Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_blocksplsda_script.R @ 1:6595c17673cb draft

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7ed137ea956b8074c34d43a5e1d46b39ddef1482-dirty
author ppericard
date Wed, 12 Jun 2019 11:22:33 -0400
parents bea08702ed51
children 0a3c83f2197a
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bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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1 #!/usr/bin/env Rscript
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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3 # Setup R error handling to go to stderr
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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4 options( show.error.messages=F, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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9 ## Get parameters ##
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10 suppressPackageStartupMessages(require(argparse))
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12 parser <- ArgumentParser(description='Run the mixOmics block.splsda function')
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bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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14 parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE, help="Block name + nb variables to select + data matrix file + variables metadata file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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15 parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE, help="Samples metadata file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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16 parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer', required=TRUE, help="Sample description column number")
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17 parser$add_argument('--ncomp', dest='ncomp', type='integer', required=TRUE, help="Number of components to include in the model")
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18 parser$add_argument('--correlation', dest='correlation', action="store_true", help="Add correlation between all blocks")
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19 parser$add_argument('--scheme', dest='scheme', required=TRUE, help="Scheme")
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20 parser$add_argument('--mode', dest='mode', required=TRUE, help="Mode")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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21 parser$add_argument('--maxiter', dest='maxiter', type='integer', required=TRUE, help="Maximum number of iterations")
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22 parser$add_argument('--scale', dest='scale', action="store_true", help="Each block is standardized to zero means and unit variances")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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23 parser$add_argument('--init', dest='init', required=TRUE, help="Init (svd or svd.single)")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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24 parser$add_argument('--tol', dest='tol', type='double', required=TRUE, help="Convergence stopping value")
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25 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", help="Should be set in particular for data with many zero values")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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26 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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27 parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
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28 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
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30 args <- parser$parse_args()
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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32 ## Print parameters
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33 print("Blocks:")
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34 print(args$blocks_list)
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35 print("Sample metadata file:")
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36 print(args$sample_metadata_in)
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37 print("Sample description column number:")
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38 print(args$sample_description_col)
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39 print("Number of components:")
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40 print(args$ncomp)
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41 print("Compute correlation between all blocks:")
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42 print(args$correlation)
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43 print("Scheme:")
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44 print(args$scheme)
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45 print("Mode:")
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46 print(args$mode)
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47 print("Max nb of iterations:")
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48 print(args$maxiter)
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49 print("Scale:")
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50 print(args$scale)
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51 print("Tol:")
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52 print(args$tol)
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53 print("near.zero.var:")
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54 print(args$nearzerovar)
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55 print("Output Rdata file:")
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56 print(args$rdata_out)
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57 print("Output sample metadata file:")
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58 print(args$sample_metadata_out)
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59 print("Output variable metadata directory:")
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60 print(args$variable_metadata_outdir)
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61
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62 ## Loading libraries
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63 suppressPackageStartupMessages(require(mixOmics))
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64
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65 ## Read sample metadata file and set description factor matrix
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66 sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1)
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67 sample_metadata_names <- row.names(sample_metadata)
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68 # print(sample_metadata_names)
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69
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70 # print("Sample metadata matrix:")
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71 # print(head(sample_metadata))
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72
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73 description_column <- ncol(sample_metadata)
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74 if(args$sample_description_col > 0)
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75 {
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76 description_column <- args$sample_description_col
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77 }
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78
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79 Y <- factor(sample_metadata[[description_column]])
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80
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81 print("Y factor matrix:")
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82 print(Y)
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83
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84 ## Read and prepare block datasets
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85 list_X <- c()
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86 keepX <- c()
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87
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88 for(i in 1:nrow(args$blocks_list))
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89 {
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90 # Read block input parameters
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91 block_name <- args$blocks_list[i,1]
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92 block_keep <- strtoi(args$blocks_list[i,2])
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93 block_data_matrix_filename <- args$blocks_list[i,3]
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94 # block_meta_var <- args$blocks_list[i,4]
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95
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96 print(sprintf("Processing block %s", block_name))
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97
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98 # Store block data matrices
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99 block_data_matrix <- t(read.table(block_data_matrix_filename, sep='\t', header=TRUE, row.names=1)) # transpose the matrix so that the samples become rows and the variables become columns
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100 block_data_matrix_names <- row.names(block_data_matrix)
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101 # print(block_data_matrix_names)
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102
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103 if(!identical(sample_metadata_names, block_data_matrix_names))
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104 {
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105 stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix")
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106 }
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107
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108 list_X[[block_name]] <- block_data_matrix
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109
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110 # Set the nb of variables to keep
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111 nb_variables = ncol(list_X[[block_name]])
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112 if(block_keep > 0)
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113 {
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114 keepX[[block_name]] <- rep(block_keep, args$ncomp)
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115 }
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116 else
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117 {
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118 keepX[[block_name]] <- rep(nb_variables, args$ncomp)
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119 }
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120 print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep))
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121 }
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122
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123 # print(list_X)
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124
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125 ## Generate design matrix
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126 block_nb <- nrow(args$blocks_list)
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127
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128 design <- matrix(0, nrow = block_nb, ncol = block_nb)
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129
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130 if(args$correlation)
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131 {
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132 design <- matrix(1, nrow = block_nb, ncol = block_nb)
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133 diag(design) <- 0
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134 }
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135
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136 # print("Design matrix:")
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137 # print(design)
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138
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139 ###################
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140 ## Main function ##
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141 ###################
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142
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143 mixomics_result <- block.splsda(X = list_X,
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144 Y = Y,
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145 ncomp = args$ncomp,
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146 keepX = keepX,
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147 design = design,
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148 scheme = args$scheme,
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149 mode = args$mode,
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150 scale = args$scale,
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151 init = args$init,
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152 tol = args$tol,
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153 max.iter = args$maxiter,
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154 near.zero.var = args$nearzerovar,
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155 all.outputs = TRUE)
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156
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157 print("Block.splsda object:")
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158 print(mixomics_result)
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159
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160 ## Save output Rdata file
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161 save(mixomics_result, file=args$rdata_out)
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162
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163 ## Save output sample metadata file
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164 # print("Block.splsda variates:")
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165 # print(mixomics_result$variates)
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166
1
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167 for(block_name in names(mixomics_result$variates))
0
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168 {
1
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169 # print(block_name)
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170 # print(mixomics_result$variates[[block_name]])
0
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171
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172 # Format the column names to add the block name and replace spaces
1
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173 colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_")
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174 # print(mixomics_result$variates[[block_name]])
0
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175
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176 # Append the new columns to the sample metadata matrix
1
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177 sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]])
0
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178 }
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179
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180 # print(sample_metadata)
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181
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182 write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
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183
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184 ## Save output variable metadata files in output directory
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185 # print("Block.splsda loadings:")
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186 # print(mixomics_result$loadings)
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187
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188 for(i in 1:nrow(args$blocks_list))
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189 {
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190 # Read again block input parameters
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191 block_name <- args$blocks_list[i,1]
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192 # block_keep <- strtoi(args$blocks_list[i,2])
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193 # block_data_matrix_filename <- args$blocks_list[i,3]
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194 block_meta_var <- args$blocks_list[i,4]
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195
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196 meta_variable <- mixomics_result$loadings[[block_name]]
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197 # print(head(meta_variable))
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198
1
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199 # Format the column names to add the block name and replace spaces
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200 colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_")
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201
0
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202 # Read input block variable metadata files if provided (optional)
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203 if(block_meta_var != "None")
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204 {
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205 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1)
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206 # print(head(input_meta_variable))
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207
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208 # Append the new columns to the variable metadata matrix
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209 meta_variable <- cbind2(input_meta_variable, meta_variable)
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210 }
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211
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212 # print(head(meta_variable))
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213
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214 block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="")
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215 write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
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216 }