Examples with EMDataSet org.baderlab.csplugins.enrichmentmap.model.EMDataSet used on opensource projects

Example 31 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class ControlPanelMediator method addNetworkView.

@SuppressWarnings("unchecked")
private void addNetworkView(CyNetworkView netView) {
    invokeOnEDT(() -> {
        EnrichmentMap map = emManager.getEnrichmentMap(netView.getModel().getSUID());
        // Is the new view an EnrichmentMap one?
        if (map != null) {
            EMViewControlPanel viewPanel = getControlPanel().addEnrichmentMapView(netView);
            if (viewPanel != null) {
                // Add listeners to the new panel's fields
                viewPanel.getQValueRadio().addActionListener(evt -> {
                    viewPanel.updateFilterPanel();
                    if (!updating)
                        filterNodesAndEdges(viewPanel, map);
                });
                viewPanel.getPValueRadio().addActionListener(evt -> {
                    viewPanel.updateFilterPanel();
                    if (!updating)
                        filterNodesAndEdges(viewPanel, map);
                });
                SliderBarPanel pvSliderPanel = viewPanel.getPValueSliderPanel();
                SliderBarPanel qvSliderPanel = viewPanel.getQValueSliderPanel();
                SliderBarPanel sSliderPanel = viewPanel.getSimilaritySliderPanel();
                if (pvSliderPanel != null)
                    pvSliderPanel.addChangeListener(evt -> {
                        if (!updating)
                            filterNodesAndEdges(viewPanel, map);
                    });
                if (qvSliderPanel != null)
                    qvSliderPanel.addChangeListener(evt -> {
                        if (!updating)
                            filterNodesAndEdges(viewPanel, map);
                    });
                if (sSliderPanel != null)
                    sSliderPanel.addChangeListener(evt -> {
                        if (!updating)
                            filterNodesAndEdges(viewPanel, map);
                    });
                viewPanel.getDataSetSelector().addPropertyChangeListener("checkedData", evt -> {
                    if (!updating) {
                        viewPanel.updateChartDataCombo();
                        filterNodesAndEdges(viewPanel, map);
                        ChartData data = (ChartData) viewPanel.getChartDataCombo().getSelectedItem();
                        Set<EMDataSet> oldDataSets = filterDataSets((Collection<AbstractDataSet>) evt.getOldValue());
                        Set<EMDataSet> newDataSets = filterDataSets((Collection<AbstractDataSet>) evt.getNewValue());
                        int oldSize = oldDataSets.size();
                        int newSize = newDataSets.size();
                        boolean updateStyle = data != null && data != ChartData.NONE && oldSize != newSize;
                        updateStyle = updateStyle || oldSize == 0 && newSize > 0;
                        updateStyle = updateStyle || oldSize > 0 && newSize == 0;
                        updateStyle = updateStyle || oldSize == 1 && newSize > 1;
                        updateStyle = updateStyle || oldSize > 1 && newSize == 1;
                        if (updateStyle)
                            updateVisualStyle(map, viewPanel);
                        else
                            netView.updateView();
                    }
                });
                viewPanel.getDataSetSelector().getAddButton().addActionListener(evt -> {
                    postAnalysisPanelMediatorProvider.get().showDialog(viewPanel, netView);
                });
                viewPanel.getDataSetSelector().getRemoveButton().addActionListener(evt -> {
                    removeSignatureDataSets(map, viewPanel);
                });
                viewPanel.getChartDataCombo().addItemListener(evt -> {
                    if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
                        updating = true;
                        try {
                            viewPanel.updateChartCombos();
                        } finally {
                            updating = false;
                        }
                        updateVisualStyle(map, viewPanel, true);
                    }
                });
                viewPanel.getChartTypeCombo().addItemListener(evt -> {
                    if (!updating && evt.getStateChange() == ItemEvent.SELECTED) {
                        updating = true;
                        try {
                            viewPanel.updateChartColorsCombo();
                            viewPanel.updateChartLabelsCheck();
                        } finally {
                            updating = false;
                        }
                        updateVisualStyle(map, viewPanel, true);
                    }
                });
                viewPanel.getChartColorsCombo().addItemListener(evt -> {
                    if (!updating && evt.getStateChange() == ItemEvent.SELECTED)
                        updateVisualStyle(map, viewPanel, true);
                });
                viewPanel.getShowChartLabelsCheck().addActionListener(evt -> {
                    if (!updating)
                        updateVisualStyle(map, viewPanel, true);
                });
                viewPanel.getPublicationReadyCheck().addActionListener(evt -> {
                    if (!updating)
                        updateVisualStyle(map, viewPanel);
                });
                viewPanel.getResetStyleButton().addActionListener(evt -> {
                    updateVisualStyle(map, viewPanel);
                });
                viewPanel.getSetEdgeWidthButton().addActionListener(evt -> {
                    showEdgeWidthDialog();
                });
                viewPanel.updateChartDataCombo();
            }
        }
    });
}

Example 32 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class HierarchicalClusterTask method cluster.

public Map<Integer, RankValue> cluster(TaskMonitor tm) {
    if (tm == null)
        tm = new NullTaskMonitor();
    tm.setTitle("Hierarchical Cluster");
    tm.setStatusMessage("Loading expression data");
    List<double[]> clusteringExpressionSet = new ArrayList<>(genes.size());
    ArrayList<Integer> labels = new ArrayList<>(genes.size());
    List<String> names = new ArrayList<>(genes.size());
    List<EMDataSet> dataSets = map.getDataSetList();
    final int expressionCount = getTotalExpressionCount(dataSets);
    for (int geneId : genes) {
        // values all default to 0.0
        double[] vals = new double[expressionCount];
        int valsIndex = 0;
        boolean found = false;
        String name = null;
        for (EMDataSet dataSet : dataSets) {
            GeneExpressionMatrix expressionSets = dataSet.getExpressionSets();
            int numConditions = expressionSets.getNumConditions() - 2;
            GeneExpression geneExpression = expressionSets.getExpressionMatrix().get(geneId);
            if (geneExpression != null) {
                found = true;
                name = geneExpression.getName();
                double[] expression = geneExpression.getExpression();
                System.arraycopy(expression, 0, vals, valsIndex, expression.length);
            }
            valsIndex += numConditions;
        }
        if (found) {
            clusteringExpressionSet.add(vals);
            labels.add(geneId);
            names.add(name);
        }
    }
    tm.setStatusMessage("Calculating Distance");
    DistanceMatrix distanceMatrix = new DistanceMatrix(genes.size());
    distanceMatrix.calcDistances(clusteringExpressionSet, distanceMetric);
    distanceMatrix.setLabels(labels);
    tm.setStatusMessage("Clustering");
    AvgLinkHierarchicalClustering clusterResult = new AvgLinkHierarchicalClustering(distanceMatrix);
    //check to see if there more than 1000 genes, if there are use eisen ordering otherwise use bar-joseph
    clusterResult.setOptimalLeafOrdering(genes.size() <= 1000);
    clusterResult.run();
    tm.setStatusMessage("Ranking");
    Map<Integer, RankValue> ranks = new HashMap<>();
    int[] order = clusterResult.getLeafOrder();
    for (int i = 0; i < order.length; i++) {
        Integer geneId = labels.get(order[i]);
        ranks.put(geneId, new RankValue(i + 1, null, false));
    }
    tm.setStatusMessage("");
    return ranks;
}

Example 33 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class ComputeSimilarityTaskParallel method startComputeSimilarities.

private Map<SimilarityKey, GenesetSimilarity> startComputeSimilarities(TaskMonitor tm, ExecutorService executor, boolean distinct, boolean compound) {
    Set<String> names = map.getAllGeneSetOfInterestNames();
    Map<String, Set<Integer>> unionedGenesets = compound ? map.unionAllGeneSetsOfInterest() : null;
    DiscreteTaskMonitor taskMonitor = discreteTaskMonitor(tm, names.size());
    String edgeType = map.getParams().getEnrichmentEdgeType();
    Map<SimilarityKey, GenesetSimilarity> similarities = new ConcurrentHashMap<>();
    Collection<EMDataSet> dataSets = map.getDataSetList();
    for (final String geneset1Name : names) {
        // Compute similarities in batches, creating a Runnable for every similarity pair would create too many objects
        executor.execute(() -> {
            loop: for (final String geneset2Name : names) {
                if (Thread.interrupted())
                    break loop;
                if (geneset1Name.equalsIgnoreCase(geneset2Name))
                    //don't compare two identical gene sets
                    continue;
                if (distinct) {
                    for (EMDataSet dataset : dataSets) {
                        SimilarityKey key = new SimilarityKey(geneset1Name, geneset2Name, edgeType, dataset.getName());
                        if (!similarities.containsKey(key)) {
                            Map<String, GeneSet> genesets = dataset.getGeneSetsOfInterest().getGeneSets();
                            GeneSet geneset1 = genesets.get(geneset1Name);
                            GeneSet geneset2 = genesets.get(geneset2Name);
                            if (geneset1 != null && geneset2 != null) {
                                // returns null if the similarity coefficient doesn't pass the cutoff
                                GenesetSimilarity similarity = computeGenesetSimilarity(map.getParams(), geneset1Name, geneset2Name, geneset1.getGenes(), geneset2.getGenes(), dataset.getName());
                                if (similarity != null) {
                                    similarities.put(key, similarity);
                                }
                            }
                        }
                    }
                }
                if (compound) {
                    SimilarityKey key = new SimilarityKey(geneset1Name, geneset2Name, edgeType, null);
                    if (!similarities.containsKey(key)) {
                        Set<Integer> geneset1 = unionedGenesets.get(geneset1Name);
                        Set<Integer> geneset2 = unionedGenesets.get(geneset2Name);
                        // returns null if the similarity coefficient doesn't pass the cutoff
                        GenesetSimilarity similarity = computeGenesetSimilarity(map.getParams(), geneset1Name, geneset2Name, geneset1, geneset2, "compound");
                        if (similarity != null) {
                            similarities.put(key, similarity);
                        }
                    }
                }
            }
            taskMonitor.inc();
        });
    }
    return similarities;
}

Example 34 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class CreateEMNetworkTask method createNodes.

private Map<String, CyNode> createNodes(CyNetwork network) {
    Map<String, CyNode> nodes = new HashMap<>();
    Map<String, Set<Integer>> geneSets = map.unionAllGeneSetsOfInterest();
    for (String genesetName : geneSets.keySet()) {
        CyNode node = network.addNode();
        nodes.put(genesetName, node);
        // Set common attributes
        CyRow row = network.getRow(node);
        row.set(CyNetwork.NAME, genesetName);
        Columns.NODE_FORMATTED_NAME.set(row, prefix, null, formatLabel(genesetName));
        // MKTODO why is this column needed?
        Columns.NODE_NAME.set(row, prefix, null, genesetName);
        Columns.NODE_GS_DESCR.set(row, prefix, null, map.findGeneSetDescription(genesetName));
        Columns.NODE_GS_TYPE.set(row, prefix, null, Columns.NODE_GS_TYPE_ENRICHMENT);
        Set<Integer> geneIds = geneSets.get(genesetName);
        List<String> genes = geneIds.stream().map(map::getGeneFromHashKey).collect(Collectors.toList());
        Columns.NODE_GENES.set(row, prefix, null, genes);
        Columns.NODE_GS_SIZE.set(row, prefix, null, genes.size());
        // Set attributes specific to each dataset
        for (EMDataSet ds : map.getDataSetList()) {
            if (ds.getGeneSetsOfInterest().getGeneSets().containsKey(genesetName))
                ds.addNodeSuid(node.getSUID());
            Map<String, EnrichmentResult> enrichmentResults = ds.getEnrichments().getEnrichments();
            EnrichmentResult result = enrichmentResults.get(genesetName);
            // if result is null it will fail both instanceof checks
            if (result instanceof GSEAResult)
                setGSEAResultNodeAttributes(row, ds.getName(), (GSEAResult) result);
            else if (result instanceof GenericResult)
                setGenericResultNodeAttributes(row, ds.getName(), (GenericResult) result);
        }
    }
    return nodes;
}

Example 35 with EMDataSet

use of org.baderlab.csplugins.enrichmentmap.model.EMDataSet in project EnrichmentMapApp by BaderLab.

the class CreateDiseaseSignatureTaskFactory method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    // Make sure that the minimum information is set in the current set of parameters
    EnrichmentMap map = emManager.getEnrichmentMap(netView.getModel().getSUID());
    StringBuilder errorBuilder = new StringBuilder();
    checkMinimalRequirements(errorBuilder, params);
    if (params.getRankTestParameters().getType().isMannWhitney() && map.getAllRanks().isEmpty())
        errorBuilder.append("Mann-Whitney requires ranks. \n");
    this.errors = errorBuilder.toString();
    if (errors.isEmpty()) {
        ControlPanelMediator controlPanelMediator = controlPanelMediatorProvider.get();
        EMStyleOptions options = controlPanelMediator.createStyleOptions(netView);
        CyCustomGraphics2<?> chart = controlPanelMediator.createChart(options);
        List<EMDataSet> dataSetList = getDataSets(map);
        TaskIterator tasks = new TaskIterator();
        tasks.append(signatureTaskFactory.create(params, map, dataSetList));
        tasks.append(applyStyleTaskFactory.create(options, chart, false));
        return tasks;
    } else {
        // MKTODO not entirely sure what to do in this case, just return an empty iterator I guess...
        return new TaskIterator(new AbstractTask() {

            @Override
            public void run(TaskMonitor taskMonitor) throws Exception {
                throw new RuntimeException(errors);
            }
        });
    }
}