# HG changeset patch
# User davidvanzessen
# Date 1447675616 18000
# Node ID 14afe3c8a3d5418b5f9213d6cdfa3372072c6e8a
# Parent  0fa1b346ab52eeb7056873e16bb79a9db3e253a4
Uploaded

diff -r 0fa1b346ab52 -r 14afe3c8a3d5 phenotype_gene_relations_plot.r
--- a/phenotype_gene_relations_plot.r	Wed Nov 11 08:36:42 2015 -0500
+++ b/phenotype_gene_relations_plot.r	Mon Nov 16 07:06:56 2015 -0500
@@ -11,6 +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)
 outdir=args[9]
 
 dat =  read.table(input, header=T, sep="\t", comment.char="#", quote = "")
@@ -62,11 +63,13 @@
 	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$ratio)
+		#dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + max(dat.sub2$ratio)
+		dat.sub2[filter,"disease.gene.order"] = dat.sub2[filter,"disease.gene.order"] + 1
 	}
 }
 
-dat.sub2[dat.sub2$disease.gene.order < max(dat.sub2$ratio),"disease.gene.order"] = 0
+#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
 
 print(paste("min ratio:", min(dat.sub2$ratio)))