Mercurial > repos > vmarcon > pcafactominer
comparison pcaFactoMineR_galaxy.R @ 0:7acfb3bdad66 draft default tip
planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
| author | vmarcon |
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| date | Thu, 18 Jan 2018 07:57:36 -0500 |
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| -1:000000000000 | 0:7acfb3bdad66 |
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| 1 #!/usr/local/bioinfo/bin/Rscript --vanilla --slave --no-site-file | |
| 2 | |
| 3 ################################################################################################ | |
| 4 # pcaFactoMineR_galaxy # | |
| 5 # # | |
| 6 # Author : Sandrine Laguerre / Marie Tremblay-Franco / Jean-Francois Martin # | |
| 7 # User : Galaxy # | |
| 8 # Original data : -- # | |
| 9 # Starting date : 24-03-2015 # | |
| 10 # Version 1 : 20-05-2015 # | |
| 11 # Version 2 : 24-02-2016 # | |
| 12 # # | |
| 13 # # | |
| 14 # Input files : dataMatrix.txt # | |
| 15 # Output files : graph_output.pdf ; # | |
| 16 # # | |
| 17 ################################################################################################ | |
| 18 | |
| 19 ##------------------------------ | |
| 20 ## Options | |
| 21 ##------------------------------ | |
| 22 strAsFacL <- options()$stringsAsFactors | |
| 23 options(stringsAsFactors = FALSE) | |
| 24 | |
| 25 ##------------------------------ | |
| 26 ## Libraries laoding | |
| 27 ##------------------------------ | |
| 28 # For parseCommandArgs function | |
| 29 library(batch) | |
| 30 library(pcaMethods) | |
| 31 library(FactoMineR) | |
| 32 | |
| 33 # R script call | |
| 34 source_local <- function(fname) | |
| 35 { | |
| 36 argv <- commandArgs(trailingOnly = FALSE) | |
| 37 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8)) | |
| 38 source(paste(base_dir, fname, sep="/")) | |
| 39 } | |
| 40 | |
| 41 #Import the different functions used for PCA | |
| 42 source_local("pcaFactoMineR_functions.R") | |
| 43 | |
| 44 ##------------------------------ | |
| 45 ## Constants | |
| 46 ##------------------------------ | |
| 47 topEnvC <- environment() | |
| 48 flagC <- "\n" | |
| 49 | |
| 50 | |
| 51 ##------------------------------ | |
| 52 ## Lecture parametres | |
| 53 ##------------------------------ | |
| 54 argLs <- parseCommandArgs(evaluate=FALSE) | |
| 55 | |
| 56 log_file <- argLs[["logOut"]] | |
| 57 # Inputs | |
| 58 # Matrice donnees | |
| 59 data <- read.table(argLs[["datafile"]],header=TRUE,sep="\t",dec=".",check.names = FALSE) | |
| 60 rownames(data) <- data[,1] | |
| 61 | |
| 62 # Facteur biologique | |
| 63 hb=0 | |
| 64 if(argLs[["factor"]] != "None") | |
| 65 { | |
| 66 metadatasample <- read.table(argLs[["samplemetadata"]],header=TRUE,sep="\t",dec=".",check.names = FALSE) | |
| 67 rownames(metadatasample) <- metadatasample[,1] | |
| 68 # Test si le facteur choisi est bien dans le samplemetadata | |
| 69 if (any(argLs[["factor"]] %in% colnames(metadatasample)) ==FALSE) | |
| 70 { | |
| 71 #log_error(simpleCondition("Factor is not in samplemetadata.")) | |
| 72 cat("<HTML><HEAD><TITLE>PCA FactoMineR report</TITLE></HEAD><BODY>\n",file=log_file,append=F,sep="") | |
| 73 cat("⚠ An error occurred while trying to read your factor table.\n<BR>",file=log_file,append=T,sep="") | |
| 74 cat("Please check that:\n<BR>",file=log_file,append=T,sep="") | |
| 75 cat("<UL>\n",file=log_file,append=T,sep="") | |
| 76 cat(" <LI> you wrote the name of the column of the factor matrix corresponding to the qualitative variable </LI>\n",file=log_file,append=T,sep="") | |
| 77 cat(" <LI> you wrote the column name correctly (it is case sensitive)</LI>\n",file=log_file,append=T,sep="") | |
| 78 cat("</UL>\n",file=log_file,append=T,sep="") | |
| 79 cat("</BODY></HTML>\n",file=log_file,append=T,sep="") | |
| 80 q(save="no",status=1) | |
| 81 } | |
| 82 # On cree une dataframe avec l’id des samples (1ere colonne de metadatasample+ le facteur choisi | |
| 83 # qui est en colonne “colfactor” | |
| 84 colfactor <- which(argLs[["factor"]] == colnames(metadatasample)) | |
| 85 facteur <- data.frame(metadatasample[,1], metadatasample[[colfactor]]) | |
| 86 facteur[[2]] <- as.factor(facteur[[2]]) | |
| 87 hb=1 | |
| 88 } | |
| 89 | |
| 90 # Appel de la fonction | |
| 91 eigenplot=0 | |
| 92 contribplot=0 | |
| 93 scoreplot=0 | |
| 94 loadingplot=0 | |
| 95 variable_in_line=0 | |
| 96 | |
| 97 if (argLs[["plotev"]]=="yes") | |
| 98 { | |
| 99 eigenplot=1 | |
| 100 } | |
| 101 | |
| 102 if (argLs[["plotcontrib"]]=="yes") | |
| 103 { | |
| 104 contribplot=1 | |
| 105 } | |
| 106 | |
| 107 | |
| 108 if (argLs[["plotindiv"]]=="yes") | |
| 109 { | |
| 110 scoreplot=1 | |
| 111 } | |
| 112 | |
| 113 | |
| 114 if (argLs[["plotvar"]]=="yes") | |
| 115 { | |
| 116 loadingplot=1 | |
| 117 } | |
| 118 | |
| 119 if (argLs[["varinline"]]=="yes") | |
| 120 { | |
| 121 variable_in_line=1 | |
| 122 } | |
| 123 | |
| 124 | |
| 125 | |
| 126 | |
| 127 | |
| 128 # Outputs | |
| 129 nomGraphe <- argLs[["outgraphpdf"]] | |
| 130 res.pca <- pca.main(ids=data,bioFact=facteur,ncp=argLs[["npc"]],hb=hb, | |
| 131 minContribution=c(argLs[["contribh"]],argLs[["contribv"]]),mainTitle=argLs[["title"]], | |
| 132 textSize=argLs[["tc"]],principalPlane=c(argLs[["pch"]],argLs[["pcv"]]),eigenplot=eigenplot, | |
| 133 contribplot=contribplot,scoreplot=scoreplot,loadingplot=loadingplot, | |
| 134 nomGraphe=argLs[["outgraphpdf"]],variable_in_line=variable_in_line,log_file=log_file) | |
| 135 | |
| 136 | |
| 137 ################################# fin ############################################## |