Release of version 0.5.2

how-to-publish.txt

@@ -6,7 +6,7 @@ Make sure you have npm installed.
 
     git pull
 
-2. Check and increment the version in the `package.json` file. E.g. version "0.5.1"
+2. Check and increment the version in the `package.json` file. E.g. version "0.5.2"
 
 3. Check if examples are working fine
 
@@ -23,14 +23,14 @@ Make sure you have npm installed.
 
 5. Commit all changes, push to repository
 
-    git commit -a -m "Release of version 0.5.1"
-    git tag -a v0.5.1 -m 'version 0.5.1'
+    git commit -a -m "Release of version 0.5.2"
+    git tag -a v0.5.2 -m 'version 0.5.2'
     git push
     git push origin --tags
 
 6. Go to GitHub and schedule a new Release
     Title: Mutations Needle Plot
     Changelog:
-    v0.5.1
+    v0.5.2
      * Selection (new)
      * Legend (new)

package.json

@@ -1,7 +1,7 @@
 {
   "name": "muts-needle-plot",
   "description": "Draws a Needle-Plot for mutation data (stacked).",
-  "version": "0.5.1",
+  "version": "0.5.2",
   "homepage": "https://github.com/bbglab/muts-needle-plot",
   "author": {
     "name": "Michael P Schroeder",

snippets/EXAMPLE.js

@@ -35,4 +35,5 @@ plotConfig = {
 };
 
 // Instantiate a plot
-p = new mutneedles(plotConfig);
+instance = new mutneedles(plotConfig);
+

snippets/EXAMPLE_AGGREGATION.js

@@ -77,7 +77,7 @@ d3.json("./data/muts.json", function(error, data){
   };
 
 // Instantiate a plot
-  p = new mutneedles(plotConfig);
+  instance =new mutneedles(plotConfig);
 
 
 });

snippets/KRAS.js

@@ -19,5 +19,5 @@ var colorMap = {
 
 var config = {maxCoord: 350, mutationData: muts, regionData: regions, target: target, legends: legends, colorMap: colorMap }
 
-var plot1 =  new mutneedles(config);
+instance =  new mutneedles(config);
 

snippets/LOGO.js

@@ -39,5 +39,5 @@ var colorMap = {
 
 var config = {maxCoord: 220, minCoord: 130, mutationData: muts, regionData: regions, target: target, legends: legends, colorMap: colorMap }
 
-var plot1 =  new mutneedles(config);
+instance =  new mutneedles(config);
 

src/js/MutsNeedlePlot.js

@@ -208,7 +208,24 @@ MutsNeedlePlot.prototype.drawLegend = function(svg) {
 
     // LEGEND
     self = this;
-    mutsScale = self.colorScale.domain(Object.keys(self.totalCategCounts));
+
+    // prepare legend categories (correct order)
+    mutCategories = [];
+    categoryColors = [];
+    allcategs = Object.keys(self.totalCategCounts); // random order
+    orderedDeclaration = self.colorScale.domain();  // wanted order
+    for (idx in orderedDeclaration) {
+        c = orderedDeclaration[idx];
+        if (allcategs.indexOf(c) > -1) {
+            mutCategories.push(c);
+            categoryColors.push(self.colorScale(c))
+        }
+    }
+
+    // create scale with correct order of categories
+    mutsScale = self.colorScale.domain(mutCategories).range(categoryColors);
+
+
     var domain = self.x.domain();
     xplacement = (domain[1] - domain[0]) * 0.75 + (domain[1] - domain[0]);
     verticalLegend = d3.svg
@@ -385,16 +402,22 @@ MutsNeedlePlot.prototype.drawNeedles = function(svg, mutationData, regionData) {
 
     formatCoord = function(coord) {
        if (coord.indexOf("-") > -1) {
-            coords = coord.split("-");
-            // place neede at middle of affected region
-            coord = Math.floor((parseInt(coords[0]) + parseInt(coords[1])) / 2);
+           coords = coord.split("-");
+
+           // place neede at middle of affected region
+           coord = Math.floor((parseInt(coords[0]) + parseInt(coords[1])) / 2);
+
+           // check for splice sites: "?-9" or "9-?"
+           if (isNaN(coord)) {
+               if (coords[0] == "?") { coord = parseInt(coords[1]) }
+               else if (coords [1] == "?") { coord = parseInt(coords[0]) }
+           }
         } else {
             coord = parseInt(coord);
         }
         return coord;
     };
 
-    getColor = this.colorScale;
     tip = this.tip;
 
     // stack needles at same pos
@@ -420,7 +443,7 @@ MutsNeedlePlot.prototype.drawNeedles = function(svg, mutationData, regionData) {
         numericCoord = formatCoord(d.coord);
         numericValue = Number(d.value);
         stickHeight = stackNeedle(numericCoord, numericValue, needlePoint);
-        category = d.category || "";
+        category = d.category || "other";
 
         if (stickHeight + numericValue > highest) {
             // set Y-Axis always to highest available
@@ -440,10 +463,10 @@ MutsNeedlePlot.prototype.drawNeedles = function(svg, mutationData, regionData) {
                 coord: numericCoord,
                 value: numericValue,
                 stickHeight: stickHeight,
-                color: getColor(category)
+                color: self.colorScale(category)
             }
         } else {
-            console.debug("discarding " + d.coord + " " + d.category)
+            console.debug("discarding " + d.coord + " " + d.category + "("+ numericCoord +")");
         }
     }
 

src/js/d3-svg-legend.js

@@ -31,7 +31,6 @@ d3.svg.legend = function() {
 
         drag = d3.behavior.drag()
             .on("drag", function(d,i) {
-                console.log(this);
                 d.x += d3.event.dx;
                 d.y += d3.event.dy;
                 d3.select(this).attr("transform", function(d,i){
@@ -229,4 +228,4 @@ d3.svg.legend = function() {
 
     return legend;
 
-}
+}