fixing support of colour and size as options for ggplot

Gruntfile.js

@@ -67,7 +67,8 @@ module.exports = function (grunt) {
 					'js/jquery.event.drag-2.2.js',
 					'js/clipboard.min.js', 'js/slick.min.js',
 					'js/js.cookie.js', 'js/d3.layout.cloud.js',
-					'js/long.js', 'js/bytebuffer.js', 'js/protobuf.js']
+					'js/long.js', 'js/bytebuffer.js', 'js/protobuf.js',
+					'js/opencpu-0.5.js', 'js/FileSaver.min.js']
 			},
 			morpheus: {
 				nonull: true,

index.html

@@ -10,6 +10,10 @@
     <title>Morpheus</title>
     <link rel="stylesheet" href="css/morpheus-latest.min.css">
     <script type="text/javascript" src="js/morpheus-external-latest.min.js"></script>
+
+    <script>
+        ocpu.seturl("http://localhost:7963/ocpu/library/morpheusR/R");
+    </script>
     <script src="js/morpheus-latest.min.js"></script>
     <script src="js/jsme/jsme.nocache.js"></script>
     <link href="https://fonts.googleapis.com/css?family=Roboto"

js/FileSaver.min.js

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+var saveAs=saveAs||function(e){"use strict";if(typeof e==="undefined"||typeof navigator!=="undefined"&&/MSIE [1-9]\./.test(navigator.userAgent)){return}var t=e.document,n=function(){return e.URL||e.webkitURL||e},r=t.createElementNS("http://www.w3.org/1999/xhtml","a"),o="download"in r,i=function(e){var t=new MouseEvent("click");e.dispatchEvent(t)},a=/constructor/i.test(e.HTMLElement),f=/CriOS\/[\d]+/.test(navigator.userAgent),u=function(t){(e.setImmediate||e.setTimeout)(function(){throw t},0)},d="application/octet-stream",s=1e3*40,c=function(e){var t=function(){if(typeof e==="string"){n().revokeObjectURL(e)}else{e.remove()}};setTimeout(t,s)},l=function(e,t,n){t=[].concat(t);var r=t.length;while(r--){var o=e["on"+t[r]];if(typeof o==="function"){try{o.call(e,n||e)}catch(i){u(i)}}}},p=function(e){if(/^\s*(?:text\/\S*|application\/xml|\S*\/\S*\+xml)\s*;.*charset\s*=\s*utf-8/i.test(e.type)){return new Blob([String.fromCharCode(65279),e],{type:e.type})}return e},v=function(t,u,s){if(!s){t=p(t)}var v=this,w=t.type,m=w===d,y,h=function(){l(v,"writestart progress write writeend".split(" "))},S=function(){if((f||m&&a)&&e.FileReader){var r=new FileReader;r.onloadend=function(){var t=f?r.result:r.result.replace(/^data:[^;]*;/,"data:attachment/file;");var n=e.open(t,"_blank");if(!n)e.location.href=t;t=undefined;v.readyState=v.DONE;h()};r.readAsDataURL(t);v.readyState=v.INIT;return}if(!y){y=n().createObjectURL(t)}if(m){e.location.href=y}else{var o=e.open(y,"_blank");if(!o){e.location.href=y}}v.readyState=v.DONE;h();c(y)};v.readyState=v.INIT;if(o){y=n().createObjectURL(t);setTimeout(function(){r.href=y;r.download=u;i(r);h();c(y);v.readyState=v.DONE});return}S()},w=v.prototype,m=function(e,t,n){return new v(e,t||e.name||"download",n)};if(typeof navigator!=="undefined"&&navigator.msSaveOrOpenBlob){return function(e,t,n){t=t||e.name||"download";if(!n){e=p(e)}return navigator.msSaveOrOpenBlob(e,t)}}w.abort=function(){};w.readyState=w.INIT=0;w.WRITING=1;w.DONE=2;w.error=w.onwritestart=w.onprogress=w.onwrite=w.onabort=w.onerror=w.onwriteend=null;return m}(typeof self!=="undefined"&&self||typeof window!=="undefined"&&window||this.content);if(typeof module!=="undefined"&&module.exports){module.exports.saveAs=saveAs}else if(typeof define!=="undefined"&&define!==null&&define.amd!==null){define([],function(){return saveAs})}
\ No newline at end of file

src/io/tcga_util.js

@@ -334,6 +334,7 @@ morpheus.TcgaUtil.getDataset = function (options) {
 					f(datasetToReturn);
 				});
 			}
+			datasetToReturn.setESSession();
 			returnDeferred.resolve(datasetToReturn);
 		});
 	return returnDeferred;

src/matrix/dataset.js

@@ -160,6 +160,33 @@ morpheus.Dataset.prototype = {
 		this.seriesArrays.push(options.array != null ? options.array
 				: morpheus.Dataset.createArray(options));
 		return this.seriesNames.length - 1;
+	},
+	setESSession : function () {
+		var _this = this;
+		if (this.esSession != null) {
+			return this.esSession;
+		}
+		else {
+			var protoMessage = morpheus.DatasetUtil.toProtoMessage(this);
+
+			var blob = new Blob(new Uint8Array(protoMessage), {type: "application/octet-stream"});
+			saveAs(blob, "test.bin");
+			var req = ocpu.call("createES", protoMessage, function (session) {
+				console.log(session);
+				_this.esSession = session;
+			}, true);
+
+			req.fail(function () {
+				alert("failed to create ExpressionSet of dataset");
+			})
 		}
+	},
+	getESSession : function () {
+		if (this.esSession == null) {
+			this.setESSession();
+		}
+		return this.esSession;
+	}
+
 };
 morpheus.Util.extend(morpheus.Dataset, morpheus.AbstractDataset);
\ No newline at end of file

src/matrix/dataset_util.js

@@ -805,3 +805,118 @@ morpheus.DatasetUtil.getNonEmptyRows = function (dataset) {
 	}
 	return rowsToKeep;
 };
+morpheus.DatasetUtil.getContentArray = function (dataset) {
+	var array = [];
+	var nr = dataset.rows;
+	var nc = dataset.columns;
+
+	for (var i = 0; i < nr; i++) {
+		for (var j = 0; j < nc; j++) {
+			array.push(dataset.getValue(i, j));
+		}
+	}
+	return array;
+};
+morpheus.DatasetUtil.getMetadataArray = function (dataset) {
+	var pDataArray = [];
+	var participantID = [];
+	var labelDescription = [];
+	var columnMeta = dataset.getColumnMetadata();
+	var n = columnMeta.getMetadataCount();
+	var m = dataset.columns;
+
+	for (var i = 0; i < n; i++) {
+		var vecI = columnMeta.get(i);
+		if (vecI.getName() == "participant_id") {
+			for (var j = 0; j < m; j++) {
+				participantID.push({
+					strval : vecI.getValue(j),
+					isNA : false
+				});
+			}
+		}
+		else {
+			for (j = 0; j < m; j++) {
+				pDataArray.push({
+					strval : vecI.getValue(j).toString(),
+					isNA : false
+				});
+			}
+			labelDescription.push({
+				strval : vecI.getName(),
+				isNA : false
+			});
+		}
+	}
+
+	var rowMeta = dataset.getRowMetadata();
+	var rowNames = [];
+	var rowNamesVec = rowMeta.getByName("id");
+	for (j = 0; j < dataset.rows; j++) {
+		rowNames.push({
+			strval : rowNamesVec.getValue(j),
+			isNA : false
+		})
+	}
+	return {pdata : pDataArray, participants : participantID, labels : labelDescription, rownames : rowNames};
+};
+morpheus.DatasetUtil.toProtoMessage = function (dataset) {
+	var array = morpheus.DatasetUtil.getContentArray(dataset);
+	var meta = morpheus.DatasetUtil.getMetadataArray(dataset);
+	var messageJSON = {
+		rclass : "LIST",
+		rexpValue : [{
+			rclass : "REAL",
+			realValue : array,
+			attrName : "dim",
+			attrValue : {
+				rclass : "INTEGER",
+				intValue : [dataset.rows, dataset.columns]
+			}
+		}, {
+			rclass : "STRING",
+			stringValue : meta.pdata,
+			attrName : "dim",
+			attrValue : {
+				rclass : "INTEGER",
+				intValue : [dataset.getColumnMetadata().getMetadataCount() - 1, dataset.columns]
+			}
+		}, {
+			rclass : "STRING",
+			stringValue : meta.labels
+		}, {
+			rclass : "STRING",
+			stringValue : meta.participants
+		}, {
+			rclass : "STRING",
+			stringValue : meta.rownames
+		}],
+		attrName : "names",
+		attrValue : {
+			rclass : "STRING",
+			stringValue : [{
+				strval : "data",
+				isNA : false
+			}, {
+				strval : "pData",
+				isNA : false
+			}, {
+				strval : "labelDescription",
+				isNA : false
+			}, {
+				strval : "colNames",
+				isNA : false
+			}, {
+				strval : "rowNames",
+				isNA : false
+			}]
+		}
+	};
+
+	ProtoBuf = dcodeIO.ProtoBuf;
+	var builder = ProtoBuf.protoFromFile("./message.proto"),
+		rexp = builder.build("rexp"),
+		REXP = rexp.REXP;
+
+	return new REXP(messageJSON);
+};
\ No newline at end of file

src/matrix/project.js

@@ -13,6 +13,7 @@ morpheus.Project = function(dataset) {
 	this.columnSelectionModel = new morpheus.SelectionModel(this, true);
 	this.rowSelectionModel = new morpheus.SelectionModel(this, false);
 	this.elementSelectionModel = new morpheus.ElementSelectionModel(this);
+
 	morpheus.Project._recomputeCalculatedFields(this.originalDataset);
 	morpheus.Project
 			._recomputeCalculatedFields(new morpheus.TransposedDatasetView(
@@ -99,6 +100,8 @@ morpheus.Project.prototype = {
 		this.columnSelectionModel.clear();
 		this.rowSelectionModel.clear();
 		this.elementSelectionModel.clear();
+		this.setESSession(dataset);
+
 		if (notify) {
 			this.trigger(morpheus.Project.Events.DATASET_CHANGED);
 		}

src/ui/heat_map_toolbar.js

@@ -253,11 +253,8 @@ morpheus.HeatMapToolBar = function (controller) {
 
 	$buttons.on('click', '[name=pca]', function () {
 		console.log("test button clicked");
-        new morpheus.PcaPlotTool({
-            project: controller.getProject(),
-            getVisibleTrackNames: _.bind(
-                controller.getVisibleTrackNames, controller)
-        });
+		new morpheus.PcaPlotTool({project : controller.getProject()});
+
 	});
 
 	var $lineOneColumn = $el.find('[data-name=lineOneColumn]');