Mercurial > repos > ethevenot > biosigner

comparison biosigner_wrapper.R @ 3:fa80bd02055f draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/biosigner.git commit 23d58cfd97411ad5d272971896914ce99e30b0ab
author ethevenot
date Tue, 06 Jun 2017 11:44:00 -0400
parents b2414be87d4b
children
comparison
equal deleted inserted replaced
2:b2414be87d4b 3:fa80bd02055f
1 #!/usr/bin/env Rscript 1 #!/usr/bin/Rscript --vanilla --slave --no-site-file
2
2 3
3 library(batch) ## parseCommandArgs 4 library(batch) ## parseCommandArgs
4 5
5 argVc <- unlist(parseCommandArgs(evaluate=FALSE)) 6 argVc <- unlist(parseCommandArgs(evaluate=FALSE))
6 7
129 tierMC <- bsnLs@tierMC 130 tierMC <- bsnLs@tierMC
130 131
131 if(!is.null(tierMC)) { 132 if(!is.null(tierMC)) {
132 plot(bsnLs, 133 plot(bsnLs,
133 tierMaxC = tierMaxC, 134 tierMaxC = tierMaxC,
134 file.pdfC = argVc["figure_tier"], 135 file.pdfC = "figure_tier.pdf",
135 .sinkC = argVc["information"]) 136 .sinkC = argVc["information"])
137 file.rename("figure_tier.pdf", argVc["figure_tier"])
136 plot(bsnLs, 138 plot(bsnLs,
137 tierMaxC = tierMaxC, 139 tierMaxC = tierMaxC,
138 typeC = "boxplot", 140 typeC = "boxplot",
139 file.pdfC = argVc["figure_boxplot"], 141 file.pdfC = "figure_boxplot.pdf",
140 .sinkC = argVc["information"]) 142 .sinkC = argVc["information"])
143 file.rename("figure_boxplot.pdf", argVc["figure_boxplot"])
141 } else { 144 } else {
142 pdf(argVc["figure_tier"]) 145 pdf(argVc["figure_tier"])
143 plot(1, bty = "n", type = "n", 146 plot(1, bty = "n", type = "n",
144 xaxt = "n", yaxt = "n", xlab = "", ylab = "") 147 xaxt = "n", yaxt = "n", xlab = "", ylab = "")
145 text(mean(par("usr")[1:2]), mean(par("usr")[3:4]), 148 text(mean(par("usr")[1:2]), mean(par("usr")[3:4]),
167 tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)] 170 tierVc <- tierFullVc[1:which(tierFullVc == tierMaxC)]
168 171
169 if(sum(tierMC %in% tierVc)) { 172 if(sum(tierMC %in% tierVc)) {
170 cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "") 173 cat("\nSignificant features from '", paste(tierVc, collapse = "', '"), "' tiers:\n", sep = "")
171 print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), , 174 print(tierMC[apply(tierMC, 1, function(rowVc) sum(rowVc %in% tierVc) > 0), ,
172 drop = FALSE]) 175 drop = FALSE])
173
174 cat("\nAccuracy:\n") 176 cat("\nAccuracy:\n")
175 print(round(getAccuracyMN(bsnLs), 3)) 177 print(round(getAccuracyMN(bsnLs), 3))
176 } else 178 } else
177 cat("\nNo significant variable found for any classifier\n") 179 cat("\nNo significant variable found for any classifier\n")
178 180
214 ##-------- 216 ##--------
215 217
216 cat("\nEnd of '", modNamC, "' Galaxy module call: ", 218 cat("\nEnd of '", modNamC, "' Galaxy module call: ",
217 as.character(Sys.time()), "\n", sep = "") 219 as.character(Sys.time()), "\n", sep = "")
218 220
221 cat("\n\n\n============================================================================")
222
223 cat("\nAdditional information about the call:\n")
224
225 cat("\n1) Parameters:\n")
226 print(cbind(value = argVc))
227
228 cat("\n2) Session Info:\n")
229 sessioninfo <- sessionInfo()
230 cat(sessioninfo$R.version$version.string,"\n")
231 cat("Main packages:\n")
232 for (pkg in names(sessioninfo$otherPkgs)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
233 cat("Other loaded packages:\n")
234 for (pkg in names(sessioninfo$loadedOnly)) { cat(paste(pkg,packageVersion(pkg)),"\t") }; cat("\n")
235
236 cat("============================================================================\n")
237
219 sink() 238 sink()
220 239
221 options(stringsAsFactors = strAsFacL) 240 options(stringsAsFactors = strAsFacL)
222 241
223 rm(list = ls()) 242 rm(list = ls())
224