Release of version 0.4.1

how-to-publish.txt

@@ -2,30 +2,29 @@ Make sure you have npm installed.
 --------------------------------------
 
 
-1. Check and increment the version in the `package.json` file. E.g. version "0.4.0"
+1. Pull from repository:
 
-2. Check if examples are working fine
+    git pull
 
-npm install (or gulp build)
-npm run sniper
+2. Check and increment the version in the `package.json` file. E.g. version "0.4.1"
 
-access http://localhost:9090/snippets/ and see the examples
+3. Check if examples are working fine
 
-3. Pull from repository:
+    npm install (or gulp build)
+    npm run sniper
 
-git pull
+    access http://localhost:9090/snippets/ and see the examples
 
 
-4. Add a git tag with the same version as in the package.json file.
-git tag -a v0.4.0 -m 'version 0.4.0'
+4. Publish the npm-module as 'bbglab' follow the instructions given by the publish command
 
+    npm publish
 
-5. Publish the npm-module as 'bbglab' follow the instructions given by the publish command
 
-npm publish
+5. Commit all changes, push to repository
 
-6. Commit all changes, push to repository 
-git commit -a -m "Release of version 0.4.0"
-git push
-git push origin --tags
+    git commit -a -m "Release of version 0.4.1"
+    git tag -a v0.4.1 -m 'version 0.4.1'
+    git push
+    git push origin --tags
 

package.json

@@ -50,6 +50,9 @@
     "vinyl-source-stream": "^1.0.0",
     "watchify": "^1.0.6"
   },
+  "biojs": {
+    "logo": "/"
+  },
   "sniper": {
     "js": [
       "/build/muts-needle-plot.js",

snippets/LOGO.js

@@ -0,0 +1,43 @@
+// BioJS-Sniper creates the DOM-element yourDiv by default
+yourDiv.innerHTML = '';
+
+// d3 & underscore are imported through the header
+// import our plot-library
+var mutneedles = require("muts-needle-plot");
+
+var target = yourDiv; // autmically generated in snippets examples
+
+var muts = [
+  { coord: "148", category : "neutral", value: 3 },
+  { coord: "150", category : "severe", value: 44 },
+  { coord: "150", category : "mild", value: 8 },
+  { coord: "152", category : "neutral", value: 2 },
+  { coord: "154", category : "neutral", value: 1 },
+  { coord: "155", category : "neutral", value: 3 },
+  { coord: "160", category : "mild", value: 4 },
+  { coord: "170", category : "severe", value: 2 },
+  { coord: "171", category : "mild", value: 30 },
+  { coord: "172", category : "mild", value: 50 }
+];
+
+var regions = {
+  "cluster 1": "145-155",
+  "cluster 2": "170-172"
+};
+
+var legends = {x: "Mutations Needle Plot", y: "# Mutations"}
+
+
+var colorMap = {
+  // mutation categories
+  "mild": "orange",
+  "severe": "red",
+  "neutral": "lightblue",
+  "cluster 1": "marine",
+  "cluster 2": "olive"
+};
+
+var config = {maxCoord: 220, minCoord: 130, mutationData: muts, regionData: regions, target: target, legends: legends, colorMap: colorMap }
+
+var plot1 =  new mutneedles(config);
+

src/js/MutsNeedlePlot.js

@@ -63,7 +63,7 @@ function MutsNeedlePlot (config) {
       .attr('class', 'd3-tip')
       .offset([-10, 0])
       .html(function(d) {
-        return "<span>" + d.value + " " + d.category +  " at " + d.coordString + "</span>";
+        return "<span>" + d.value + " " + d.category +  " at coord. " + d.coordString + "</span>";
       });
 
     var svg = d3.select(targetElement).append("svg")
@@ -94,6 +94,7 @@ function MutsNeedlePlot (config) {
 MutsNeedlePlot.prototype.drawRegions = function(svg, regionData) {
 
     var maxCoord = this.maxCoord;
+    var minCoord = this.minCoord;
     var buffer = this.buffer;
     var colors = this.colorMap;
     var y = this.y;
@@ -134,9 +135,9 @@ MutsNeedlePlot.prototype.drawRegions = function(svg, regionData) {
             .insert("g", ":first-child")
             .attr("class", "regionsBG")
             .append("rect")
-            .attr("x", x(0) )
+            .attr("x", x(minCoord) )
             .attr("y", y(0) + bg_offset )
-            .attr("width", x(maxCoord) - x(0) )
+            .attr("width", x(maxCoord) - x(minCoord) )
             .attr("height", 10);