Examples with HeatMapTableModel org.baderlab.csplugins.enrichmentmap.view.heatmap.table.HeatMapTableModel used on opensource projects

Example 1 with HeatMapTableModel

use of org.baderlab.csplugins.enrichmentmap.view.heatmap.table.HeatMapTableModel in project EnrichmentMapApp by BaderLab.

the class HeatMapMainPanel method addRankings.

private void addRankings() {
    HeatMapTableModel model = (HeatMapTableModel) table.getModel();
    EnrichmentMap map = model.getEnrichmentMap();
    AddRanksDialog dialog = ranksDialogFactory.create(map);
    Optional<String> ranksName = dialog.open();
    if (ranksName.isPresent()) {
        this.moreRankOptions = parent.getMediator().getDataSetRankOptions(map);
    }
}

Example 2 with HeatMapTableModel

use of org.baderlab.csplugins.enrichmentmap.view.heatmap.table.HeatMapTableModel in project EnrichmentMapApp by BaderLab.

the class HeatMapMainPanel method createTableHeader.

private void createTableHeader(int expressionColumnWidth) {
    JTableHeader header = table.getTableHeader();
    header.setReorderingAllowed(false);
    HeatMapTableModel tableModel = (HeatMapTableModel) table.getModel();
    TableColumnModel columnModel = table.getColumnModel();
    TableCellRenderer vertRenderer = new ColumnHeaderVerticalRenderer();
    TableCellRenderer vertRendererPheno1 = new ColumnHeaderVerticalRenderer(EMStyleBuilder.Colors.LIGHTEST_PHENOTYPE_1);
    TableCellRenderer vertRendererPheno2 = new ColumnHeaderVerticalRenderer(EMStyleBuilder.Colors.LIGHTEST_PHENOTYPE_2);
    TableColumn rankColumn = columnModel.getColumn(HeatMapTableModel.RANK_COL);
    rankColumn.setHeaderRenderer(columnHeaderRankOptionRendererFactory.create(this, HeatMapTableModel.RANK_COL));
    rankColumn.setPreferredWidth(100);
    ((TableRowSorter<?>) table.getRowSorter()).setSortable(HeatMapTableModel.RANK_COL, false);
    int colCount = tableModel.getColumnCount();
    for (int col = HeatMapTableModel.DESC_COL_COUNT; col < colCount; col++) {
        EMDataSet dataset = tableModel.getDataSet(col);
        String pheno1 = dataset.getEnrichments().getPhenotype1();
        String pheno2 = dataset.getEnrichments().getPhenotype2();
        Optional<String> pheno = tableModel.getPhenotype(col);
        TableCellRenderer renderer;
        if (pheno.filter(p -> p.equals(pheno1)).isPresent())
            renderer = vertRendererPheno1;
        else if (pheno.filter(p -> p.equals(pheno2)).isPresent())
            renderer = vertRendererPheno2;
        else
            renderer = vertRenderer;
        TableColumn column = columnModel.getColumn(col);
        column.setHeaderRenderer(renderer);
        column.setPreferredWidth(expressionColumnWidth);
    }
}

Example 3 with HeatMapTableModel

use of org.baderlab.csplugins.enrichmentmap.view.heatmap.table.HeatMapTableModel in project EnrichmentMapApp by BaderLab.

the class ExportTXTAction method actionPerformed.

@Override
public void actionPerformed(ActionEvent ae) {
    File file = promptForFile();
    if (file == null)
        return;
    HeatMapTableModel tableModel = (HeatMapTableModel) table.getModel();
    boolean leadingEdgeOnly = promptForLeadingEdgeOnly(tableModel);
    try (BufferedWriter out = new BufferedWriter(new FileWriter(file))) {
        int numCols = tableModel.getColumnCount();
        // Print column headers
        out.append(tableModel.getColumnName(HeatMapTableModel.GENE_COL));
        out.append("\t");
        // Skip the ranks column
        for (int col = HeatMapTableModel.DESC_COL_COUNT; col < numCols; col++) {
            out.append(tableModel.getColumnName(col));
            out.append(col == numCols - 1 ? "\n" : "\t");
        }
        RowSorter<?> sorter = table.getRowSorter();
        int numViewRows = sorter.getViewRowCount();
        // Print table data
        for (int viewRow = 0; viewRow < numViewRows; viewRow++) {
            int modelRow = sorter.convertRowIndexToModel(viewRow);
            if (leadingEdgeOnly && !tableModel.getRankValue(modelRow).isSignificant())
                continue;
            out.append(tableModel.getValueAt(modelRow, HeatMapTableModel.GENE_COL).toString());
            out.append("\t");
            for (int col = HeatMapTableModel.DESC_COL_COUNT; col < numCols; col++) {
                out.append(tableModel.getValueAt(modelRow, col).toString());
                out.append(col == numCols - 1 ? "\n" : "\t");
            }
        }
    } catch (IOException e) {
        JOptionPane.showMessageDialog(jframeProvider.get(), e.getMessage(), "Error writing file", JOptionPane.ERROR_MESSAGE);
        e.printStackTrace();
    }
}

Example 4 with HeatMapTableModel

use of org.baderlab.csplugins.enrichmentmap.view.heatmap.table.HeatMapTableModel in project EnrichmentMapApp by BaderLab.

the class HeatMapMainPanel method updateSetting_RankOption.

public void updateSetting_RankOption(RankingOption rankOption) {
    selectedRankOption = rankOption;
    List<String> genes = getGenes(getOperator());
    HeatMapTableModel tableModel = (HeatMapTableModel) table.getModel();
    EnrichmentMap map = tableModel.getEnrichmentMap();
    List<Integer> geneIds = genes.stream().map(map::getHashFromGene).collect(Collectors.toList());
    CompletableFuture<Optional<Map<Integer, RankValue>>> rankingFuture = rankOption.computeRanking(geneIds);
    if (rankingFuture != null) {
        rankingFuture.whenComplete((ranking, ex) -> {
            if (ranking.isPresent()) {
                tableModel.setRanking(rankOption.getName(), ranking.get());
                table.getColumnModel().getColumn(HeatMapTableModel.RANK_COL).setHeaderValue(rankOption);
            } else {
                tableModel.setRanking(rankOption.getName(), null);
                table.getColumnModel().getColumn(HeatMapTableModel.RANK_COL).setHeaderValue(new RankOptionErrorHeader(rankOption));
            }
            table.getTableHeader().repaint();
        });
    }
    settingChanged();
}

Example 5 with HeatMapTableModel

use of org.baderlab.csplugins.enrichmentmap.view.heatmap.table.HeatMapTableModel in project EnrichmentMapApp by BaderLab.

the class HeatMapMainPanel method reset.

public void reset(EnrichmentMap map, HeatMapParams params, List<RankingOption> moreRankOptions, Set<String> union, Set<String> intersection) {
    isResetting = true;
    this.clusterRankOption = parent.getMediator().getClusterRankOption(map);
    this.moreRankOptions = moreRankOptions.isEmpty() ? Arrays.asList(RankingOption.none()) : moreRankOptions;
    unionGenes = new ArrayList<>(union);
    unionGenes.sort(Comparator.naturalOrder());
    interGenes = new ArrayList<>(intersection);
    interGenes.sort(Comparator.naturalOrder());
    operatorCombo.removeActionListener(operatorActionListener);
    normCombo.removeActionListener(normActionListener);
    showValuesCheck.removeActionListener(showValueActionListener);
    // Update Combo Boxes
    operatorCombo.removeAllItems();
    operatorCombo.addItem(new ComboItem<>(Operator.UNION, "All (" + union.size() + ")"));
    operatorCombo.addItem(new ComboItem<>(Operator.INTERSECTION, "Common (" + intersection.size() + ")"));
    operatorCombo.setSelectedItem(ComboItem.of(params.getOperator()));
    normCombo.setSelectedItem(ComboItem.of(params.getTransform()));
    selectedRankOption = getRankOptionFromParams(params);
    // Update the setings panel
    settingsPanel.update(params);
    showValuesCheck.setSelected(params.isShowValues());
    // Update the Table
    clearTableHeader();
    List<String> genesToUse = params.getOperator() == Operator.UNION ? unionGenes : interGenes;
    List<? extends SortKey> sortKeys = table.getRowSorter().getSortKeys();
    HeatMapTableModel tableModel = new HeatMapTableModel(map, null, genesToUse, params.getTransform());
    table.setModel(tableModel);
    updateSetting_ShowValues(params.isShowValues());
    try {
        table.getRowSorter().setSortKeys(sortKeys);
    } catch (IllegalArgumentException e) {
    }
    // Re-compute the ranking
    updateSetting_RankOption(selectedRankOption);
    operatorCombo.addActionListener(operatorActionListener);
    normCombo.addActionListener(normActionListener);
    showValuesCheck.addActionListener(showValueActionListener);
    isResetting = false;
}