Replace KEGG1_enrichment.R

scripts/KEGG1_enrichment.R

@@ -13,7 +13,7 @@
 #source("https://bioconductor.org/biocLite.R")
 #biocLite(c("KEGGREST", "org.At.tair.db", "Rgraphviz","clusterProfile"))
 #if (!requireNamespace("BiocManager", quietly = TRUE))
-  install.packages("BiocManager")
+#  install.packages("BiocManager")
 #BiocManager::install("org.At.tair.db")
 #BiocManager::install("signatureSearch")
 #BiocManager::install("clusterProfiler")
@@ -45,7 +45,7 @@ all_geneIDs <- keys(org.At.tair.db)
 #Read DE file
 #MULTIPLE SAMPLES IN ONE FILE
 #read file with p adj value data
-de_multiple<- read.delim("multiple_input.txt",stringsAsFactors = F,row.names = 1) 
+#de_multiple<- read.delim("multiple_input.txt",stringsAsFactors = F,row.names = 1) 
 de_multiple<- read.delim(args[1],stringsAsFactors = F,row.names = 1)
 sample_names <-colnames(de_multiple)
 
@@ -72,7 +72,7 @@ for(leaf in sample_names){
     table = paste(current_leaf,"KEGG1",sep="_")
     table = paste(table,"txt",sep=".")
     write.table(enrich_k, col.names=T, row.names=F,
-                file = paste("/enrichment/",table,sep=""), sep ="\t",quote = F)
+                file = paste("enrichment/",table,sep=""), sep ="\t",quote = F)
     }