changeset 15:dc0b132f1919 draft

Uploaded

--- a/phenotype_gene_relations_plot.r	Wed Sep 23 04:38:03 2015 -0400
+++ b/phenotype_gene_relations_plot.r	Fri Oct 09 09:04:06 2015 -0400
@@ -82,8 +82,12 @@
 dev.off()
 
 dat.sub4 = dat[disease.in.omt & dat$diseaseId %in% dat.sub3$diseaseId, c("diseaseId", "OMT.5.name")]
+dat.sub4 = dat.sub4[!duplicated(dat.sub4),]
 dat.sub4$value = 1
-p = ggplot(dat.sub4, aes(diseaseId, OMT.5.name)) + geom_tile(aes(fill = value), colour = "white") + scale_fill_gradient(low = "red",high = "red")
+dat.sub4.freq = data.frame(table(as.character(dat.sub4$diseaseId)))
+names(dat.sub4.freq) = c("diseaseId", "diseaseId.order")
+dat.sub4 = merge(dat.sub4, dat.sub4.freq, by="diseaseId")
+p = ggplot(dat.sub4, aes(reorder(diseaseId, -diseaseId.order), OMT.5.name)) + geom_tile(aes(fill = value), colour = "white") + scale_fill_gradient(low = "red",high = "red")
 
 p = p + theme(axis.text.x = element_text(angle = 45, hjust = 1), legend.position="none")
 
@@ -91,12 +95,27 @@
 print(p)
 dev.off()
 
-disease.gene.url = dat[OMTs & disease.in.omt & inheritance.filter ,c("diseaseId", "gene.symbol", "url")]
+#order the table the same as the first plot x axis
+disease.gene.url = dat[OMTs & disease.in.omt & inheritance.filter ,c("disease.gene", "diseaseId", "gene.symbol", "url")]
 disease.gene.url = disease.gene.url[!duplicated(disease.gene.url),]
+disease.gene.url = merge(disease.gene.url, dat.sub2.order, by="disease.gene")
+disease.gene.url = disease.gene.url[order(-disease.gene.url$disease.gene.order),]
+disease.gene.url = disease.gene.url[,c("diseaseId", "gene.symbol", "url")]
 
 names(disease.gene.url) = c("Disease ID","Gene Symbol","URL")
 
-write.table(disease.gene.url, "disease_gene_url.txt", quote=F, sep="\t", row.names=F, col.names=T)
+write.table(disease.gene.url, "disease_gene_url_1.txt", quote=F, sep="\t", row.names=F, col.names=T)
+
+
+disease.gene.url = dat[OMTs & disease.in.omt & inheritance.filter ,c("diseaseId", "gene.symbol", "url")]
+disease.gene.url = disease.gene.url[!duplicated(disease.gene.url),]
+disease.gene.url = merge(disease.gene.url, dat.sub4.freq, by.x="diseaseId", by.y="diseaseId")
+disease.gene.url = disease.gene.url[order(-disease.gene.url$diseaseId.order),]
+disease.gene.url = disease.gene.url[,c("diseaseId", "gene.symbol", "url")]
+
+names(disease.gene.url) = c("Disease ID","Gene Symbol","URL")
+
+write.table(disease.gene.url, "disease_gene_url_2.txt", quote=F, sep="\t", row.names=F, col.names=T)
 
 
 
@@ -119,8 +138,3 @@
 
 
 
-
-
-
-
-

--- a/phenotype_gene_relations_plot.sh	Wed Sep 23 04:38:03 2015 -0400
+++ b/phenotype_gene_relations_plot.sh	Fri Oct 09 09:04:06 2015 -0400
@@ -1,3 +1,4 @@
+#!/usr/bin/env bash
 set -e
 
 dir="$(cd "$(dirname "$0")" && pwd)"
@@ -43,7 +44,10 @@
 while read diseaseId gene url
 	do
 		if [[ "$first" == "true" ]] ; then
-			echo "<thead><tr><th>$diseaseId</th><th>$gene</th><th>$url</th></tr></thead>" >> $html
+			echo "<thead>" >> $html
+			echo "<tr><th colspan='3'>Disease.gene/Group.name</th></tr>" >> $html
+			echo "<tr><th>$diseaseId</th><th>$gene</th><th>$url</th></tr>" >> $html
+			echo "</thead>" >> $html
 			first="false"
 			continue
 		fi
@@ -52,5 +56,25 @@
 		echo "<td>$gene</td>" >> $html
 		echo "<td><a href='$url'>$url</a></td>" >> $html
 		echo "</tr>" >> $html
-done < "${outdir}/disease_gene_url.txt"
+done < "${outdir}/disease_gene_url_1.txt"
+
+echo "<table border='1'>" >> $html
+first="true"
+while read diseaseId gene url
+	do
+		if [[ "$first" == "true" ]] ; then
+			echo "<thead>" >> $html
+			echo "<tr><th colspan='3'>OMT.5.name/Disease</th></tr>" >> $html
+			echo "<tr><th>$diseaseId</th><th>$gene</th><th>$url</th></tr>" >> $html
+			echo "</thead>" >> $html
+			first="false"
+			continue
+		fi
+		echo "<tr>" >> $html
+		echo "<td>$diseaseId</td>" >> $html
+		echo "<td>$gene</td>" >> $html
+		echo "<td><a href='$url'>$url</a></td>" >> $html
+		echo "</tr>" >> $html
+done < "${outdir}/disease_gene_url_2.txt"
+
 echo "</center>" >> $html