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planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
author vmarcon
date Thu, 18 Jan 2018 07:57:36 -0500
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1 #!/usr/local/bioinfo/bin/Rscript --vanilla --slave --no-site-file
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2
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3 ################################################################################################
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4 # pcaFactoMineR_galaxy #
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5 # #
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6 # Author : Sandrine Laguerre / Marie Tremblay-Franco / Jean-Francois Martin #
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7 # User : Galaxy #
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8 # Original data : -- #
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9 # Starting date : 24-03-2015 #
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10 # Version 1 : 20-05-2015 #
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11 # Version 2 : 24-02-2016 #
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12 # #
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13 # #
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14 # Input files : dataMatrix.txt #
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15 # Output files : graph_output.pdf ; #
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16 # #
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17 ################################################################################################
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18
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19 ##------------------------------
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20 ## Options
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21 ##------------------------------
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22 strAsFacL <- options()$stringsAsFactors
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23 options(stringsAsFactors = FALSE)
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24
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25 ##------------------------------
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26 ## Libraries laoding
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27 ##------------------------------
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28 # For parseCommandArgs function
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29 library(batch)
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30 library(pcaMethods)
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31 library(FactoMineR)
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32
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33 # R script call
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34 source_local <- function(fname)
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35 {
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36 argv <- commandArgs(trailingOnly = FALSE)
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37 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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38 source(paste(base_dir, fname, sep="/"))
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39 }
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40
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41 #Import the different functions used for PCA
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42 source_local("pcaFactoMineR_functions.R")
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43
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44 ##------------------------------
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45 ## Constants
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46 ##------------------------------
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47 topEnvC <- environment()
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48 flagC <- "\n"
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49
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50
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51 ##------------------------------
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52 ## Lecture parametres
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53 ##------------------------------
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54 argLs <- parseCommandArgs(evaluate=FALSE)
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55
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56 log_file <- argLs[["logOut"]]
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57 # Inputs
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58 # Matrice donnees
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59 data <- read.table(argLs[["datafile"]],header=TRUE,sep="\t",dec=".",check.names = FALSE)
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60 rownames(data) <- data[,1]
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61
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62 # Facteur biologique
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63 hb=0
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64 if(argLs[["factor"]] != "None")
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65 {
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66 metadatasample <- read.table(argLs[["samplemetadata"]],header=TRUE,sep="\t",dec=".",check.names = FALSE)
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67 rownames(metadatasample) <- metadatasample[,1]
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68 # Test si le facteur choisi est bien dans le samplemetadata
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69 if (any(argLs[["factor"]] %in% colnames(metadatasample)) ==FALSE)
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70 {
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71 #log_error(simpleCondition("Factor is not in samplemetadata."))
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72 cat("<HTML><HEAD><TITLE>PCA FactoMineR report</TITLE></HEAD><BODY>\n",file=log_file,append=F,sep="")
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73 cat("&#9888 An error occurred while trying to read your factor table.\n<BR>",file=log_file,append=T,sep="")
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74 cat("Please check that:\n<BR>",file=log_file,append=T,sep="")
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75 cat("<UL>\n",file=log_file,append=T,sep="")
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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="")
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77 cat(" <LI> you wrote the column name correctly (it is case sensitive)</LI>\n",file=log_file,append=T,sep="")
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78 cat("</UL>\n",file=log_file,append=T,sep="")
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79 cat("</BODY></HTML>\n",file=log_file,append=T,sep="")
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80 q(save="no",status=1)
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81 }
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82 # On cree une dataframe avec l’id des samples (1ere colonne de metadatasample+ le facteur choisi
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83 # qui est en colonne “colfactor”
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84 colfactor <- which(argLs[["factor"]] == colnames(metadatasample))
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85 facteur <- data.frame(metadatasample[,1], metadatasample[[colfactor]])
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86 facteur[[2]] <- as.factor(facteur[[2]])
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87 hb=1
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88 }
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89
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90 # Appel de la fonction
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91 eigenplot=0
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92 contribplot=0
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93 scoreplot=0
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94 loadingplot=0
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95 variable_in_line=0
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96
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97 if (argLs[["plotev"]]=="yes")
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98 {
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99 eigenplot=1
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100 }
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101
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102 if (argLs[["plotcontrib"]]=="yes")
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103 {
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104 contribplot=1
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105 }
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106
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107
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108 if (argLs[["plotindiv"]]=="yes")
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109 {
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110 scoreplot=1
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111 }
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112
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113
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114 if (argLs[["plotvar"]]=="yes")
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115 {
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116 loadingplot=1
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117 }
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118
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119 if (argLs[["varinline"]]=="yes")
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120 {
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121 variable_in_line=1
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122 }
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123
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124
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125
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126
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127
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128 # Outputs
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129 nomGraphe <- argLs[["outgraphpdf"]]
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130 res.pca <- pca.main(ids=data,bioFact=facteur,ncp=argLs[["npc"]],hb=hb,
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131 minContribution=c(argLs[["contribh"]],argLs[["contribv"]]),mainTitle=argLs[["title"]],
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132 textSize=argLs[["tc"]],principalPlane=c(argLs[["pch"]],argLs[["pcv"]]),eigenplot=eigenplot,
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133 contribplot=contribplot,scoreplot=scoreplot,loadingplot=loadingplot,
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134 nomGraphe=argLs[["outgraphpdf"]],variable_in_line=variable_in_line,log_file=log_file)
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135
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136
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137 ################################# fin ##############################################