Examples with CyMatrix edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix used on opensource projects

Example 6 with CyMatrix

use of edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix in project clusterMaker2 by RBVI.

the class TransClustCluster method run.

/**
 * Perform the actual clustering.  For TransClust, there are really
 * two steps:
 * 	1) Assign all of the connected components
 * 	2) Do the TransClust clustering.
 *
 * There is also an optional approach called evolutionary parameter
 * tuning, which takes a lot longer and is probably less relevant for
 * the Cytoscape integration.
 *
 * @param monitor the TaskMonitor to use
 */
public void run(TaskMonitor monitor) {
    monitor.setTitle("Performing Transitivity clustering");
    this.monitor = monitor;
    if (network == null)
        network = clusterManager.getNetwork();
    // Make sure to update the context
    context.setNetwork(network);
    NodeCluster.init();
    CyMatrix matrix = context.edgeAttributeHandler.getMatrix();
    if (matrix == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
        return;
    }
    updateSettings();
    runTransClust = new RunTransClust(matrix, context.edgeAttributeHandler.edgeCutOff.getValue(), monitor);
    if (canceled)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
    createGroups = context.advancedAttributes.createGroups;
    // Cluster the nodes
    List<NodeCluster> clusters = runTransClust.run(monitor, network);
    // Canceled?
    if (clusters == null)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, GROUP_ATTRIBUTE);
    monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
    params = new ArrayList<String>();
    context.edgeAttributeHandler.setParams(params);
    List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
    results = new AbstractClusterResults(network, clusters);
    monitor.setStatusMessage("Done.  TransClust results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !context.edgeAttributeHandler.selectedOnly));
    }
}

Example 7 with CyMatrix

use of edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix in project clusterMaker2 by RBVI.

the class RunSCPS method getSMat.

// Get Connected Components, cluster all components <= |5|, and connect the remaining components with random lowscoring edges
public DoubleMatrix2D getSMat(CyMatrix distanceMatrix) {
    // Matrix prior to filtration modification
    DoubleMatrix2D unfiltered_mat = distanceMatrix.getColtMatrix();
    // Size of newly created Umat after filtering of small components
    int sMat_rows = 0;
    HashMap<Integer, List<CyNode>> filtered_cmap = new HashMap<Integer, List<CyNode>>();
    // Connected Componets
    Map<Integer, List<CyNode>> cMap = MatrixUtils.findConnectedComponents(distanceMatrix);
    IntArrayList rowList = new IntArrayList();
    IntArrayList columnList = new IntArrayList();
    DoubleArrayList valueList = new DoubleArrayList();
    // Iterate through connected components
    int component_size_sum = 0;
    for (List<CyNode> component : cMap.values()) {
        numComponents += 1;
        // Size <= 5. Automatically create cluster and increment clusterCount.
        if (component.size() <= 5) {
            NodeCluster iCluster = new NodeCluster(component);
            iCluster.setClusterNumber(this.clusterCount);
            // iCluster.add(component,this.clusterCount);
            this.clusterMap.put(new Integer(clusterCount), iCluster);
            this.clusterCount++;
        } else {
            // iterate through components and assign them index mappings in new uMatrix
            component_size_sum += component.size();
            System.out.println("Normal Component size " + component.size() + " Total Sum " + component_size_sum);
            for (int i = 0; i < component.size(); i++) {
                CyNode n = component.get(i);
                int node_id = this.nodes.indexOf(n);
                // set mapping of new matrix index to old index
                setMap(node_id, sMat_rows);
                sMat_rows++;
            }
        }
    }
    DoubleMatrix2D sMat = DoubleFactory2D.sparse.make(sMat_rows, sMat_rows);
    // set diagnols of sMat to one
    for (int i = 0; i < sMat_rows; i++) sMat.set(i, i, 1);
    // iterate through nonzero edges. If both nodes in new index map, transfer the edge to new matrix
    unfiltered_mat.getNonZeros(rowList, columnList, valueList);
    for (int i = 0; i < rowList.size(); i++) {
        int row_id = rowList.get(i);
        int column_id = columnList.get(i);
        int new_row_id = getMap_new(row_id);
        int new_column_id = getMap_new(column_id);
        double value = valueList.get(i);
        // Set symmetrically the values in new matrix
        if (new_row_id > -1 && new_column_id > -1) {
            sMat.set(new_row_id, new_column_id, value);
            sMat.set(new_column_id, new_row_id, value);
        }
    }
    return sMat;
}

Example 8 with CyMatrix

use of edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix in project clusterMaker2 by RBVI.

the class APCluster method run.

public void run(TaskMonitor monitor) {
    monitor.setTitle("Performing AP cluster");
    this.monitor = monitor;
    if (network == null)
        network = clusterManager.getNetwork();
    // Make sure to update the context
    context.setNetwork(network);
    NodeCluster.init();
    CyMatrix matrix = context.edgeAttributeHandler.getMatrix();
    if (matrix == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
        return;
    }
    // Update our tunable results
    clusterAttributeName = context.getClusterAttribute();
    createGroups = context.advancedAttributes.createGroups;
    if (canceled)
        return;
    // Cluster the nodes
    runAP = new RunAP(matrix, context.lambda, context.preference, context.rNumber, monitor, debug);
    if (canceled)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
    List<NodeCluster> clusters = runAP.run(network, monitor);
    // Canceled?
    if (clusters == null)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, GROUP_ATTRIBUTE);
    monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
    params = new ArrayList<String>();
    context.edgeAttributeHandler.setParams(params);
    setParams(params);
    List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
    results = new AbstractClusterResults(network, clusters);
    monitor.showMessage(TaskMonitor.Level.INFO, "Done.  AP results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !context.edgeAttributeHandler.selectedOnly));
    }
}

Example 9 with CyMatrix

use of edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix in project clusterMaker2 by RBVI.

the class MCLCluster method run.

public void run(TaskMonitor monitor) {
    monitor.setTitle("Performing MCL cluster");
    this.monitor = monitor;
    if (network == null)
        network = clusterManager.getNetwork();
    context.setNetwork(network);
    NodeCluster.init();
    CyMatrix matrix = context.edgeAttributeHandler.getMatrix();
    if (matrix == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
        return;
    }
    // Update our tunable results
    clusterAttributeName = context.getClusterAttribute();
    createGroups = context.advancedAttributes.createGroups;
    if (canceled)
        return;
    // Cluster the nodes
    runMCL = new RunMCL(matrix, context.inflation_parameter, context.iterations, context.clusteringThresh, context.maxResidual, context.maxThreads, context.forceDecliningResidual, monitor);
    runMCL.setDebug(false);
    if (canceled)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Clustering...");
    // results = runMCL.run(monitor);
    List<NodeCluster> clusters = runMCL.run(network, monitor);
    // Canceled?
    if (clusters == null)
        return;
    monitor.showMessage(TaskMonitor.Level.INFO, "Removing groups");
    // Remove any leftover groups from previous runs
    removeGroups(network, GROUP_ATTRIBUTE);
    monitor.showMessage(TaskMonitor.Level.INFO, "Creating groups");
    params = new ArrayList<String>();
    context.edgeAttributeHandler.setParams(params);
    List<List<CyNode>> nodeClusters = createGroups(network, clusters, GROUP_ATTRIBUTE);
    results = new AbstractClusterResults(network, clusters);
    monitor.showMessage(TaskMonitor.Level.INFO, "MCL results:\n" + results);
    if (context.vizProperties.showUI) {
        monitor.showMessage(TaskMonitor.Level.INFO, "Creating network");
        insertTasksAfterCurrentTask(new NewNetworkView(network, clusterManager, true, context.vizProperties.restoreEdges, !context.edgeAttributeHandler.selectedOnly));
    }
}

Example 10 with CyMatrix

use of edu.ucsf.rbvi.clusterMaker2.internal.api.CyMatrix in project clusterMaker2 by RBVI.

the class RunBiMine method getASR.

private double getASR(BETNode<Integer> node) {
    List<Integer> genes = node.getGenes();
    List<Integer> conditions = node.getConditions();
    // Matrix data = new Matrix(network,genes.size(),conditions.size());
    CyMatrix data = CyMatrixFactory.makeSmallMatrix(network, genes.size(), conditions.size());
    for (int i = 0; i < genes.size(); i++) {
        for (int j = 0; j < conditions.size(); j++) {
            data.setValue(i, j, matrix.getValue(genes.get(i), conditions.get(j)));
        // data_t.setValue(j, i, matrix.getValue(genes.get(i), conditions.get(j)));
        }
    }
    double asr = 0.0;
    double asr_g = 0.0;
    double asr_c = 0.0;
    for (int i = 0; i < genes.size(); i++) {
        for (int j = i + 1; j < genes.size(); j++) {
            // asr_g += geneRho[genes.get(i)][genes.get(j)];
            asr_g += getSpearmansRho(data, i, j);
        }
    }
    asr_g /= genes.size() * (genes.size() - 1);
    /*
		for(int i = 0; i < conditions.size(); i++){			
			for(int j = i+1; j < conditions.size(); j++){
				//asr_c += conditionRho[conditions.get(i)][conditions.get(j)];
				asr_c += getSpearmansRho(data_t,i,j);
			}
		}
		asr_c /= conditions.size()*(conditions.size()-1);
		*/
    // asr = 2*Math.max(asr_g, asr_c);
    asr = 2 * asr_g;
    return asr;
}