Merge pull request #160 from aertslab/157-display-trajectory

157-display-trajectory

README.md

@@ -1,11 +1,18 @@
-# SCope v1.1.0: Visualization of large-scale and high dimensional single cell data
+# SCope v1.2.0: Visualization of large-scale and high dimensional single cell data
 <img src="images/SCope_Logo.png" width="640">
 
 SCope is a fast visualization tool for large-scale and high dimensional scRNA-seq datasets.
 Currently the data format supported by SCope is `.loom`. This file format for very large omics datasets is maintained by the Linnarsson Lab through the `loompy` Python package (https://github.com/linnarsson-lab/loompy).
 
 ## Version History
 
+July 6, 2018
+
+* Version 1.2.0
+   * Changes:
+     * Add feature to display trajectory data in the viewer. Currently the only way we provide to add trajectory data to .loom files is through [SCopeLoomR](https://github.com/aertslab/SCopeLoomR/).
+
+
 July 4, 2018
 
 * Version 1.1.0

VERSION

@@ -1 +1 @@
-1.1.0
+1.2.0

opt/setup.py

@@ -5,7 +5,7 @@
                         'scope-server = scopeserver.dataserver:dev'
                         ]
                     },
-      version='1.1.0',
+      version='1.2.0',
       description='SCope Data Server: a server to load and serve the data to the SCope Client',
       url='',
       author='Maxime De Waegeneer',

package.json

@@ -1,6 +1,6 @@
 {
   "name": "SCope",
-  "version": "1.1.0",
+  "version": "1.2.0",
   "description": "Visualization tool for large-scale and high dimensional single-cell data",
   "main": "index.js",
   "scripts": {

src/components/AppSidebar.jsx

@@ -124,6 +124,14 @@ class AppSidebar extends Component {
 							<Menu.Item>
 								<Dropdown inline value={activeCoordinates} options={coordinates} onChange={this.setActiveCoordinates.bind(this)} />
 							</Menu.Item>
+							{ BackendAPI.hasActiveCoordinatesTrajectory() &&
+							<div>
+							<Menu.Item>Trajectory</Menu.Item>
+							<Menu.Item>
+								<Checkbox toggle label="Hide" checked={settings.hideTrajectory} onChange={this.toggleHideTrajectory.bind(this)} />
+							</Menu.Item>
+							</div>
+							}
 						</Menu.Menu>
 					}
 					{ showTransforms &&
@@ -399,6 +407,17 @@ class AppSidebar extends Component {
 		});
 	}
 
+
+	toggleHideTrajectory() {
+		let settings = BackendAPI.setSetting('hideTrajectory', !this.state.settings.hideTrajectory);
+		this.setState({settings: settings});
+		ReactGA.event({
+			category: 'settings',
+			action: 'toggle hide trajectory',
+			label: settings.hideTrajectory ? 'on' : 'off'
+		});
+	}
+
 	setActiveCoordinates(evt, coords) {
 		BackendAPI.setActiveCoordinates(coords.value);
 		this.setState({ activeCoordinates: coords.value });

src/components/common/API.jsx

@@ -49,6 +49,7 @@ class API {
 		this.featureChangeListeners = {};
 
 		this.settings = {
+			hideTrajectory: false,
 			sortCells: true,
 			hasLogTransform: true,
 			hasCpmNormalization: false,
@@ -107,7 +108,7 @@ class API {
 			'activeLooms',
 			'activeCoordinates',
 			'features', 'gene', 'regulon', 'compare', 'feature', 'featureType', 'threshold', 'type', 'metadata', 'description',
-			'settings', 'hasCpmNormalization', 'hasLogTransform', 'sortCells', 'dissociateViewers',
+			'settings', 'hasCpmNormalization', 'hasLogTransform', 'sortCells', 'dissociateViewers', 'hideTrajectory', 
 			'viewerTool',
 			'viewerSelections',
 			'viewerTransform',
@@ -243,6 +244,14 @@ class API {
 		return this.loomFiles[this.activeLooms[0]];
 	}
 
+	getActiveLoomMetadataEmbeddings() {
+		return this.loomFiles[this.activeLooms[0]].cellMetaData.embeddings;
+	}
+
+	getActiveLoomMetaDataEmbedding() {
+		return this.getActiveLoomMetadataEmbeddings().filter(x => x.id == this.getActiveCoordinates())[0]
+	}
+
 	onActiveLoomChange(listener) {
 		this.activeLoomChangeListeners.push(listener);
 	}
@@ -258,6 +267,14 @@ class API {
 		return this.activeCoordinates;
 	}
 
+	hasActiveCoordinatesTrajectory() {
+		return this.getActiveLoomMetaDataEmbedding().trajectory != null
+	}
+
+	getActiveCoordinatesTrajectory() {
+		return this.getActiveLoomMetaDataEmbedding().trajectory
+	}
+
 	queryLoomFiles(uuid, callback) {
 		let query = {
 			UUID: uuid