List of usage examples for org.jfree.chart.axis CategoryAxis CategoryAxis
public CategoryAxis()
From source file:weka.core.ChartUtils.java
/** * Create a box plot from summary data (mean, median, q1, q3, min, max, * minOutlier, maxOutlier, list of outliers) * /*from w ww . ja va2 s.c o m*/ * @param summary summary data * @param outliers list of outlier values * @param additionalArgs additional options to the renderer * @return a box plot chart * @throws Exception if a problem occurs */ protected static JFreeChart getBoxPlotFromSummaryData(List<Double> summary, List<Double> outliers, List<String> additionalArgs) throws Exception { if (summary.size() != 8) { throw new Exception("Expected 8 values in the summary argument: mean, median, " + "q1, q3, min, max, minOutlier, maxOutlier"); } String plotTitle = "Box Plog"; String userTitle = getOption(additionalArgs, "-title"); plotTitle = (userTitle != null) ? userTitle : plotTitle; String xLabel = getOption(additionalArgs, "-x-label"); xLabel = xLabel == null ? "" : xLabel; String yLabel = getOption(additionalArgs, "-y-label"); yLabel = yLabel == null ? "" : yLabel; DefaultBoxAndWhiskerCategoryDataset dataset = new DefaultBoxAndWhiskerCategoryDataset(); Double mean = summary.get(0); Double median = summary.get(1); Double q1 = summary.get(2); Double q3 = summary.get(3); Double min = summary.get(4); Double max = summary.get(5); Double minOutlier = summary.get(6); Double maxOutlier = summary.get(7); if (mean.isNaN() || median.isNaN() || min.isNaN() || max.isNaN() || q1.isNaN() || q3.isNaN()) { throw new Exception("NaN in summary data - can't generate box plot"); } BoxAndWhiskerItem item = new BoxAndWhiskerItem(mean, median, q1, q3, min, max, minOutlier, maxOutlier, outliers); dataset.add(item, "", ""); CategoryAxis xAxis = new CategoryAxis(); NumberAxis yAxis = new NumberAxis(); yAxis.setAutoRangeIncludesZero(false); BoxAndWhiskerRenderer renderer = new BoxAndWhiskerRenderer(); renderer.setFillBox(false); renderer.setMaximumBarWidth(0.15); CategoryPlot plot = new CategoryPlot(dataset, xAxis, yAxis, renderer); JFreeChart chart = new JFreeChart(plotTitle, new Font("SansSerif", Font.BOLD, 12), plot, false); return chart; }
From source file:org.jax.pubarray.server.restful.GraphingResource.java
/** * Create a graph for the given configuration * @param graphConfiguration//from w w w . ja v a 2 s. com * the key * @return * the graph */ @SuppressWarnings("unchecked") private JFreeChart createProbeIntensityGraph(ProbeIntensityGraphConfiguration graphConfiguration) { try { Connection connection = this.getConnection(); String[] probeIds = graphConfiguration.getProbeIds(); double[][] probeDataRows = new double[probeIds.length][]; for (int i = 0; i < probeIds.length; i++) { probeDataRows[i] = this.persistenceManager.getDataRowForProbeID(connection, probeIds[i]); } TableColumnMetadata orderBy = graphConfiguration.getOrderProbesBy(); final List<Comparable> orderByItems; if (orderBy != null) { LOG.info("We are ordering by: " + orderBy); orderByItems = this.persistenceManager.getDesignDataColumn(connection, orderBy); } else { orderByItems = null; } TableMetadata metadata = this.persistenceManager.getDataTableMetadata(connection); final CategoryDataset categoryDataset; if (graphConfiguration.getGroupReplicates()) { switch (graphConfiguration.getGroupedGraphType()) { case BOX_PLOT: { categoryDataset = new DefaultBoxAndWhiskerCategoryDataset(); } break; case SCATTER_PLOT: { categoryDataset = new DefaultMultiValueCategoryDataset(); } break; default: throw new IllegalArgumentException( "don't know how to deal with plot type: " + graphConfiguration.getGroupedGraphType()); } } else { categoryDataset = new DefaultCategoryDataset(); } // iterate through all of the selected probesets List<QualifiedColumnMetadata> termsOfInterest = Arrays.asList(graphConfiguration.getTermsOfInterest()); for (int rowIndex = 0; rowIndex < probeDataRows.length; rowIndex++) { double[] currRow = probeDataRows[rowIndex]; assert currRow.length == metadata.getColumnMetadata().length - 1; // should we log2 transform the data? if (graphConfiguration.getLog2TransformData()) { for (int i = 0; i < currRow.length; i++) { currRow[i] = Math.log(currRow[i]) / LOG2_FACTOR; } } // iterate through the columns in the data table (each column // represents a different array) List<ComparableContainer<Double, Comparable>> rowElemList = new ArrayList<ComparableContainer<Double, Comparable>>(); for (int colIndex = 0; colIndex < currRow.length; colIndex++) { // we use +1 indexing here because we want to skip over // the probesetId metadata and get right to the // array intensity metadata TableColumnMetadata colMeta = metadata.getColumnMetadata()[colIndex + 1]; // check to see if we need to skip this data if (!graphConfiguration.getIncludeDataFromAllArrays()) { // if it's one of the "terms of interest" we will keep // it. we're using a brute force search here boolean keepThisOne = false; for (QualifiedColumnMetadata termOfInterest : termsOfInterest) { if (termOfInterest.getTableName().equals(metadata.getTableName()) && termOfInterest.getName().equals(colMeta.getName())) { keepThisOne = true; break; } } if (!keepThisOne) { continue; } } final String columnName = colMeta.getName(); final Comparable columnKey; if (orderByItems == null) { columnKey = columnName; } else { // the ordering will be done on the selected // "order by" design criteria columnKey = new ComparableContainer<String, Comparable>(columnName, orderByItems.get(colIndex), !graphConfiguration.getGroupReplicates()); // TODO remove me!!!! System.out.println("For array " + columnName + " the order by " + "value is: " + orderByItems.get(colIndex)); // end of remove me } rowElemList .add(new ComparableContainer<Double, Comparable>(currRow[colIndex], columnKey, false)); } Collections.sort(rowElemList); if (graphConfiguration.getGroupReplicates()) { switch (graphConfiguration.getGroupedGraphType()) { case BOX_PLOT: { DefaultBoxAndWhiskerCategoryDataset dataset = (DefaultBoxAndWhiskerCategoryDataset) categoryDataset; for (int i = 0; i < rowElemList.size(); i++) { List<Double> groupList = new ArrayList<Double>(); groupList.add(rowElemList.get(i).getElement()); Comparable colKey = rowElemList.get(i).getComparable(); i++; for (; i < rowElemList.size() && rowElemList.get(i).getComparable().equals(colKey); i++) { groupList.add(rowElemList.get(i).getElement()); } i--; dataset.add(groupList, probeIds[rowIndex], colKey); } } break; case SCATTER_PLOT: { DefaultMultiValueCategoryDataset dataset = (DefaultMultiValueCategoryDataset) categoryDataset; for (int i = 0; i < rowElemList.size(); i++) { List<Double> groupList = new ArrayList<Double>(); groupList.add(rowElemList.get(i).getElement()); Comparable colKey = rowElemList.get(i).getComparable(); i++; for (; i < rowElemList.size() && rowElemList.get(i).getComparable().equals(colKey); i++) { groupList.add(rowElemList.get(i).getElement()); } i--; dataset.add(groupList, probeIds[rowIndex], colKey); } } break; } } else { DefaultCategoryDataset dataset = (DefaultCategoryDataset) categoryDataset; for (ComparableContainer<Double, Comparable> rowElem : rowElemList) { dataset.addValue(rowElem.getElement(), probeIds[rowIndex], rowElem.getComparable()); } } } CategoryAxis xAxis = new CategoryAxis(); if (graphConfiguration.getGroupReplicates() && orderBy != null) { xAxis.setLabel(orderBy.getName()); } else { if (orderBy != null) { xAxis.setLabel("Arrays (Ordered By " + orderBy.getName() + ")"); } else { xAxis.setLabel("Arrays"); } } xAxis.setCategoryLabelPositions(CategoryLabelPositions.UP_90); final NumberAxis yAxis; if (graphConfiguration.getLog2TransformData()) { yAxis = new NumberAxis("log2(Intensity)"); } else { yAxis = new NumberAxis("Intensity"); } yAxis.setAutoRange(true); yAxis.setAutoRangeIncludesZero(false); // TODO: this is a HACK to deal with auto-range bug in JFreeChart // which occurs when doing the grouped scatter plot if (graphConfiguration.getGroupReplicates() && graphConfiguration.getGroupedGraphType() == GroupedGraphType.SCATTER_PLOT) { double minVal = Double.POSITIVE_INFINITY; double maxVal = Double.NEGATIVE_INFINITY; for (double[] dataRow : probeDataRows) { for (double datum : dataRow) { if (datum > maxVal) { maxVal = datum; } if (datum < minVal) { minVal = datum; } } if (minVal != Double.POSITIVE_INFINITY && maxVal != Double.NEGATIVE_INFINITY && minVal != maxVal) { yAxis.setAutoRange(false); double margin = (maxVal - minVal) * 0.02; Range yRange = new Range(minVal - margin, maxVal + margin); yAxis.setRange(yRange); } } } // END HACK final CategoryItemRenderer renderer; if (graphConfiguration.getGroupReplicates()) { switch (graphConfiguration.getGroupedGraphType()) { case BOX_PLOT: { BoxAndWhiskerRenderer boxRenderer = new BoxAndWhiskerRenderer(); boxRenderer.setMaximumBarWidth(0.03); renderer = boxRenderer; } break; case SCATTER_PLOT: { renderer = new ScatterRenderer(); } break; default: throw new IllegalArgumentException( "don't know how to deal with plot type: " + graphConfiguration.getGroupedGraphType()); } } else { renderer = new LineAndShapeRenderer(); } Plot plot = new CategoryPlot(categoryDataset, xAxis, yAxis, renderer); return new JFreeChart("Intensity Values", plot); } catch (SQLException ex) { LOG.log(Level.SEVERE, "failed to generate image", ex); return null; } }