Mercurial > repos > proteore > proteore_topgo
changeset 9:8f5025a35a84 draft
planemo upload commit 9d3e0b226140b566fc529fd0ffe7aa9e8388c6e5-dirty
| author | proteore |
|---|---|
| date | Fri, 21 Sep 2018 05:35:46 -0400 |
| parents | f325701409e6 |
| children | 511b060e9890 |
| files | enrichment_v3.R topGO.xml |
| diffstat | 2 files changed, 9 insertions(+), 5 deletions(-) [+] |
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--- a/enrichment_v3.R Wed Sep 19 09:23:51 2018 -0400 +++ b/enrichment_v3.R Fri Sep 21 05:35:46 2018 -0400 @@ -30,9 +30,10 @@ # results file, barplot.png for the barplot image file and dotplot.png for the # dotplot image file +options(warn=-1) #TURN OFF WARNINGS !!!!!! # loading topGO library -library(topGO) +suppressMessages(library(topGO)) # Read file and return file content as data.frame readfile = function(filename, header) { @@ -88,6 +89,10 @@ stop("Not enough/Too many arguments", call. = FALSE) } +#save(options.args,file="/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda") +#load("/home/dchristiany/proteore_project/ProteoRE/tools/topGO/args.Rda") + + typeinput = options.args[1] listfile = options.args[2] onto = as.character(options.args[3]) @@ -348,16 +353,15 @@ createDotPlot(cut_result, onto) } - return(TRUE) } # Load R library ggplot2 to plot graphs -library(ggplot2) +suppressMessages(library(ggplot2)) # Launch enrichment analysis -allresult = goEnrichment(geneuniverse,sample,onto) +allresult = suppressMessages(goEnrichment(geneuniverse,sample,onto)) result = allresult[1][[1]] myGOdata = allresult[2][[1]] if (!is.null(result)){