Examples with VisualStyle org.cytoscape.view.vizmap.VisualStyle used on opensource projects

Example 96 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project clusterMaker2 by RBVI.

the class RankingPanel method createClusterImage.

/**
 * Convert a network to an image.  This is used by the MCODEResultsPanel.
 *
 * @param cluster Input network to convert to an image
 * @param height  Height that the resulting image should be
 * @param width   Width that the resulting image should be
 * @param layouter Reference to the layout algorithm
 * @param layoutNecessary Determinant of cluster size growth or shrinkage, the former requires layout
 * @return The resulting image
 */
public Image createClusterImage(final NodeCluster cluster, final int height, final int width, SpringEmbeddedLayouter layouter, boolean layoutNecessary) {
    // System.out.println("CCI: inside method");
    final CyRootNetwork root = clusterManager.getService(CyRootNetworkManager.class).getRootNetwork(network);
    // need to create a method get the subnetwork for a cluster
    final CyNetwork net = cluster.getSubNetwork(network, root, SavePolicy.DO_NOT_SAVE);
    // System.out.println("CCI: after getting root and network ");
    // Progress reporters.
    // There are three basic tasks, the progress of each is calculated and then combined
    // using the respective weighting to get an overall progress global progress
    // setting up the nodes and edges is deemed as 25% of the whole task
    int weightSetupNodes = 20;
    int weightSetupEdges = 5;
    // layout it is 70%
    double weightLayout = 75.0;
    double goalTotal = weightSetupNodes + weightSetupEdges;
    if (layoutNecessary) {
        goalTotal += weightLayout;
    }
    // keeps track of progress as a percent of the totalGoal
    double progress = 0;
    final VisualStyle vs = getClusterStyle();
    // System.out.println("CCI: after getClusterStyle");
    final CyNetworkView clusterView = createNetworkView(net, vs);
    // System.out.println("CCI: after createNetworkView");
    clusterView.setVisualProperty(NETWORK_WIDTH, new Double(width));
    clusterView.setVisualProperty(NETWORK_HEIGHT, new Double(height));
    for (View<CyNode> nv : clusterView.getNodeViews()) {
        if (interrupted) {
            // problems the next time around
            if (layouter != null)
                layouter.resetDoLayout();
            resetLoading();
            return null;
        }
        // Node position
        final double x;
        final double y;
        // first prevents the program from throwing a null pointer exception in the second condition)
        if (cluster.getView() != null && cluster.getView().getNodeView(nv.getModel()) != null) {
            // If it does, then we take the layout position that was already generated for it
            x = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_X_LOCATION);
            y = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_Y_LOCATION);
        } else {
            // Otherwise, randomize node positions before layout so that they don't all layout in a line
            // (so they don't fall into a local minimum for the SpringEmbedder)
            // If the SpringEmbedder implementation changes, this code may need to be removed
            // size is small for many default drawn graphs, thus +100
            x = (clusterView.getVisualProperty(NETWORK_WIDTH) + 100) * Math.random();
            y = (clusterView.getVisualProperty(NETWORK_HEIGHT) + 100) * Math.random();
            if (!layoutNecessary) {
                goalTotal += weightLayout;
                progress /= (goalTotal / (goalTotal - weightLayout));
                layoutNecessary = true;
            }
        }
        nv.setVisualProperty(NODE_X_LOCATION, x);
        nv.setVisualProperty(NODE_Y_LOCATION, y);
    // Might be specific to MCODE
    /*
			// Node shape
			if (cluster.getSeedNode() == nv.getModel().getSUID()) {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.RECTANGLE);
			} else {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.ELLIPSE);
			}
			 */
    /*
			// Update loader
			if (loader != null) {
				progress += 100.0 * (1.0 / (double) clusterView.getNodeViews().size()) *
							((double) weightSetupNodes / (double) goalTotal);
				loader.setProgress((int) progress, "Setup: nodes");
			}

			*/
    }
    if (clusterView.getEdgeViews() != null) {
        for (int i = 0; i < clusterView.getEdgeViews().size(); i++) {
            if (interrupted) {
                // logger.error("Interrupted: Edge Setup");
                if (layouter != null)
                    layouter.resetDoLayout();
                resetLoading();
                return null;
            }
        /*
				if (loader != null) {
					progress += 100.0 * (1.0 / (double) clusterView.getEdgeViews().size()) *
								((double) weightSetupEdges / (double) goalTotal);
					loader.setProgress((int) progress, "Setup: edges");
				}
				*/
        }
    }
    if (layoutNecessary) {
        if (layouter == null) {
            layouter = new SpringEmbeddedLayouter();
        }
        layouter.setGraphView(clusterView);
        // The doLayout method should return true if the process completes without interruption
        if (!layouter.doLayout(weightLayout, goalTotal, progress)) {
            // Otherwise, if layout is not completed, set the interruption to false, and return null, not an image
            resetLoading();
            return null;
        }
    }
    final Image image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
    final Graphics2D g = (Graphics2D) image.getGraphics();
    SwingUtilities.invokeLater(new Runnable() {

        // @Override
        public void run() {
            try {
                final Dimension size = new Dimension(width, height);
                JPanel panel = new JPanel();
                panel.setPreferredSize(size);
                panel.setSize(size);
                panel.setMinimumSize(size);
                panel.setMaximumSize(size);
                panel.setBackground((Color) vs.getDefaultValue(NETWORK_BACKGROUND_PAINT));
                JWindow window = new JWindow();
                window.getContentPane().add(panel, BorderLayout.CENTER);
                RenderingEngine<CyNetwork> re = renderingEngineFactory.createRenderingEngine(panel, clusterView);
                vs.apply(clusterView);
                clusterView.fitContent();
                clusterView.updateView();
                window.pack();
                window.repaint();
                re.createImage(width, height);
                re.printCanvas(g);
                g.dispose();
                if (clusterView.getNodeViews().size() > 0) {
                    cluster.setView(clusterView);
                }
            } catch (Exception ex) {
                throw new RuntimeException(ex);
            }
        }
    });
    layouter.resetDoLayout();
    resetLoading();
    return image;
}

Example 97 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project clusterMaker2 by RBVI.

the class RankingPanelTask method setNodeColors.

private void setNodeColors() {
    String rankingAlgorithmName = getRankingAlgorithmName();
    VisualStyle vs = ViewUtils.copyStyle(manager, ViewUtils.getCurrentVisualStyle(manager), "_removeThis");
    vs.setTitle("Ranking results colors");
    VisualMappingFunctionFactory vmff = manager.getService(VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
    ContinuousMapping mapping = (ContinuousMapping) vmff.createVisualMappingFunction(rankingAlgorithmName, Double.class, BasicVisualLexicon.NODE_FILL_COLOR);
    Color color1 = new Color(170, 221, 221);
    Color color2 = new Color(212, 229, 212);
    Color color3 = new Color(255, 238, 204);
    Color color4 = new Color(255, 195, 178);
    Color color5 = new Color(255, 153, 153);
    double belowAverage = NodeCluster.getAverageRankScore(clusters) / 2.0;
    double overAverage = NodeCluster.getMaxRankScore(clusters) / 2.0;
    BoundaryRangeValues<Paint> range1 = new BoundaryRangeValues<>(color1, color1, color2);
    BoundaryRangeValues<Paint> range2 = new BoundaryRangeValues<>(color3, color4, color5);
    mapping.addPoint(belowAverage, range1);
    mapping.addPoint(overAverage, range2);
    vs.addVisualMappingFunction(mapping);
    ViewUtils.setVisualStyle(manager, manager.getNetworkView(), vs);
}

Example 98 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project clusterMaker2 by RBVI.

the class ResultsPanel method createClusterImage.

/**
 * Convert a network to an image.  This is used by the MCODEResultsPanel.
 *
 * @param cluster Input network to convert to an image
 * @param height  Height that the resulting image should be
 * @param width   Width that the resulting image should be
 * @param layouter Reference to the layout algorithm
 * @param layoutNecessary Determinant of cluster size growth or shrinkage, the former requires layout
 * @return The resulting image
 */
public Image createClusterImage(final NodeCluster cluster, final int height, final int width, SpringEmbeddedLayouter layouter, boolean layoutNecessary) {
    // System.out.println("CCI: inside method");
    final CyRootNetwork root = clusterManager.getService(CyRootNetworkManager.class).getRootNetwork(network);
    // need to create a method get the subnetwork for a cluster
    final CyNetwork net = cluster.getSubNetwork(network, root, SavePolicy.DO_NOT_SAVE);
    // System.out.println("CCI: after getting root and network ");
    // Progress reporters.
    // There are three basic tasks, the progress of each is calculated and then combined
    // using the respective weighting to get an overall progress global progress
    // setting up the nodes and edges is deemed as 25% of the whole task
    int weightSetupNodes = 20;
    int weightSetupEdges = 5;
    // layout it is 70%
    double weightLayout = 75.0;
    double goalTotal = weightSetupNodes + weightSetupEdges;
    if (layoutNecessary) {
        goalTotal += weightLayout;
    }
    // keeps track of progress as a percent of the totalGoal
    double progress = 0;
    final VisualStyle vs = getClusterStyle();
    // System.out.println("CCI: after getClusterStyle");
    final CyNetworkView clusterView = createNetworkView(net, vs);
    // System.out.println("CCI: after createNetworkView");
    clusterView.setVisualProperty(NETWORK_WIDTH, new Double(width));
    clusterView.setVisualProperty(NETWORK_HEIGHT, new Double(height));
    for (View<CyNode> nv : clusterView.getNodeViews()) {
        if (interrupted) {
            // problems the next time around
            if (layouter != null)
                layouter.resetDoLayout();
            resetLoading();
            return null;
        }
        // Node position
        final double x;
        final double y;
        // first prevents the program from throwing a null pointer exception in the second condition)
        if (cluster.getView() != null && cluster.getView().getNodeView(nv.getModel()) != null) {
            // If it does, then we take the layout position that was already generated for it
            x = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_X_LOCATION);
            y = cluster.getView().getNodeView(nv.getModel()).getVisualProperty(NODE_Y_LOCATION);
        } else {
            // Otherwise, randomize node positions before layout so that they don't all layout in a line
            // (so they don't fall into a local minimum for the SpringEmbedder)
            // If the SpringEmbedder implementation changes, this code may need to be removed
            // size is small for many default drawn graphs, thus +100
            x = (clusterView.getVisualProperty(NETWORK_WIDTH) + 100) * Math.random();
            y = (clusterView.getVisualProperty(NETWORK_HEIGHT) + 100) * Math.random();
            if (!layoutNecessary) {
                goalTotal += weightLayout;
                progress /= (goalTotal / (goalTotal - weightLayout));
                layoutNecessary = true;
            }
        }
        nv.setVisualProperty(NODE_X_LOCATION, x);
        nv.setVisualProperty(NODE_Y_LOCATION, y);
    // Might be specific to MCODE
    /*
			// Node shape
			if (cluster.getSeedNode() == nv.getModel().getSUID()) {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.RECTANGLE);
			} else {
				nv.setLockedValue(NODE_SHAPE, NodeShapeVisualProperty.ELLIPSE);
			}
			 */
    /*
			// Update loader
			if (loader != null) {
				progress += 100.0 * (1.0 / (double) clusterView.getNodeViews().size()) *
							((double) weightSetupNodes / (double) goalTotal);
				loader.setProgress((int) progress, "Setup: nodes");
			}
			
			*/
    }
    if (clusterView.getEdgeViews() != null) {
        for (int i = 0; i < clusterView.getEdgeViews().size(); i++) {
            if (interrupted) {
                // logger.error("Interrupted: Edge Setup");
                if (layouter != null)
                    layouter.resetDoLayout();
                resetLoading();
                return null;
            }
        /*
				if (loader != null) {
					progress += 100.0 * (1.0 / (double) clusterView.getEdgeViews().size()) *
								((double) weightSetupEdges / (double) goalTotal);
					loader.setProgress((int) progress, "Setup: edges");
				}
				*/
        }
    }
    if (layoutNecessary) {
        if (layouter == null) {
            layouter = new SpringEmbeddedLayouter();
        }
        layouter.setGraphView(clusterView);
        // The doLayout method should return true if the process completes without interruption
        if (!layouter.doLayout(weightLayout, goalTotal, progress)) {
            // Otherwise, if layout is not completed, set the interruption to false, and return null, not an image
            resetLoading();
            return null;
        }
    }
    final Image image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);
    final Graphics2D g = (Graphics2D) image.getGraphics();
    SwingUtilities.invokeLater(new Runnable() {

        // @Override
        public void run() {
            try {
                final Dimension size = new Dimension(width, height);
                JPanel panel = new JPanel();
                panel.setPreferredSize(size);
                panel.setSize(size);
                panel.setMinimumSize(size);
                panel.setMaximumSize(size);
                panel.setBackground((Color) vs.getDefaultValue(NETWORK_BACKGROUND_PAINT));
                JWindow window = new JWindow();
                window.getContentPane().add(panel, BorderLayout.CENTER);
                RenderingEngine<CyNetwork> re = renderingEngineFactory.createRenderingEngine(panel, clusterView);
                vs.apply(clusterView);
                clusterView.fitContent();
                clusterView.updateView();
                window.pack();
                window.repaint();
                re.createImage(width, height);
                re.printCanvas(g);
                g.dispose();
                if (clusterView.getNodeViews().size() > 0) {
                    cluster.setView(clusterView);
                }
            } catch (Exception ex) {
                throw new RuntimeException(ex);
            }
        }
    });
    layouter.resetDoLayout();
    resetLoading();
    return image;
}

Example 99 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project PhenomeScape by soulj.

the class PhenomeExpress method run.

@Override
public void run(TaskMonitor taskMonitor) throws Exception {
    taskMonitor.setTitle("Running PhenomeExpress");
    taskMonitor.setStatusMessage("Preparing Networks");
    long time = System.currentTimeMillis();
    inputCheck();
    setUpNetworks();
    double[] relativeWeighting = { 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8 };
    double[] alphas = { 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8 };
    double[] piValues = proteinNetwork.getPivalues();
    Map<String, Integer> phenotypeMap = phenomeNetwork.getName2IndexMap();
    double[] phenoArray = new double[phenomeNetwork.getName2IndexMap().size()];
    selectedPhenotypes = new ArrayList<Phenotype>();
    boolean first = true;
    for (Phenotype phenotype : phenotypes) {
        if (phenotype.getSelected()) {
            if (first) {
                phenotypeSelected = phenotype.getID();
                phenotypeNamesSelected = phenotype.getName();
                selectedPhenotypes.add(phenotype);
                phenoArray[phenotypeMap.get(phenotype.getID())] = 1.0;
                first = false;
            } else {
                phenotypeSelected = phenotypeSelected + " ," + phenotype.getID();
                phenotypeNamesSelected = phenotypeNamesSelected + " ," + phenotype.getName();
                phenoArray[phenotypeMap.get(phenotype.getID())] = 1.0;
                selectedPhenotypes.add(phenotype);
            }
        }
    }
    Map<CyNode, Integer> map = proteinNetwork.getNode2IndexMap();
    int size = proteinNetwork.getNetwork().getNodeCount();
    int[] occuranceArray = new int[size];
    HashMap<CyNode, Protein> node2Protein = new HashMap<CyNode, Protein>();
    if (cancelled) {
        return;
    }
    taskMonitor.setStatusMessage("Calculating Activity Scores");
    taskMonitor.setProgress(0.0);
    double progress = 0.0;
    SparseRowMatrix adjMatrix = SparseRowMatrix.create(size, size);
    double[] transitionProbs = { 0.5, 0.6, 0.7, 0.8 };
    for (double transitionProb : transitionProbs) {
        TransitionMatrix transitionMatrix = new TransitionMatrix(phenomeNetwork.normalise(transitionProb, phenoGeneNetwork), proteinNetwork.normalise(transitionProb, phenoGeneNetwork), phenoGeneNetwork.normaliseT(transitionProb), phenoGeneNetwork.normalise(transitionProb));
        for (double weighting : relativeWeighting) {
            if (cancelled) {
                return;
            }
            transitionMatrix.prepareVector(piValues, phenoArray, weighting);
            for (double alpha : alphas) {
                progress += 0.0051;
                taskMonitor.setProgress(progress);
                double[] pageRankResults = transitionMatrix.pageRank(alpha);
                HashMap<Integer, Protein> index2ProteinMap = proteinNetwork.getIndex2ProteinMap();
                for (int i = 0; i < index2ProteinMap.size(); i++) {
                    Protein protein = index2ProteinMap.get(i);
                    protein.setValue(pageRankResults[i]);
                }
                List<Protein> proteinList = new ArrayList<Protein>(index2ProteinMap.values());
                Collections.sort(proteinList, new DescendingScoreComparator());
                int rank = 0;
                for (Protein protein : proteinList) {
                    rank++;
                    protein.setRank(rank);
                    node2Protein.put(protein.getNode(), protein);
                }
                Collections.sort(proteinList, new DescendingScoreComparator());
                GIGA giga = new GIGA(proteinList, node2Protein, proteinNetwork, maxNetworkSize);
                giga.compute();
                for (GIGACluster cluster : giga.getClusters()) {
                    for (CyNode node : cluster.getCluster()) {
                        Integer index = map.get(node);
                        AVector row = adjMatrix.getRow(index);
                        if (!row.isMutable()) {
                            row = row.mutable();
                        }
                        for (CyNode node2 : cluster.getCluster()) {
                            Integer index2 = map.get(node2);
                            row.set(index2, row.get(index2) + 1.0);
                            occuranceArray[index2]++;
                        }
                        adjMatrix.replaceRow(index, row);
                    }
                }
            }
        }
    }
    if (cancelled) {
        return;
    }
    taskMonitor.setProgress(1.0);
    taskMonitor.setStatusMessage("Creating Consensus Subnetworks");
    AMatrix cooccuranceMat = adjMatrix.transposeInnerProduct(adjMatrix);
    for (int i = 0; i < size; i++) {
        AVector row = cooccuranceMat.getRow(i);
        if (row.elementSum() > 0) {
            row.divide(occuranceArray[i]);
            Index nonSparse = row.nonSparseIndex();
            for (int j = 0; j < nonSparse.length(); j++) {
                if (row.get(nonSparse.get(j)) < 1.0) {
                    row.set(nonSparse.get(j), 0.0);
                }
            }
            cooccuranceMat.replaceRow(i, row.sparse());
        }
    }
    ConnectedComponentAnalyser CCA = new ConnectedComponentAnalyser(node2Protein);
    ArrayList<PhenomeExpressSubnetwork> subnetworks = CCA.ccFromAdjMatrix(adjMatrix, proteinNetwork);
    Iterator<PhenomeExpressSubnetwork> it = subnetworks.iterator();
    while (it.hasNext()) {
        PhenomeExpressSubnetwork subnetwork = it.next();
        if (subnetwork.getNodeList().size() < this.minNetSize) {
            it.remove();
        }
    }
    if (cancelled) {
        return;
    }
    taskMonitor.setStatusMessage("Calculating Subnetwork Significance");
    subnetworksSignificance(subnetworks);
    taskMonitor.setStatusMessage("Visualising Subnetworks");
    List<Double> foldChangeValues = proteinNetwork.getNodeTable().getColumn(foldChange).getValues(Double.class);
    double fcMax = Collections.max(foldChangeValues);
    double fcMin = Collections.min(foldChangeValues);
    // Apply the visual style to a NetworkView
    VizStyle vizStyle = new VizStyle();
    VisualStyle vs = vizStyle.createVizStyle(cyServiceRegistrar, geneName, foldChange, fcMax, fcMin);
    this.property = getNodeLabelPositionProperty();
    vs.setDefaultValue(property, property.parseSerializableString("N,S,c,0.0,0.0"));
    VisualMappingManager visualMappingManager = cyServiceRegistrar.getService(VisualMappingManager.class);
    visualMappingManager.setCurrentVisualStyle(vs);
    ArrayList<CyNetworkView> networkViewList = new ArrayList<CyNetworkView>();
    Iterator<PhenomeExpressSubnetwork> it2 = subnetworks.iterator();
    CyNetworkManager networkManager = cyServiceRegistrar.getService(CyNetworkManager.class);
    CyNetworkViewFactory networkViewFactory = cyServiceRegistrar.getService(CyNetworkViewFactory.class);
    CyLayoutAlgorithmManager layoutManager = cyServiceRegistrar.getService(CyLayoutAlgorithmManager.class);
    CyApplicationManager cyApplicationManager = cyServiceRegistrar.getService(CyApplicationManager.class);
    CyLayoutAlgorithm layout = layoutManager.getLayout("force-directed");
    Map<String, Object> settings = new HashMap<String, Object>();
    settings.put("defaultSpringLength", 5.0);
    settings.put("defaultSpringNodeMass", 2.0);
    TunableSetter setter = cyServiceRegistrar.getService(TunableSetter.class);
    Object context = layout.createLayoutContext();
    setter.applyTunables(context, settings);
    GOTermAnalyser2 goTermAnalyser = new GOTermAnalyser2(proteinNetwork, species);
    while (it2.hasNext()) {
        PhenomeExpressSubnetwork subnet = it2.next();
        if (subnet.getPvalue() > this.threshold) {
            it2.remove();
        } else {
            goTermAnalyser.calculateGOTermPValues(subnet, proteinNetwork);
            String subnetworkName = NetworkUtils.getUniqueNetworkName(cyServiceRegistrar, networkName + "_" + subnet.getBestGOTerm());
            subnet.setName(subnetworkName);
            CySubNetwork subnetwork = NetworkUtils.createSubNetwork(((CySubNetwork) proteinNetwork.getNetwork()).getRootNetwork(), subnet.getNodeList());
            subnetwork.getRow(subnetwork).set(CyNetwork.NAME, subnetworkName);
            addSeedPhenotypes(subnetwork);
            networkManager.addNetwork(subnetwork);
            CyNetworkViewManager viewManager = cyServiceRegistrar.getService(CyNetworkViewManager.class);
            CyNetworkView nv = networkViewFactory.createNetworkView(subnetwork);
            viewManager.addNetworkView(nv);
            cyApplicationManager.setCurrentNetworkView(nv);
            for (CyNode phenoNode : phenotypesAdded) {
                View<CyNode> nodeView = nv.getNodeView(phenoNode);
                nodeView.setLockedValue(BasicVisualLexicon.NODE_SHAPE, NodeShapeVisualProperty.RECTANGLE);
                nodeView.setLockedValue(BasicVisualLexicon.NODE_FILL_COLOR, Color.BLUE);
            }
            for (CyEdge phenoEdge : phenoEdges) {
                View<CyEdge> edgeView = nv.getEdgeView(phenoEdge);
                edgeView.setLockedValue(BasicVisualLexicon.EDGE_LINE_TYPE, LineTypeVisualProperty.DOT);
                edgeView.setLockedValue(BasicVisualLexicon.EDGE_PAINT, Color.BLUE);
            }
            networkViewList.add(nv);
            Set<View<CyNode>> nodeSet = Collections.emptySet();
            cyServiceRegistrar.getService(TaskManager.class).execute(layout.createTaskIterator(nv, context, nodeSet, null));
        }
    }
    CyEventHelper cyEventHelper = cyServiceRegistrar.getService(CyEventHelper.class);
    for (CyNetworkView nv : networkViewList) {
        visualMappingManager.setVisualStyle(vs, nv);
        vs.apply(nv);
        cyEventHelper.flushPayloadEvents();
        cyApplicationManager.setCurrentNetworkView(nv);
        nv.updateView();
    }
    phenomeNetwork = null;
    proteinNetwork = null;
    ResultsPanel resultsPanel = (ResultsPanel) CytoPanelUtils.getCytoPanel(cyServiceRegistrar, ResultsPanel.class, CytoPanelName.EAST);
    resultsPanel.newTableData(getResultsSummary(subnetworks), getParameterList());
    CytoPanelUtils.showCytoPanel(cyServiceRegistrar, CytoPanelName.EAST);
}

Example 100 with VisualStyle

use of org.cytoscape.view.vizmap.VisualStyle in project PhenomeScape by soulj.

the class VizStyle method createVizStyle.

public VisualStyle createVizStyle(CyServiceRegistrar cyServiceRegistrar, String geneName, String foldchangeName, double maxFC, double minFC) {
    // To get references to services in CyActivator class
    VisualMappingManager vmmServiceRef = cyServiceRegistrar.getService(VisualMappingManager.class);
    VisualStyleFactory visualStyleFactoryServiceRef = cyServiceRegistrar.getService(VisualStyleFactory.class);
    VisualMappingFunctionFactory vmfFactoryC = cyServiceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=continuous)");
    VisualMappingFunctionFactory vmfFactoryD = cyServiceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=discrete)");
    VisualMappingFunctionFactory vmfFactoryP = cyServiceRegistrar.getService(VisualMappingFunctionFactory.class, "(mapping.type=passthrough)");
    // To create a new VisualStyle object and set the mapping function
    VisualStyle vs = visualStyleFactoryServiceRef.createVisualStyle("PhenomeScape");
    // Use pass-through mapping to create the node label
    PassthroughMapping nameMapping = (PassthroughMapping) vmfFactoryP.createVisualMappingFunction(geneName, String.class, BasicVisualLexicon.NODE_LABEL);
    vs.addVisualMappingFunction(nameMapping);
    vs.setDefaultValue(BasicVisualLexicon.NODE_SIZE, 15.0);
    // RenderingEngineManager renderingEngineManager = cyServiceRegistrar.getService(RenderingEngineManager.class);
    // CyNetworkViewManager viewManager = cyServiceRegistrar.getService(CyNetworkViewManager.class);
    // CyNetworkViewFactory networkViewFactory = cyServiceRegistrar.getService(CyNetworkViewFactory.class);
    // Set<CyNetworkView> views = viewManager.getNetworkViewSet();
    // CyNetworkView networkView = views.iterator().next();
    // Collection<RenderingEngine<?>> engines = renderingEngineManager.getAllRenderingEngines();
    // VisualLexicon lex = engines.iterator().next().getVisualLexicon();
    // VisualProperty prop = lex.lookup(CyNode.class, "NODE_LABEL_POSITION");
    // Object value = prop.parseSerializableString("S,N,c,0.0,5.0"); // Put the north of the label on the southeast corner of the node
    // vs.setDefaultValue(prop, value);
    // Set the node size to smaller than the default
    // Set node color map to attribute "FoldChange"
    ContinuousMapping mapping = (ContinuousMapping) vmfFactoryC.createVisualMappingFunction(foldchangeName, Double.class, BasicVisualLexicon.NODE_FILL_COLOR);
    // Define the points
    BoundaryRangeValues<Paint> brv1 = new BoundaryRangeValues<Paint>(Color.GREEN, Color.GREEN, Color.WHITE);
    BoundaryRangeValues<Paint> brv2 = new BoundaryRangeValues<Paint>(Color.GREEN, Color.WHITE, Color.RED);
    BoundaryRangeValues<Paint> brv3 = new BoundaryRangeValues<Paint>(Color.RED, Color.RED, Color.RED);
    // Set the points
    // TODO add the point size and text postition
    mapping.addPoint(minFC, brv1);
    mapping.addPoint(0.0, brv2);
    mapping.addPoint(maxFC, brv3);
    // add the mapping to visual style
    vs.addVisualMappingFunction(mapping);
    // Add the new style to the VisualMappingManager
    vmmServiceRef.addVisualStyle(vs);
    return (vs);
}