Create_Boxplot.bsh

/* Create_Boxplot.bsh
 * IJ BAR: https://github.com/tferr/Scripts#scripts
 *
 * Displays a box-and-whisker plot from data in the IJ Results table using BAR and the
 * JFreeChart library, bundled with Fiji. The displayed plot is highly customized to
 * exemplify JFreeChart[1] scripting and how to integrate JFreeChart graphs in ImageJ.
 * It also exemplifies how to use BAR to export JFreeCharts as vector graphics.
 *
 * NB: Data can be split into series. In addition to Minimum--[Q1|Median|Q3]--Maximum
 * and Average (filled ellipses), other properties are also plotted, as per [2]:
 *   - Outliers (presence highlighted by open ellipses), values outside the 'regular
 *     range' defined as:
 *         Q1 - 2.0*IQR > Lower Outliers < Q1 - 1.5*IQR
 *         Q3 + 1.5*IQR > Higher Outliers < Q3 + 2.0*IQR
 *   - Far-outs (presence highlighted by open triangles), extreme values defined as:
 *         Lower Far-outs < Q1 - 2.0*IQR
 *         Upper Far-outs > Q3 + 2.0*IQR
 *
 * [1] http://www.jfree.org/jfreechart/api/javadoc/
 * [2] http://www.jfree.org/jfreechart/api/javadoc/src-html/org/jfree/data/statistics/BoxAndWhiskerCalculator.html
 *
 * Tiago Ferreira, v1.0.0 2015.08.12
 * //TODO: NB The copy command in contextual menu raises a java.io.IOException in Mac OS
 */

import bar.Utils;
import bar.PlotUtils;
import ij.IJ;
import ij.WindowManager;
import ij.gui.GenericDialog;
import ij.measure.ResultsTable;
import ij.plugin.frame.PlugInFrame;
import org.jfree.chart.ChartFactory;
import org.jfree.chart.ChartPanel;
import org.jfree.chart.plot.PlotOrientation;
import org.jfree.data.statistics.DefaultBoxAndWhiskerCategoryDataset;
import java.util.Arrays;
import java.util.ArrayList;
import java.util.HashSet;


/** Prompts user to specify which ResultsTable columns to use as input */
boolean setupDataset(ResultsTable rt) {
	if (rt==null)
		return false;

	// Extract column headings w/ numeric data (ignore "Label" column, if present)
	headings = rt.getHeadings();
	numIdx = (rt.getLabel(0)!=null || headings[0].equals("Label")) ? 1 : 0;
	numHeadings = Arrays.copyOfRange(headings, numIdx, headings.length);
	numItems = headings.length - numIdx;
	numChoices = new boolean[numItems];

	gd = new GenericDialog("Boxplot Builder");
	cols = (numItems<6) ? 1 : 3;
	rows = (numItems%cols>0) ? numItems/cols+1 : numItems/cols;
	gd.addCheckboxGroup(rows, cols, numHeadings, numChoices, new String[]{"Measurements:"});
	gd.setInsets(0, 0, 20);
	gd.addCheckbox("Plot_all (Select all measurements)", false);
	seriesList = new ArrayList(Arrays.asList(headings));
	seriesList.add(0, "*None*");
	gd.addChoice("Group data by:", seriesList.toArray(new String[numItems+1]), null);
	gd.addHelp("https://github.com/tferr/Scripts/tree/master/Data_Analysis#create-boxplot");
	gd.showDialog();
	if (gd.wasCanceled())
		return false;
	IJ.showStatus("Building Plot...");

	// Retrieve options from prompt
	for (i=0; i<numItems; i++)
		numChoices[i] = gd.getNextBoolean();
	plotAll = gd.getNextBoolean();
	super.sColumn = seriesList.get(gd.getNextChoiceIndex());

	// Specify categories. "Label" column is not taken into account
	for (i=0; i<numItems; i++)
		if (numChoices[i] || plotAll)
			super.categories.add(numHeadings[i]);

	// Determine if data has to be split and specify series. The "Label" columnn (first
	// non-numeric column in ResultsTable) is special because it is accessed using
	// dedicated methods even when its heading has been renamed (at least with IJ1.45a)
	super.singleSeries = super.sColumn.equals("*None*");
	super.sColIsLabel = !super.singleSeries &&
		(super.sColumn.equals("Label") || rt.getColumnIndex(super.sColumn)==rt.COLUMN_NOT_FOUND);
	if (super.singleSeries)
		super.series.add("");
	else if (super.sColIsLabel) {
		for (i=0; i<rt.getCounter(); i++)
			super.series.add(rt.getLabel(i));
	} else for (i=0; i<rt.getCounter(); i++)
		super.series.add(rt.getStringValue(super.sColumn, i));

	return true;
}

/** Assesses if the specified row of <tt>sColumn</tt> equals the specified string */
boolean rowMatches(int row, String s) {
	if (super.singleSeries)
		return true;
	else if (super.sColIsLabel)
		return super.rt.getLabel(row).equals(s);
	else
		return super.rt.getStringValue(super.sColumn, row).equals(s);
}


ArrayList categories = new ArrayList();	// Holds categories list
HashSet series = new HashSet();	// Holds series list (unique items)
String sColumn = "Label";		// Heading of column defining groups (series)
boolean sColIsLabel = true;		// Flag tracking if sColumn is the "Label" column
boolean singleSeries = false;	// Flag tracking if multiple groups (series) exist
PlugInFrame frame;				// Frame displaying the analysis
String TITLE = "Box Plot";		// Frame title

// Retrieve valid data from the Results table
rt = Utils.getResultsTable();

// Prepare dataset: Specify categories and series
if (!setupDataset(rt))
	return;
dataset = new DefaultBoxAndWhiskerCategoryDataset();

// Assemble dataset: Populate lists
n = rt.getCounter();
for (s : series) {
	for (c : categories) {
		values = new ArrayList();
		for (row=0; row<n; row++)
			if (rowMatches(row, s))
				values.add(rt.getValue(c, row));
		dataset.add(values, s, c);
	}
}

// Create JFreeChart. Analysis is now complete
chart = ChartFactory.createBoxAndWhiskerChart(
	null, // chart title
	null, // Category axis label
	null, // Numeric axis label
	dataset, // The BoxAndWhiskerCategoryDataset
	!singleSeries // Flag controlling legend display
);

// Tweak: Register frame in WindowManager and reuse it as needed
if (WindowManager.getWindow(TITLE) == null) {
	frame = new PlugInFrame(TITLE);
	WindowManager.addWindow(frame);
} else {
	frame = WindowManager.getFrame(TITLE);
	frame.removeAll();
}

// Tweak: Render plot mimicking look and feel of ij.gui.Plot
plot = chart.getPlot();
renderer = plot.getRenderer();
plot.setBackgroundPaint(java.awt.Color.WHITE);
plot.setRangeGridlinePaint(java.awt.Color.LIGHT_GRAY);
plot.setOutlineVisible(false);
renderer.setUseOutlinePaintForWhiskers(true);
renderer.setMaximumBarWidth(0.40);
if (singleSeries)
	renderer.setSeriesPaint(0, Color.LIGHT_GRAY);
if (chart.getLegend()!=null)
	chart.getLegend().setFrame(org.jfree.chart.block.BlockBorder.NONE);

// Tweak: Resize ChartPanel. Tilt to landscape when plotting large datasets
cp = new ChartPanel(chart);
nItems = series.size() * categories.size();
width = Math.min(100 + nItems * 50, 600);
height = width * 4 / 3;
if (nItems>10) {
	plot.setOrientation(PlotOrientation.HORIZONTAL);
	cp.setPreferredSize(new java.awt.Dimension(height, width));
} else
	cp.setPreferredSize(new java.awt.Dimension(width, height));

// Tweak: Ensure chart is always drawn and not scaled to avoid rendering artifacts
cp.setMinimumDrawWidth(0);
cp.setMaximumDrawWidth(Integer.MAX_VALUE);
cp.setMinimumDrawHeight(0);
cp.setMaximumDrawHeight(Integer.MAX_VALUE);

// Tweak: Make JTooltips displaying computed data less transient
cp.setDismissDelay(5 * cp.getDismissDelay());

// Tweak: Support mouse wheel and provide feedback in IJ while navigating ChartPanel
cp.setMouseWheelEnabled(true);
cp.addMouseMotionListener(new MouseAdapter() {
	public void mouseMoved(MouseEvent me) {
		p = me.getPoint();
		plotArea = cp.getScreenDataArea();
		sPos = (plot.getOrientation()==PlotOrientation.VERTICAL) ? p.getY() : p.getX();
		pPos = plot.getRangeAxis().java2DToValue(sPos, plotArea, plot.getRangeAxisEdge());
		IJ.showStatus(IJ.d2s(pPos,3) +"... Mouse over datasets for details | Right-click for options...");
	}
});

// Tweak: Add right-click options for SVG and PDF export
menu = cp.getPopupMenu();
menu.addSeparator();
mi = new JMenuItem("Export as PDF...");
mi.addActionListener(new ActionListener() {
	public void actionPerformed(ActionEvent e) {
		PlotUtils.exportChartAsPDF(chart, cp.getBounds());
	}
});
menu.add(mi);
mi = new JMenuItem("Export as SVG...");
mi.addActionListener(new ActionListener() {
	public void actionPerformed(ActionEvent e) {
		PlotUtils.exportChartAsSVG(chart, cp.getBounds());
	}
});
menu.add(mi);

// Display analysis
frame.add(cp);
frame.pack();
ij.gui.GUI.center(frame);
frame.setVisible(true);