# HG changeset patch
# User davidvanzessen
# Date 1447675960 18000
# Node ID bce9fdf89e48413d80c902160e395faa985a7a0e
# Parent  14afe3c8a3d5418b5f9213d6cdfa3372072c6e8a
Uploaded

diff -r 14afe3c8a3d5 -r bce9fdf89e48 phenotype_gene_relations_plot.r
--- a/phenotype_gene_relations_plot.r	Mon Nov 16 07:06:56 2015 -0500
+++ b/phenotype_gene_relations_plot.r	Mon Nov 16 07:12:40 2015 -0500
@@ -11,7 +11,7 @@
 omt5=strsplit(args[6], ",")[[1]]
 inheritance=strsplit(args[7], ",")[[1]]
 orderby.list=as.character(args[8])
-orderby = ifelse(nchar(orderby) == 0, "1", orderby)
+orderby.list = ifelse(orderby.list == "None", "1", orderby.list)
 outdir=args[9]
 
 dat =  read.table(input, header=T, sep="\t", comment.char="#", quote = "")
@@ -63,13 +63,11 @@
 	filter = dat.sub2$GROUP.CODE == as.numeric(orderby) & dat.sub2$ratio != 0
 	print(paste("orderby:",orderby, "+1:", sum(filter)))
 	if(sum(filter) > 0){
-		#dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + max(dat.sub2$ratio)
-		dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + 1
+		dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + max(dat.sub2$ratio)
 	}
 }
 
-#dat.sub2[dat.sub2$disease.gene.order < max(dat.sub2$ratio),"disease.gene.order"] = 0
-dat.sub2[dat.sub2$disease.gene.order < 1,"disease.gene.order"] = 0
+dat.sub2[dat.sub2$disease.gene.order <= max(dat.sub2$ratio),"disease.gene.order"] = 0
 
 print(paste("min ratio:", min(dat.sub2$ratio)))