Mercurial > repos > cristian > rbgoa
diff GO_MWU.R @ 1:f7287f82602f draft
"planemo upload commit 486235d6560c9e95bd42152ad19bf7c3941cdc1b"
author | cristian |
---|---|
date | Tue, 19 Apr 2022 08:28:43 +0000 |
parents | 91261b42c07e |
children | 5acf9dfdfa27 |
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--- a/GO_MWU.R Thu Apr 14 13:28:05 2022 +0000 +++ b/GO_MWU.R Tue Apr 19 08:28:43 2022 +0000 @@ -120,6 +120,17 @@ source_local("gomwu.functions.R") + +nn <- strsplit(opt$input, "[/.]") +if (length(nn[[1]]) == 3) { + dir <- nn[[1]][1] + name <- nn[[1]][2] + ext <- nn[[1]][3] +} else if (length(nn[[1]]) == 2) { + dir <- "." + name <- nn[[1]][1] + ext <- nn[[1]][2] +} # It might take a few minutes for MF and BP. Do not rerun it if you just want # to replot the data with different cutoffs, go straight to gomwuPlot. If you # change any of the numeric values below, delete the files that were generated @@ -145,7 +156,7 @@ # ----------- Plotting results # change this to a pdf output -pdf() +pdf(paste0(dir,"/","Rplots.pdf")) results <- gomwuPlot(opt$input, opt$goAnnotations, opt$goDivision, # genes with the measure value exceeding this will be counted as "good genes". @@ -168,7 +179,7 @@ # if there are too many categories displayed, try make it more stringent with level1 = 0.05,level2=0.01,level3=0.001. # text representation of results, with actual adjusted p-values -write.table(results[[1]], "results.tsv", sep = "\t") +write.table(results[[1]], paste0(dir, "/", "results.tsv"), sep = "\t") # ------- extracting representative GOs @@ -212,7 +223,7 @@ } } -mwus <- read.table(paste("MWU", opt$goDivision, opt$input, sep = "_"), header = T) +mwus <- read.table(paste0(dir,"/",paste("MWU", opt$goDivision, name, sep = "_"), ".", ext), header = T) best_GOs <- mwus[mwus$name %in% annots, ] -write.table(best_GOs, "best_go.tsv", sep = "\t") +write.table(best_GOs, paste0(dir, "/","best_go.tsv"), sep = "\t") dev.off()