Made standardisation before kmeans optional

In the clustering menu, an switch has been added with which this
behaviour can be switched. Closes #6.

R.ICoVeR/R/cluster.R

@@ -17,7 +17,7 @@
 # along with this program.  If not, see <http://www.gnu.org/licenses/>.
 
 # cluster.kmeans(vars=c("M4", "M20", "M28", "M36", "M40", "M44", "M48"), identifier="kmeans_30_7", centers=30)
-cluster.kmeans <- function(rows = c(), vars, identifier, centers = NA, iter.max=10) {
+cluster.kmeans <- function(rows = c(), vars, identifier, centers = NA, iter.max=10, standardize = T) {
   clusterData <- data.get(rows, vars)
   clusterRows <- clusterData$row
   clusterData$row <- NULL
@@ -25,7 +25,7 @@ cluster.kmeans <- function(rows = c(), vars, identifier, centers = NA, iter.max=
   if (is.na(centers)) centers <- floor(sqrt(nrow(clusterData)))
 
   # Make sure that the data is standardised
-  clusterData <- scale(clusterData)
+  if (standardize) clusterData <- scale(clusterData)
 
   clusters <- as.factor(stats::kmeans(clusterData, centers, iter.max)$cluster)
   clusters <- data.frame(row = clusterRows, cluster = clusters)

R.ICoVeR/inst/www/js/controllers/clusterconfigctrl.js

@@ -48,6 +48,7 @@ angular.module('contigBinningApp.controllers')
       method: $scope.options.methods[0],
       identifier: $scope.options.methods[0].name + '_' + previousCentersCount + '_0',
       centers: previousCentersCount, // NOTE: The naming is kmeans specific
+      standardize: true,
       variables: []
     };
 
@@ -59,6 +60,10 @@ angular.module('contigBinningApp.controllers')
       $modalInstance.close($scope.specified);
     };
 
+    $scope.hideStandardization = function () {
+      return $scope.specified.method.name !== "kmeans";
+    };
+
     $scope.hideCenters = function () {
       if ($scope.specified.method.name !== "kmeans") {
         previousCentersCount = $scope.specified.centers;

R.ICoVeR/inst/www/js/controllers/clusterctrl.js

@@ -42,11 +42,12 @@ angular.module('contigBinningApp.controllers')
       //        every clustering method we add.
       if (config.method.name === "kmeans") {
         args.centers = config.centers;
+        args.standardize = config.standardize;
       } else if (config.method.name !== "correlation") {
         //FIXME get rid of this hard coded value, change it to a simple else
         throw "Unknown clustering method: " + config.method.name;
       }
-
+      
       Analytics.cluster(
         config.method.name,
         _.map(config.variables,

R.ICoVeR/inst/www/js/templates/clusterconfig.html

@@ -38,6 +38,16 @@
         </div>
       </div>
     </fieldset>
+    <fieldset>
+      <div class="form-group">
+        <div class="col-sm-3" ng-hide="hideStandardization()"></div>
+        <div class="col-sm-9">
+          <button type="button" class="btn btn-sm btn-default" ng-model="specified.standardize" btn-checkbox btn-checkbox-true="true" btn-checkbox-false="false" ng-hide="hideStandardization()">
+            Standardize data before clustering
+          </button>
+        </div>
+      </div>
+    </fieldset>
     <fieldset>
       <div class="from-group">
         <label class="col-sm-3 control-label" for="inpIdentifier">Cluster variables:</label>