Mercurial > repos > iuc > masigpro
diff masigpro.R @ 2:db04ba860dab draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/masigpro commit 54ebbdebc9861af600371928cb9915095941c231
| author | iuc |
|---|---|
| date | Thu, 13 Jul 2017 18:23:17 -0400 |
| parents | cc96abdef027 |
| children | 402e0b9cfd87 |
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--- a/masigpro.R Thu Jun 01 11:10:22 2017 -0400 +++ b/masigpro.R Thu Jul 13 18:23:17 2017 -0400 @@ -92,6 +92,7 @@ make_option("--significant_intercept", type="character", default="dummy"), make_option("--cluster_data", type="integer", default=1), make_option(c("-k", "--k"), type="integer", default=9), + make_option("--print_cluster", type="logical", default=FALSE), make_option("--cluster_method", type="character", default="hclust"), make_option("--distance", type="character", default="cor"), make_option("--agglo_method", type="character", default="ward.D"), @@ -143,6 +144,17 @@ show.lines = opt$show_lines, cexlab = opt$cexlab, legend = opt$legend) +if (opt$print_cluster) { + for (i in 1:length(results$sig.genes)) { + + colname <- paste(names(results$sig.genes)[i], "cluster", sep = "_") + + results$summary[colname] <- "" + results$summary[[colname]][1:length(results$sig.genes[[i]]$sig.profiles$`cluster$cut`)] <- + results$sig.genes[[i]]$sig.profiles$`cluster$cut` + } +} + filename <- opt$outfile write.table((results$summary), file=filename, sep="\t", quote=FALSE,