Mercurial > repos > ppericard > viscorvar

annotate mixomics_blocksplsda.R @ 2:c8533e9298e5 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
author ppericard
date Fri, 23 Oct 2020 10:15:56 +0000
parents
children 88c1fd2ac110
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c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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1 #!/usr/bin/env Rscript
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c8533e9298e5 "planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 8cb5630238352459037b3647eebfabb5554566f6-dirty"
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3 # Setup R error handling to go to stderr
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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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14 parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE,
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15 help="Block name + nb variables to select + data matrix file + variables metadata file")
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16 parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE,
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17 help="Samples metadata file")
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18 parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer',
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19 default=0, help="Sample description column number")
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20 parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2,
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21 help="Number of components to include in the model")
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22 parser$add_argument('--correlation', dest='correlation', action="store_true",
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23 help="Add correlation between all blocks")
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24 parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme")
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25 parser$add_argument('--mode', dest='mode', default="regression", help="Mode")
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26 parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100,
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27 help="Maximum number of iterations")
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28 parser$add_argument('--scale', dest='scale', action="store_true",
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29 help="Each block is standardized to zero means and unit variances")
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30 parser$add_argument('--check_missing_values', dest='check_missing_values', action="store_true",
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31 help="Check for missing values and raise an error")
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32 parser$add_argument('--init', dest='init', default="svd",
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33 help="Init (svd or svd.single)")
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34 parser$add_argument('--tol', dest='tol', type='double', default=1e-06,
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35 help="Convergence stopping value")
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36 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true",
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37 help="Should be set in particular for data with many zero values")
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38 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
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39 # parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
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40 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
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41
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42 args <- parser$parse_args()
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43
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44 ## Print parameters
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45 print("Blocks:")
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46 print(args$blocks_list)
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47 print("Sample metadata file:")
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48 print(args$sample_metadata_in)
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49 print("Sample description column number:")
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50 print(args$sample_description_col)
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51 print("Number of components:")
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52 print(args$ncomp)
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53 print("Compute correlation between all blocks:")
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54 print(args$correlation)
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55 print("Scheme:")
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56 print(args$scheme)
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57 print("Mode:")
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58 print(args$mode)
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59 print("Max nb of iterations:")
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60 print(args$maxiter)
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61 print("Scale:")
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62 print(args$scale)
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63 print("Check for missing values:")
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64 print(args$check_missing_values)
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65 print("Tol:")
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66 print(args$tol)
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67 print("near.zero.var:")
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68 print(args$nearzerovar)
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69 print("Output Rdata file:")
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70 print(args$rdata_out)
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71 # print("Output sample metadata file:")
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72 # print(args$sample_metadata_out)
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73 print("Output variable metadata directory:")
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74 print(args$variable_metadata_outdir)
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75
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76 ## Loading libraries
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77 suppressPackageStartupMessages(require(mixOmics))
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78
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79 ## Read sample metadata file and set description factor matrix
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80 sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1)
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81 sample_metadata_names <- row.names(sample_metadata)
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82 # print(sample_metadata_names)
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83
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84 # print("Sample metadata matrix:")
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85 # print(head(sample_metadata))
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86
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87 description_column <- ncol(sample_metadata)
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88 if(args$sample_description_col > 0)
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89 {
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90 description_column <- args$sample_description_col
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91 }
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92
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93 Y <- factor(sample_metadata[[description_column]])
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94
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95 print("Y factor matrix:")
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96 print(Y)
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97
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98 ## Read and prepare block datasets
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99 list_X <- c()
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100 keepX <- c()
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101
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102 for(i in 1:nrow(args$blocks_list))
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103 {
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104 # Read block input parameters
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105 block_name <- args$blocks_list[i,1]
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106 block_keep <- strtoi(args$blocks_list[i,2])
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107 block_data_matrix_filename <- args$blocks_list[i,3]
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108 # block_meta_var <- args$blocks_list[i,4]
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109
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110 print(sprintf("Processing block %s", block_name))
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111
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112 # Store block data matrices
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113 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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114 block_data_matrix_names <- row.names(block_data_matrix)
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115 # print(block_data_matrix_names)
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116
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117 if(!identical(sample_metadata_names, block_data_matrix_names))
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118 {
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119 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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120 }
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121
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122 if(any(is.na(block_data_matrix)))
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123 {
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124 stop(sprintf("Block %s contains missing values. We recommend not to perform data integration with missing values. If you want to force run, change the advanced parameter 'Check for missing values' to 'No'.", block_name))
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125 }
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126
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127 list_X[[block_name]] <- block_data_matrix
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128
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129 # Set the nb of variables to keep
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130 nb_variables = ncol(list_X[[block_name]])
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131 if(block_keep > 0)
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132 {
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133 keepX[[block_name]] <- rep(block_keep, args$ncomp)
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134 }
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135 else
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136 {
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137 keepX[[block_name]] <- rep(nb_variables, args$ncomp)
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138 }
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139 print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep))
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140 }
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141
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142 # print(list_X)
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143
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144 ## Generate design matrix
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145 block_nb <- nrow(args$blocks_list)
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146
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147 design <- matrix(0, nrow = block_nb, ncol = block_nb)
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148
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149 if(args$correlation)
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150 {
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151 design <- matrix(1, nrow = block_nb, ncol = block_nb)
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152 diag(design) <- 0
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153 }
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154
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155 # print("Design matrix:")
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156 # print(design)
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157
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158 ###################
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159 ## Main function ##
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160 ###################
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161
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162 mixomics_result <- block.splsda(X = list_X,
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163 Y = Y,
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164 ncomp = args$ncomp,
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165 keepX = keepX,
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166 design = design,
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167 scheme = args$scheme,
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168 mode = args$mode,
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169 scale = args$scale,
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170 init = args$init,
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171 tol = args$tol,
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172 max.iter = args$maxiter,
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173 near.zero.var = args$nearzerovar,
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174 all.outputs = TRUE)
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175
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176 print("Block.splsda object:")
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177 print(mixomics_result)
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178 print(attributes(mixomics_result))
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179
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180 ## Save output Rdata file
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181 save(mixomics_result, file=args$rdata_out)
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182
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183 # R script call
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184 source_local <- function(fname)
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185 {
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186 argv <- commandArgs(trailingOnly = FALSE)
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187 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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188 source(paste(base_dir, fname, sep="/"))
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189 }
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190
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191 # Load library
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192 source_local("mixomics_blocksplsda_additional_funct.R")
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193
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194
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195 list_union_selected_block_variables = unionSelectBlockVariables(mixomics_result)
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196
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197 ## Save output sample metadata file
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198 # print("Block.splsda variates:")
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199 # print(mixomics_result$variates)
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200
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201 # for(block_name in names(mixomics_result$variates))
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202 # {
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203 # # print(block_name)
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204 # # print(mixomics_result$variates[[block_name]])
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205
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206 # # Format the column names to add the block name and replace spaces
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207 # colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_")
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208 # # print(mixomics_result$variates[[block_name]])
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209
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210 # # Append the new columns to the sample metadata matrix
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211 # sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]])
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212 # }
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213
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214 # print(sample_metadata)
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215
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216 # write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
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217
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218 ## Save output variable metadata files in output directory
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219 # print("Block.splsda loadings:")
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220 # print(mixomics_result$loadings)
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221
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222 for(i in 1:nrow(args$blocks_list))
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223 {
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224 # Read again block input parameters
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225 block_name <- args$blocks_list[i,1]
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226 # block_keep <- strtoi(args$blocks_list[i,2])
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227 # block_data_matrix_filename <- args$blocks_list[i,3]
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228 block_meta_var <- args$blocks_list[i,4]
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229
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230 print(sprintf("Saving block %s output metavar", block_name))
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231
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232
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233 meta_variable <- list_union_selected_block_variables[[i]]
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234 colnames(meta_variable) <- "block.splsda_var_select"
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235
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236 # meta_variable <- mixomics_result$loadings[[block_name]]
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237 # print(head(meta_variable))
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238
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239 # Format the column names to add the block name and replace spaces
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240 # colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_")
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241
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242 # Read input block variable metadata files if provided (optional)
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243 if(block_meta_var != "None")
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244 {
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245 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1)
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246 # print(head(input_meta_variable))
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247
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248 # Append the new columns to the variable metadata matrix
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249 meta_variable <- cbind2(input_meta_variable, meta_variable)
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250 }
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251
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252 # print(head(meta_variable))
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253
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254 block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="")
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255 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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256 }