Fixed problem with GO enrichment analysis.

rules/GenePrioritization.smk

@@ -4,10 +4,10 @@ rule do_GO_analysis:
         gene_list="Reports/Genes_{tool}.txt"
     output:
         table="GO/Enriched_GOs_{tool}.txt",                 #Add gene names to table
-        plot="GO/Enriched_GOs_{tool}.png"
+        #plot="GO/Enriched_GOs_{tool}.png"
     params:
         organism="hsapiens",    #default is human
-        ontology="BP",           #MF, BP, CC or all
+        ontology="all",           #MF, BP, CC or all
         gene_ID_to_GO=os.path.join(workflow.basedir, config["ID_to_GO"]) if config["ID_to_GO"].startswith("input_files") else config["ID_to_GO"]
     benchmark:
         "Benchmarks/topGO." + str(datetime.datetime.now()).replace(" ", "_") + ".txt"

wrappers/topgo/wrapper.R

@@ -40,21 +40,20 @@ test.stat <- new("weightCount", testStatistic = GOFisherTest, name = "Fisher tes
 resultWeight <- getSigGroups(GOdata, test.stat)
 
 #Make table with results
-allRes <- GenTable(GOdata, classic = resultFisher,
-                   #KS = resultKS,
+allRes <- GenTable(GOdata, classic = resultFisher, #KS = resultKS,
                    weight = resultWeight,
-                   orderBy = "weight", ranksOf = "classic") #, topNodes = 50)
+                   orderBy = "weight", ranksOf = "classic", topNodes = 50)
 write.table(allRes, file=snakemake@output[[1]], quote=FALSE, sep="\t", eol = "\n")
 
 #Visualize GO term relationships
-png(snakemake@output[[1]])
+#png(snakemake@output[[2]])
 #showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo ='all')
-printGraph(GOdata, resultFisher, firstSigNodes = 10, fn.prefix = "tGO", useInfo = "all", pdfSW = TRUE)
-dev.off()
+#printGraph(GOdata, resultFisher, firstSigNodes = 10, fn.prefix = "tGO", useInfo = "all", pdfSW = TRUE)
+#dev.off()
 
 #Print most significant genes
-ann.genes <- genesInTerm(GOdata)
-str(ann.genes)
-fisher.go <- names(score(resultFisher))[1:5]
-fisher.ann.genes <- genesInTerm(sampleGOdata, whichGO=fisher.go)
-print(fisher.ann.genes)
+#ann.genes <- genesInTerm(GOdata)
+#str(ann.genes)
+#fisher.go <- names(score(resultFisher))[1:5]
+#fisher.ann.genes <- genesInTerm(GOdata, whichGO=fisher.go)
+#print(fisher.ann.genes)