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

Example 21 with CyMatrix

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

the class RunPCA method calculateLoadingMatrix.

private Matrix calculateLoadingMatrix(CyMatrix matrix) {
    int rows = eigenVectors.length;
    int columns = eigenVectors[0].length;
    Matrix loading = CyMatrixFactory.makeSmallMatrix(matrix.getNetwork(), rows, columns);
    // loading.initialize(rows, columns, new double[rows][columns]);
    IntStream.range(0, rows).parallel().forEach(row -> {
        for (int column = columns - 1, newCol = 0; column >= 0; column--, newCol++) {
            loading.setValue(row, newCol, eigenVectors[row][column] * Math.sqrt(Math.abs(eigenValues[column])));
        }
    });
    loading.setRowLabels(Arrays.asList(matrix.getColumnLabels()));
    for (int column = 0; column < columns; column++) {
        loading.setColumnLabel(column, "PC " + (column + 1));
    }
    return loading;
}

Example 22 with CyMatrix

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

the class PCoA method run.

public void run(TaskMonitor monitor) {
    monitor.setTitle("Running Principal Coordinate Analysis");
    this.monitor = monitor;
    long start = System.currentTimeMillis();
    if (network == null)
        network = clusterManager.getNetwork();
    context.setNetwork(network);
    CyMatrix matrix = context.edgeAttributeHandler.getMatrix();
    if (matrix == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't get distance matrix: no attribute value?");
        return;
    }
    if (canceled)
        return;
    PCoAContext.NegEigenHandling neg = context.neg.getSelectedValue();
    // Cluster the nodes
    runpcoa = new RunPCoA(manager, matrix, network, networkView, context, neg.getValue(), monitor);
    runpcoa.run();
    if (canceled)
        return;
    long duration = System.currentTimeMillis() - start;
    monitor.showMessage(TaskMonitor.Level.INFO, "PCoA completed in " + duration + "ms");
}

Example 23 with CyMatrix

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

the class ResultPanelPCA method valueChanged.

public void valueChanged(ListSelectionEvent e) {
    ListSelectionModel lsm = (ListSelectionModel) e.getSource();
    // Get the rows
    int[] rowIndices = table.getSelectedRows();
    Map<CyNode, CyNode> selectedMap = new HashMap<CyNode, CyNode>();
    double threshold = 0.02;
    // Get the clusters
    for (int index = 0; index < rowIndices.length; index++) {
        int row = rowIndices[index];
        CyMatrix matrix = components[row];
        for (int i = 0; i < matrix.nRows(); i++) {
            for (int j = 0; j < matrix.nColumns(); j++) {
                if (matrix.getValue(i, j) > threshold) {
                    CyNode node = matrix.getRowNode(i);
                    selectedMap.put(node, node);
                    break;
                }
            }
        }
    // System.out.println("PC is selected");
    }
    // Select the nodes
    for (CyNode node : network.getNodeList()) {
        if (selectedMap.containsKey(node))
            network.getRow(node).set(CyNetwork.SELECTED, true);
        else
            network.getRow(node).set(CyNetwork.SELECTED, false);
    }
    // I wish we didn't need to do this, but if we don't, the selection
    // doesn't update
    networkView.updateView();
}

Example 24 with CyMatrix

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

the class BicFinder method run.

public void run(TaskMonitor monitor) {
    this.monitor = monitor;
    monitor.setTitle("Performing " + getName());
    List<String> nodeAttributeList = context.attributeList.getNodeAttributeList();
    String edgeAttribute = context.attributeList.getEdgeAttribute();
    clusterAttributeName = "BicFinder_Bicluster";
    if (network.getRow(network, CyNetwork.LOCAL_ATTRS).getTable().getColumn(ClusterManager.CLUSTER_ATTRIBUTE) == null) {
        network.getRow(network, CyNetwork.LOCAL_ATTRS).getTable().createColumn(ClusterManager.CLUSTER_ATTRIBUTE, String.class, false);
    }
    network.getRow(network, CyNetwork.LOCAL_ATTRS).set(ClusterManager.CLUSTER_ATTRIBUTE, clusterAttributeName);
    if (nodeAttributeList == null && edgeAttribute == null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must select either one edge column or two or more node columns");
        return;
    }
    if (nodeAttributeList != null && nodeAttributeList.size() > 0 && edgeAttribute != null) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Can't have both node and edge columns selected");
        return;
    }
    if (context.selectedOnly && CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, true).size() < 3) {
        monitor.showMessage(TaskMonitor.Level.ERROR, "Must have at least three nodes to cluster");
        return;
    }
    createGroups = context.createGroups;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        // To make debugging easier, sort the attribute list
        Collections.sort(nodeAttributeList);
    }
    // Get our attributes we're going to use for the cluster
    String[] attributeArray;
    if (nodeAttributeList != null && nodeAttributeList.size() > 0) {
        attributeArray = new String[nodeAttributeList.size()];
        int i = 0;
        for (String attr : nodeAttributeList) {
            attributeArray[i++] = "node." + attr;
        }
    } else {
        attributeArray = new String[1];
        attributeArray[0] = "edge." + edgeAttribute;
    }
    monitor.setStatusMessage("Initializing");
    resetAttributes(network, SHORTNAME);
    // Create a new clusterer
    RunBicFinder algorithm = new RunBicFinder(network, attributeArray, monitor, context);
    String resultsString = "BicFinder results:";
    // Cluster the nodes
    monitor.setStatusMessage("Clustering nodes");
    Integer[] rowOrder = algorithm.cluster(false);
    CyMatrix biclusterMatrix = algorithm.getBiclusterMatrix();
    int[] clusters = new int[biclusterMatrix.nRows()];
    createBiclusterGroups(algorithm.getClusterNodes());
    // createGroups(network,biclusterMatrix,1, clusters, "bicfinder");
    updateAttributes(network, SHORTNAME, rowOrder, attributeArray, getAttributeList(), algorithm.getBiclusterMatrix());
    createBiclusterTable(algorithm.getClusterNodes(), algorithm.getClusterAttrs());
    // System.out.println(resultsString);
    if (context.showUI) {
        insertTasksAfterCurrentTask(new BiclusterView(clusterManager));
    }
}

Example 25 with CyMatrix

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

the class RunBicFinder method getASR.

private double getASR(List<Integer> genes, List<Integer> conditions) {
    CyMatrix data = CyMatrixFactory.makeSmallMatrix(network, genes.size(), conditions.size());
    // Matrix data_t = new Matrix(network,conditions.size(),genes.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 += getSpearmansRho(data, i, j);
        }
    }
    asr_g /= genes.size() * (genes.size() - 1);
    /*
		for(int i = 0; i < genes.size(); i++){
			for(int j = i+1; j < genes.size(); j++){
				asr_c += conditionRho[conditions.get(i)][conditions.get(j)];
			}
		}
		asr_c /= conditions.size()*(conditions.size()-1);

		asr = 2*Math.max(asr_g, asr_c);
		*/
    asr = 2 * asr_g;
    return asr;
}