Mercurial > repos > ppericard > viscorvar

annotate mixomics_blocksplsda.R @ 5:88c1fd2ac110 draft default tip

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 21d09ff286a496ff475f32626d88dd42423ae663"
author ppericard
date Tue, 07 Sep 2021 10:40:08 +0000
parents c8533e9298e5
children
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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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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$add_argument('--maxiter', dest='maxiter', type='integer', default=100,
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26 help="Maximum number of iterations")
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27 parser$add_argument('--scale', dest='scale', action="store_true",
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28 help="Each block is standardized to zero means and unit variances")
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29 parser$add_argument('--check_missing_values', dest='check_missing_values', action="store_true",
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30 help="Check for missing values and raise an error")
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31 parser$add_argument('--init', dest='init', default="svd",
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32 help="Init (svd or svd.single)")
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33 parser$add_argument('--tol', dest='tol', type='double', default=1e-06,
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34 help="Convergence stopping value")
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35 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true",
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36 help="Should be set in particular for data with many zero values")
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37 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
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38 # parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
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39 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
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41 args <- parser$parse_args()
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43 ## Print parameters
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44 print("Blocks:")
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45 print(args$blocks_list)
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46 print("Sample metadata file:")
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47 print(args$sample_metadata_in)
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48 print("Sample description column number:")
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49 print(args$sample_description_col)
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50 print("Number of components:")
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51 print(args$ncomp)
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52 print("Compute correlation between all blocks:")
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53 print(args$correlation)
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54 print("Scheme:")
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55 print(args$scheme)
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56 print("Max nb of iterations:")
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57 print(args$maxiter)
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58 print("Scale:")
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59 print(args$scale)
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60 print("Check for missing values:")
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61 print(args$check_missing_values)
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62 print("Tol:")
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63 print(args$tol)
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64 print("near.zero.var:")
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65 print(args$nearzerovar)
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66 print("Output Rdata file:")
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67 print(args$rdata_out)
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68 # print("Output sample metadata file:")
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69 # print(args$sample_metadata_out)
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70 print("Output variable metadata directory:")
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71 print(args$variable_metadata_outdir)
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73 ## Loading libraries
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74 suppressPackageStartupMessages(require(mixOmics))
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75
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76 ## Read sample metadata file and set description factor matrix
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77 sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1)
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78 sample_metadata_names <- row.names(sample_metadata)
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79 # print(sample_metadata_names)
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80
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81 # print("Sample metadata matrix:")
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82 # print(head(sample_metadata))
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83
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84 description_column <- ncol(sample_metadata)
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85 if(args$sample_description_col > 0)
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86 {
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87 description_column <- args$sample_description_col
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88 }
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89
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90 Y <- factor(sample_metadata[[description_column]])
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91
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92 print("Y factor matrix:")
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93 print(Y)
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94
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95 ## Read and prepare block datasets
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96 list_X <- c()
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97 keepX <- c()
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98
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99 for(i in 1:nrow(args$blocks_list))
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100 {
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101 # Read block input parameters
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102 block_name <- args$blocks_list[i,1]
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103 block_keep <- strtoi(args$blocks_list[i,2])
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104 block_data_matrix_filename <- args$blocks_list[i,3]
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105 # block_meta_var <- args$blocks_list[i,4]
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106
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107 print(sprintf("Processing block %s", block_name))
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108
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109 # Store block data matrices
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110 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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111 block_data_matrix_names <- row.names(block_data_matrix)
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112 # print(block_data_matrix_names)
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113
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114 if(!identical(sample_metadata_names, block_data_matrix_names))
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115 {
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116 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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117 }
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118
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119 if(any(is.na(block_data_matrix)))
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120 {
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121 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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122 }
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123
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124 list_X[[block_name]] <- block_data_matrix
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125
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126 # Set the nb of variables to keep
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127 nb_variables = ncol(list_X[[block_name]])
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128 if(block_keep > 0)
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129 {
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130 keepX[[block_name]] <- rep(block_keep, args$ncomp)
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131 }
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132 else
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133 {
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134 keepX[[block_name]] <- rep(nb_variables, args$ncomp)
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135 }
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136 print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep))
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137 }
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138
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139 # print(list_X)
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140
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141 ## Generate design matrix
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142 block_nb <- nrow(args$blocks_list)
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143
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144 design <- matrix(0, nrow = block_nb, ncol = block_nb)
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145
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146 if(args$correlation)
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147 {
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148 design <- matrix(1, nrow = block_nb, ncol = block_nb)
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149 diag(design) <- 0
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150 }
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151
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152 # print("Design matrix:")
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153 # print(design)
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154
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155 ###################
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156 ## Main function ##
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157 ###################
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158
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159 mixomics_result <- block.splsda(X = list_X,
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160 Y = Y,
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161 ncomp = args$ncomp,
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162 keepX = keepX,
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163 design = design,
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164 scheme = args$scheme,
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165 scale = args$scale,
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166 init = args$init,
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167 tol = args$tol,
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168 max.iter = args$maxiter,
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169 near.zero.var = args$nearzerovar,
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170 all.outputs = TRUE)
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171
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172 print("Block.splsda object:")
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173 print(mixomics_result)
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174 print(attributes(mixomics_result))
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175
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176 ## Save output Rdata file
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177 save(mixomics_result, file=args$rdata_out)
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178
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179 # R script call
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180 source_local <- function(fname)
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181 {
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182 argv <- commandArgs(trailingOnly = FALSE)
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183 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
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184 source(paste(base_dir, fname, sep="/"))
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185 }
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186
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187 # Load library
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188 source_local("mixomics_blocksplsda_additional_funct.R")
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189
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190
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191 list_union_selected_block_variables = unionSelectBlockVariables(mixomics_result)
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192
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193 ## Save output sample metadata file
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194 # print("Block.splsda variates:")
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195 # print(mixomics_result$variates)
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196
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197 # for(block_name in names(mixomics_result$variates))
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198 # {
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199 # # print(block_name)
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200 # # print(mixomics_result$variates[[block_name]])
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201
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202 # # Format the column names to add the block name and replace spaces
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203 # colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_")
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204 # # print(mixomics_result$variates[[block_name]])
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205
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206 # # Append the new columns to the sample metadata matrix
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207 # sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]])
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208 # }
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209
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210 # print(sample_metadata)
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211
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212 # write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
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213
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214 ## Save output variable metadata files in output directory
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215 # print("Block.splsda loadings:")
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216 # print(mixomics_result$loadings)
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217
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218 for(i in 1:nrow(args$blocks_list))
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219 {
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220 # Read again block input parameters
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221 block_name <- args$blocks_list[i,1]
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222 # block_keep <- strtoi(args$blocks_list[i,2])
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223 # block_data_matrix_filename <- args$blocks_list[i,3]
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224 block_meta_var <- args$blocks_list[i,4]
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225
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226 print(sprintf("Saving block %s output metavar", block_name))
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227
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228
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229 meta_variable <- list_union_selected_block_variables[[i]]
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230 colnames(meta_variable) <- "block.splsda_var_select"
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231
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232 # meta_variable <- mixomics_result$loadings[[block_name]]
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233 # print(head(meta_variable))
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234
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235 # Format the column names to add the block name and replace spaces
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236 # colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_")
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237
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238 # Read input block variable metadata files if provided (optional)
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239 if(block_meta_var != "None")
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240 {
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241 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1)
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242 # print(head(input_meta_variable))
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243
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244 # Append the new columns to the variable metadata matrix
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245 meta_variable <- cbind2(input_meta_variable, meta_variable)
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246 }
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247
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248 # print(head(meta_variable))
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249
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250 block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="")
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251 write.table(meta_variable, file = paste(args$variable_metadata_outdir,block_meta_var_output_filename, sep='/'), quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
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252 }