames(varDF), , drop = FALSE]
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	445 varDF <- cbind.data.frame(varDF, pCompDF)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	446
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	447 ## sampleMetadata
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	448
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	449 samDF <- cbind.data.frame(sampleMetadata = rownames(samDF),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	450 samDF)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	451 write.table(samDF,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	452 file = argVc["sampleMetadata_out"],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	453 quote = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	454 row.names = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	455 sep = "\t")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	456
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	457 ## variableMetadata
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	458
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	459 varDF <- cbind.data.frame(variableMetadata = rownames(varDF),
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	460 varDF)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	461 write.table(varDF,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	462 file = argVc["variableMetadata_out"],
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	463 quote = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	464 row.names = FALSE,
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	465 sep = "\t")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	466
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	467 # Output ropLs
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	468 if (!is.null(argVc['ropls_out']) && !is.na(argVc['ropls_out']))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	469 save(ropLs, file = argVc['ropls_out'])
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	470
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	471 ## Closing
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	472 ##--------
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	473
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	474 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	475 as.character(Sys.time()), "\n", sep = "")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	476
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	477 cat("\n\n\n============================================================================")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	478 cat("\nAdditional information about the call:\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	479 cat("\n1) Parameters:\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	480 print(cbind(value = argVc))
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	481
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	482 cat("\n2) Session Info:\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	483 sessioninfo <- sessionInfo()
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	484 cat(sessioninfo$R.version$version.string,"\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	485 cat("Main packages:\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	486 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	487 cat("Other loaded packages:\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	488 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	489
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	490 cat("============================================================================\n")
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	491
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	492 sink()
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	493
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	494 options(stringsAsFactors = strAsFacL)
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	495
b2b02fb81a0a planemo upload for repository https://github.com/eschen42/multivariate/tree/dump_rdata forked from https://github.com/workflow4metabolomics/multivariate.git commit 2ace6612c83223925e25d38bce9530f90f20a602-dirty eschen42 parents: diff changeset	496 rm(list = ls())

Mercurial > repos > eschen42 > multivariate

annotate multivariate_wrapper.R @ 0:b2b02fb81a0a draft default tip