Mercurial > repos > ppericard > mixomics_blocksplsda

annotate mixomics_blocksplsda_script.R @ 6:bc28839b17fb draft default tip

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planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit f2b28f1a77491a26f8ac753b3623400d8485470a
author ppericard
date Tue, 10 Mar 2020 06:51:08 -0400
parents 1ee8d2c20c0a
children
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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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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 ) } )
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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6 # we need that to not crash galaxy with an UTF8 error on German LC settings.
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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7 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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9 ## Get parameters ##
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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10 suppressPackageStartupMessages(require(argparse))
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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12 parser <- ArgumentParser(description='Run the mixOmics block.splsda function')
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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13
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1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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14 parser$add_argument('--block', dest='blocks_list', nargs=4, action="append", required=TRUE,
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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15 help="Block name + nb variables to select + data matrix file + variables metadata file")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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16 parser$add_argument('--sample_metadata_in', dest='sample_metadata_in', required=TRUE,
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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17 help="Samples metadata file")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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18 parser$add_argument('--sample_description_col', dest='sample_description_col', type='integer',
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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19 default=0, help="Sample description column number")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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20 parser$add_argument('--ncomp', dest='ncomp', type='integer', default=2,
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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21 help="Number of components to include in the model")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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22 parser$add_argument('--correlation', dest='correlation', action="store_true",
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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23 help="Add correlation between all blocks")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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24 parser$add_argument('--scheme', dest='scheme', default="horst", help="Scheme")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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25 parser$add_argument('--mode', dest='mode', default="regression", help="Mode")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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26 parser$add_argument('--maxiter', dest='maxiter', type='integer', default=100,
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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27 help="Maximum number of iterations")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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28 parser$add_argument('--scale', dest='scale', action="store_true",
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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29 help="Each block is standardized to zero means and unit variances")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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30 parser$add_argument('--init', dest='init', default="svd",
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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31 help="Init (svd or svd.single)")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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32 parser$add_argument('--tol', dest='tol', type='double', default=1e-06,
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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33 help="Convergence stopping value")
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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34 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true",
1ee8d2c20c0a planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 25773bd7a90072f9782df823969b282e4fe29252
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35 help="Should be set in particular for data with many zero values")
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36 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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37 parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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38 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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40 args <- parser$parse_args()
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42 ## Print parameters
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43 print("Blocks:")
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44 print(args$blocks_list)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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45 print("Sample metadata file:")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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46 print(args$sample_metadata_in)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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47 print("Sample description column number:")
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48 print(args$sample_description_col)
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49 print("Number of components:")
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50 print(args$ncomp)
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51 print("Compute correlation between all blocks:")
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52 print(args$correlation)
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53 print("Scheme:")
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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54 print(args$scheme)
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55 print("Mode:")
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56 print(args$mode)
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57 print("Max nb of iterations:")
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58 print(args$maxiter)
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59 print("Scale:")
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60 print(args$scale)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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61 print("Tol:")
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62 print(args$tol)
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63 print("near.zero.var:")
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64 print(args$nearzerovar)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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65 print("Output Rdata file:")
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66 print(args$rdata_out)
bea08702ed51 planemo upload for repository https://github.com/bilille/galaxy-mixomics-blocksplsda commit 7595141b2b760d3c9781f350abd2aa76a0644b1a
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67 print("Output sample metadata file:")
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68 print(args$sample_metadata_out)
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69 print("Output variable metadata directory:")
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70 print(args$variable_metadata_outdir)
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72 ## Loading libraries
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73 suppressPackageStartupMessages(require(mixOmics))
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74
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75 ## Read sample metadata file and set description factor matrix
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76 sample_metadata <- read.table(args$sample_metadata_in, sep='\t', header=TRUE, row.names=1)
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77 sample_metadata_names <- row.names(sample_metadata)
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78 # print(sample_metadata_names)
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79
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80 # print("Sample metadata matrix:")
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81 # print(head(sample_metadata))
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82
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83 description_column <- ncol(sample_metadata)
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84 if(args$sample_description_col > 0)
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85 {
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86 description_column <- args$sample_description_col
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87 }
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88
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89 Y <- factor(sample_metadata[[description_column]])
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90
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91 print("Y factor matrix:")
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92 print(Y)
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93
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94 ## Read and prepare block datasets
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95 list_X <- c()
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96 keepX <- c()
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97
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98 for(i in 1:nrow(args$blocks_list))
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99 {
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100 # Read block input parameters
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101 block_name <- args$blocks_list[i,1]
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102 block_keep <- strtoi(args$blocks_list[i,2])
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103 block_data_matrix_filename <- args$blocks_list[i,3]
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104 # block_meta_var <- args$blocks_list[i,4]
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105
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106 print(sprintf("Processing block %s", block_name))
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107
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108 # Store block data matrices
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109 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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110 block_data_matrix_names <- row.names(block_data_matrix)
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111 # print(block_data_matrix_names)
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112
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113 if(!identical(sample_metadata_names, block_data_matrix_names))
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114 {
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115 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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116 }
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117
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118 list_X[[block_name]] <- block_data_matrix
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119
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120 # Set the nb of variables to keep
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121 nb_variables = ncol(list_X[[block_name]])
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122 if(block_keep > 0)
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123 {
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124 keepX[[block_name]] <- rep(block_keep, args$ncomp)
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125 }
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126 else
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127 {
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128 keepX[[block_name]] <- rep(nb_variables, args$ncomp)
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129 }
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130 print(sprintf("Block %s contains %d variables and %d will be selected", block_name, nb_variables, block_keep))
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131 }
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132
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133 # print(list_X)
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134
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135 ## Generate design matrix
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136 block_nb <- nrow(args$blocks_list)
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137
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138 design <- matrix(0, nrow = block_nb, ncol = block_nb)
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139
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140 if(args$correlation)
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141 {
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142 design <- matrix(1, nrow = block_nb, ncol = block_nb)
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143 diag(design) <- 0
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144 }
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145
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146 # print("Design matrix:")
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147 # print(design)
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148
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149 ###################
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150 ## Main function ##
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151 ###################
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152
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153 mixomics_result <- block.splsda(X = list_X,
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154 Y = Y,
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155 ncomp = args$ncomp,
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156 keepX = keepX,
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157 design = design,
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158 scheme = args$scheme,
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159 mode = args$mode,
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160 scale = args$scale,
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161 init = args$init,
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162 tol = args$tol,
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163 max.iter = args$maxiter,
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164 near.zero.var = args$nearzerovar,
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165 all.outputs = TRUE)
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166
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167 print("Block.splsda object:")
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168 print(mixomics_result)
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169
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170 ## Save output Rdata file
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171 save(mixomics_result, file=args$rdata_out)
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172
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173 ## Save output sample metadata file
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174 # print("Block.splsda variates:")
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175 # print(mixomics_result$variates)
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176
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177 for(block_name in names(mixomics_result$variates))
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178 {
1
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179 # print(block_name)
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180 # print(mixomics_result$variates[[block_name]])
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181
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182 # Format the column names to add the block name and replace spaces
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183 colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_")
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184 # print(mixomics_result$variates[[block_name]])
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185
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186 # Append the new columns to the sample metadata matrix
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187 sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]])
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188 }
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189
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190 # print(sample_metadata)
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191
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192 write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
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193
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194 ## Save output variable metadata files in output directory
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195 # print("Block.splsda loadings:")
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196 # print(mixomics_result$loadings)
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197
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198 for(i in 1:nrow(args$blocks_list))
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199 {
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200 # Read again block input parameters
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201 block_name <- args$blocks_list[i,1]
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202 # block_keep <- strtoi(args$blocks_list[i,2])
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203 # block_data_matrix_filename <- args$blocks_list[i,3]
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204 block_meta_var <- args$blocks_list[i,4]
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205
3
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206 print(sprintf("Saving block %s output metavar", block_name))
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207
0
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208 meta_variable <- mixomics_result$loadings[[block_name]]
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209 # print(head(meta_variable))
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210
1
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211 # Format the column names to add the block name and replace spaces
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212 colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_")
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213
0
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214 # Read input block variable metadata files if provided (optional)
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215 if(block_meta_var != "None")
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216 {
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217 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1)
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218 # print(head(input_meta_variable))
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219
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220 # Append the new columns to the variable metadata matrix
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221 meta_variable <- cbind2(input_meta_variable, meta_variable)
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222 }
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223
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224 # print(head(meta_variable))
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225
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226 block_meta_var_output_filename <- paste("mixomics_blocksplsda_block_", block_name, "_variable_metadata.tsv", sep="")
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227 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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228 }