Mercurial > repos > ppericard > viscorvar

comparison mixomics_blocksplsda_script.R @ 1:e93350dc99f1 draft

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"planemo upload for repository https://gitlab.com/bilille/galaxy-viscorvar commit 1eda261d4fe137d6e8806b0c6af7eaf12d11ac95"
author ppericard
date Thu, 15 Oct 2020 12:22:25 +0000
parents d0b77b926863
children
comparison
equal deleted inserted replaced
0:d0b77b926863 1:e93350dc99f1
34 parser$add_argument('--tol', dest='tol', type='double', default=1e-06, 34 parser$add_argument('--tol', dest='tol', type='double', default=1e-06,
35 help="Convergence stopping value") 35 help="Convergence stopping value")
36 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true", 36 parser$add_argument('--nearzerovar', dest='nearzerovar', action="store_true",
37 help="Should be set in particular for data with many zero values") 37 help="Should be set in particular for data with many zero values")
38 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file") 38 parser$add_argument('--rdata_out', dest='rdata_out', required=TRUE, help="Output Rdata file")
39 parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file") 39 # parser$add_argument('--sample_metadata_out', dest='sample_metadata_out', required=TRUE, help="Output sample metadata file")
40 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory") 40 parser$add_argument('--variable_metadata_outdir', dest='variable_metadata_outdir', required=TRUE, help="Output variable metadata directory")
41 41
42 args <- parser$parse_args() 42 args <- parser$parse_args()
43 43
44 ## Print parameters 44 ## Print parameters
66 print(args$tol) 66 print(args$tol)
67 print("near.zero.var:") 67 print("near.zero.var:")
68 print(args$nearzerovar) 68 print(args$nearzerovar)
69 print("Output Rdata file:") 69 print("Output Rdata file:")
70 print(args$rdata_out) 70 print(args$rdata_out)
71 print("Output sample metadata file:") 71 # print("Output sample metadata file:")
72 print(args$sample_metadata_out) 72 # print(args$sample_metadata_out)
73 print("Output variable metadata directory:") 73 print("Output variable metadata directory:")
74 print(args$variable_metadata_outdir) 74 print(args$variable_metadata_outdir)
75 75
76 ## Loading libraries 76 ## Loading libraries
77 suppressPackageStartupMessages(require(mixOmics)) 77 suppressPackageStartupMessages(require(mixOmics))
115 # print(block_data_matrix_names) 115 # print(block_data_matrix_names)
116 116
117 if(!identical(sample_metadata_names, block_data_matrix_names)) 117 if(!identical(sample_metadata_names, block_data_matrix_names))
118 { 118 {
119 stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix") 119 stop("Sample names must be the same and in the same order in the sample metadata matrix and the block data matrix")
120 }
121
122 if(any(is.na(block_data_matrix)))
123 {
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))
120 } 125 }
121 126
122 list_X[[block_name]] <- block_data_matrix 127 list_X[[block_name]] <- block_data_matrix
123 128
124 # Set the nb of variables to keep 129 # Set the nb of variables to keep
173 print(attributes(mixomics_result)) 178 print(attributes(mixomics_result))
174 179
175 ## Save output Rdata file 180 ## Save output Rdata file
176 save(mixomics_result, file=args$rdata_out) 181 save(mixomics_result, file=args$rdata_out)
177 182
183 # R script call
184 source_local <- function(fname)
185 {
186 argv <- commandArgs(trailingOnly = FALSE)
187 base_dir <- dirname(substring(argv[grep("--file=", argv)], 8))
188 source(paste(base_dir, fname, sep="/"))
189 }
190
191 # Load library
192 source_local("additional_functions_block_splsda.R")
193
194
195
196 list_union_selected_block_variables = unionSelectBlockVariables(mixomics_result)
197
178 ## Save output sample metadata file 198 ## Save output sample metadata file
179 # print("Block.splsda variates:") 199 # print("Block.splsda variates:")
180 # print(mixomics_result$variates) 200 # print(mixomics_result$variates)
181 201
182 for(block_name in names(mixomics_result$variates)) 202 # for(block_name in names(mixomics_result$variates))
183 { 203 # {
184 # print(block_name) 204 # # print(block_name)
185 # print(mixomics_result$variates[[block_name]]) 205 # # print(mixomics_result$variates[[block_name]])
186 206
187 # Format the column names to add the block name and replace spaces 207 # # Format the column names to add the block name and replace spaces
188 colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_") 208 # colnames(mixomics_result$variates[[block_name]]) <- paste("block.splsda_variates", block_name, gsub(" ", "_", colnames(mixomics_result$variates[[block_name]])), sep = "_")
189 # print(mixomics_result$variates[[block_name]]) 209 # # print(mixomics_result$variates[[block_name]])
190 210
191 # Append the new columns to the sample metadata matrix 211 # # Append the new columns to the sample metadata matrix
192 sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]]) 212 # sample_metadata <- cbind2(sample_metadata, mixomics_result$variates[[block_name]])
193 } 213 # }
194 214
195 # print(sample_metadata) 215 # print(sample_metadata)
196 216
197 write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA) 217 # write.table(sample_metadata, file = args$sample_metadata_out, quote = TRUE, sep = "\t", row.names = TRUE, col.names = NA)
198 218
199 ## Save output variable metadata files in output directory 219 ## Save output variable metadata files in output directory
200 # print("Block.splsda loadings:") 220 # print("Block.splsda loadings:")
201 # print(mixomics_result$loadings) 221 # print(mixomics_result$loadings)
202 222
208 # block_data_matrix_filename <- args$blocks_list[i,3] 228 # block_data_matrix_filename <- args$blocks_list[i,3]
209 block_meta_var <- args$blocks_list[i,4] 229 block_meta_var <- args$blocks_list[i,4]
210 230
211 print(sprintf("Saving block %s output metavar", block_name)) 231 print(sprintf("Saving block %s output metavar", block_name))
212 232
213 meta_variable <- mixomics_result$loadings[[block_name]] 233
234 meta_variable <- list_union_selected_block_variables[[i]]
235 colnames(meta_variable) <- "block.splsda_var_select"
236
237 # meta_variable <- mixomics_result$loadings[[block_name]]
214 # print(head(meta_variable)) 238 # print(head(meta_variable))
215 239
216 # Format the column names to add the block name and replace spaces 240 # Format the column names to add the block name and replace spaces
217 colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_") 241 # colnames(meta_variable) <- paste("block.splsda_loadings", gsub(" ", "_", colnames(meta_variable)), sep = "_")
218 242
219 # Read input block variable metadata files if provided (optional) 243 # Read input block variable metadata files if provided (optional)
220 if(block_meta_var != "None") 244 if(block_meta_var != "None")
221 { 245 {
222 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1) 246 input_meta_variable <- read.table(block_meta_var, sep='\t', header=TRUE, row.names=1)