From 9e9c22aae22428fa29ec1995930d55eae8b4dc5c Mon Sep 17 00:00:00 2001
From: corywang <cory.wang@uconn.edu>
Date: Fri, 17 Apr 2015 11:10:41 -0400
Subject: [PATCH] Added above/below colored genes based on score

---
 Tile2contentsnpplotter.txt | 14 ++++++-------
 VQI_GenomeBrowser.js       | 40 +++++++++++++++++++++-----------------
 2 files changed, 29 insertions(+), 25 deletions(-)

diff --git a/Tile2contentsnpplotter.txt b/Tile2contentsnpplotter.txt
index 8ecf41e..064ff93 100644
--- a/Tile2contentsnpplotter.txt
+++ b/Tile2contentsnpplotter.txt
@@ -10,27 +10,27 @@ chr9_gl000198_random	77493	77494	.	0	+
 chr4_gl000193_random	86356	86357	.	0	+
 chr4_gl000193_random	86519	86520	.	0	+
 chr1	896004	896005	.	0	+
-chr1	976170	976171	.	0	+
+chr1	976170	976171	.	-.4	+
 chr1	1198674	1198675	.	0	+
-chr1	1250433	1250434	.	0	+
+chr1	1250433	1250434	.	1	+
 chr1	1597292	1597293	rs79791328	0	+
 chr1	1597292	1597293	rs79791328	0	+
 chr1	1688189	1688190	.	0	+
 chr1	1897981	1897982	.	0	+
-chr1	1987060	1987061	.	0	+
+chr1	1987060	1987061	.	-3	+
 chr1	3555382	3555383	.	0	+
-chr1	3692443	3692444	.	0	+
+chr1	3692443	3692444	.	1	+
 chr1	6142182	6142183	.	0	+
 chr1	9027765	9027766	.	0	+
 chr1	9785114	9785115	.	0	+
 chr1	12025665	12025666	.	0	+
 chr1	12320683	12320684	.	0	+
-chr1	12780679	12780680	.	0	+
+chr1	12780679	12780680	.	1	+
 chr1	16053894	16053895	.	0	+
 chr1	16580123	16580124	.	0	+
-chr1	17555405	17555406	.	0	+
+chr1	17555405	17555406	.	.5	+
 chr1	18016317	18016318	.	0	+
-chr1	18017563	18017564	.	0	+
+chr1	18017563	18017564	.	1	+
 chr1	21103040	21103041	.	0	+
 chr1	21582581	21582582	rs79178176	0	+
 chr1	22055122	22055123	rs151180337	0	+
diff --git a/VQI_GenomeBrowser.js b/VQI_GenomeBrowser.js
index d266286..b0d01ff 100755
--- a/VQI_GenomeBrowser.js
+++ b/VQI_GenomeBrowser.js
@@ -603,11 +603,20 @@ function VQI_GenomeBrowser(id) {
         })
         //.attr("transform", "translate(" + 0 + "," + thisY + ")");
 
+                //Just a line
+        trackGroup.selectAll("line").data([name], function (d) {
+            return d;
+        }).enter().append("line")
+                .attr("x1", 0)
+                .attr("y1", 0)
+                .attr("x2", width)
+                .attr("y2", 0)
+                .style("stroke", "blue")
+                .style("stroke-opacity" , 0.5);
 
         trackGroup.selectAll("text").data([name], function (d) {
             return d;
         }).enter().append("text")
-                .attr("class", name)
                 .attr("x", 0)
                 .attr("y", -trackHeight / 2 - bufferSpace / 2)
                 .attr("font-family", "sans-serif")
@@ -647,7 +656,7 @@ function VQI_GenomeBrowser(id) {
                     .append("xhtml:body")
                     .html("<form><input type=checkbox id=check class=" + name + "/></form>")
                     .on("click", function (d, i) {
-                        console.log(trackGroup.select("#check").node().checked);
+                        //console.log(trackGroup.select("#check").node().checked);
                         xAxisSelection.call(xAxis);//I have no idea why it won't redraw the checkbox unless I call this
                     });
         }
@@ -722,17 +731,6 @@ function VQI_GenomeBrowser(id) {
 
     var addCpgTrack = function (data, name) {
 
-        //Just a line
-        graphRegion.selectAll("g").data([name], function (d) {
-            return d;
-        })
-                .append("line")
-                .attr("x1", 0)
-                .attr("y1", 0)
-                .attr("x2", width)
-                .attr("y2", 0)
-                .style("stroke", "blue");
-
         var trackScalableGroup = graphRegion.selectAll("g").data([name], function (d) {
             return d;
         }).select("g.scalable");
@@ -846,14 +844,20 @@ function VQI_GenomeBrowser(id) {
                 .attr("x", function (d) {
                     return fullXScale(d[indexArray.start]);
                 })
-                .attr("y", -1)
+                .attr("y", function (d) {
+                    return d[indexArray.score] > 0 ? -5 : 0;
+                })
                 .attr("height", 5)
                 .attr("width", function (d) {
                     return fullXScale(d[indexArray.end]) - fullXScale(d[indexArray.start]);
                 })
                 .style("fill-opacity", "1")
-                .style("stroke", "black")
-                .style("fill", "black")
+                .style("stroke", function (d) {
+                    return d[indexArray.score] > 0 ? "red" : "green";
+                })
+                .style("fill", function (d) {
+                    return d[indexArray.score] > 0 ? "red" : "green";
+                })
                 .style("vector-effect", "non-scaling-stroke")
                 .attr("class", "scalable")
         /*.attr("x1", function (d) {
@@ -914,8 +918,8 @@ function VQI_GenomeBrowser(id) {
                     .attr("x", function (d) {
                         return fullXScale(d[indexArray.start]);
                     })
-                    .attr("y", -trackHeight / 2)
-                    .attr("height", trackHeight)
+                    .attr("y", -2.5)
+                    .attr("height", 5)
                     .attr("width", function (d) {
                         return fullXScale(d[indexArray.end]) - fullXScale(d[indexArray.start]);
                     })