Mercurial > repos > proteore > proteore_clusterprofiler
changeset 8:ea5fecd4aa69 draft
planemo upload commit 229c140e131039467e2797f656d9acf916907dd7-dirty
| author | proteore |
|---|---|
| date | Tue, 18 Sep 2018 09:49:55 -0400 |
| parents | b25f272d3505 |
| children | 60a3897346e0 |
| files | GO-enrich.R cluster_profiler.xml |
| diffstat | 2 files changed, 4 insertions(+), 5 deletions(-) [+] |
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--- a/GO-enrich.R Tue Sep 18 09:20:27 2018 -0400 +++ b/GO-enrich.R Tue Sep 18 09:49:55 2018 -0400 @@ -77,8 +77,6 @@ #if there are enriched GopTerms if (length(ego$ID)>0){ - print ('ego') - print (ego@result$Description) ego@result$Description <- sapply(ego@result$Description, function(x) {ifelse(nchar(x)>100, substr(x,1,100),x)},USE.NAMES = FALSE) nb_max_char = max_str_length_10_first(ego$Description) width = width_by_max_char(nb_max_char) @@ -97,8 +95,9 @@ p <- barplot(ego) print(p) dev.off() + + } return(ego) - } } else { warning(paste("No Go terms enriched (EGO) found for ",ontology,"ontology"),immediate. = TRUE,noBreaks. = TRUE,call. = FALSE) } @@ -268,7 +267,7 @@ if (args$go_enrich == "true") { ego<-enrich.GO(gene, universe_gene, orgdb, onto, pval_cutoff, qval_cutoff,plot) output_path = paste("cluster_profiler_EGO_",onto,".csv",sep="") - write.table(ego, output_path, append = TRUE, sep="\t", row.names = FALSE, quote=FALSE) + write.table(ego, output_path, sep="\t", row.names = FALSE, quote=FALSE) } } }
--- a/cluster_profiler.xml Tue Sep 18 09:20:27 2018 -0400 +++ b/cluster_profiler.xml Tue Sep 18 09:49:55 2018 -0400 @@ -1,4 +1,4 @@ -<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.18.3"> +<tool id="cluter_profiler" name="clusterProfiler" version="2018.09.18.4"> <description> GO terms classification and enrichment analysis </description>