Heatmap trace (#66)

src/cli/Figure_Generation/ThreeColorHeatMapCLI.java

@@ -76,7 +76,7 @@ static class MaxGroup {
 	@Option(names = {"-0", "--include-zeros"}, description = "used with `-p` flag, indicating exclusion of zero values when calculating percentile thresholds")
 	private boolean includeZeros = false;
 
-	@ArgGroup(multiplicity = "0..1", heading = "%nSelect heatmap colors:%n")
+	@ArgGroup(multiplicity = "0..1", exclusive=false, heading = "%nSelect heatmap colors:%n")
 	private ColorGroup color = new ColorGroup();
 	static class ColorGroup {
 		@Option(names = {"-cn", "--color-min"}, description = "Color indicating minimum values (default=YELLOW) For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
@@ -88,7 +88,20 @@ static class ColorGroup {
 		@Option(names = {"-ca", "--color-nan"}, description = "Color indicating not-a-number values (default=GRAY) For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
 		private String nan = null;
 	}
-
+
+	@ArgGroup(multiplicity = "0..1", exclusive=false, heading = "%nSelect transparency of heatmap colors (alpha channel):%n")
+	private AlphaGroup alpha = new AlphaGroup();
+	static class AlphaGroup {
+		@Option(names = {"-tn", "--transparent-min"}, description = "Value indicating transparency of minimum values, 0 to 255 (default=255)\n")
+		private int min = 255;
+		@Option(names = {"-td", "--transparent-mid"}, description = "Value indicating transparency of middle values, 0 to 255  (default=255)\n")
+		private int mid = 255;
+		@Option(names = {"-tx", "--transparent-max"}, description = "Value indicating transparency of maximum values, 0 to 255  (default=255)\n")
+		private int max = 255;
+		@Option(names = {"-ta", "--transparent-nan"}, description = "Value indicating transparency of not-a-number values, 0 to 255  (default=255)\n")
+		private int nan = 255;
+	}
+
 	String scaleType = "treeview";
 	//Colors from JavaTreeview microarray software
 	Color CMAX = new Color(254,255,0,255);
@@ -217,6 +230,16 @@ private String validateInput() throws IOException {
 			System.err.println("Decoding NaN color: 0x" + color.nan);
 			CNAN = Color.decode("0x" + color.nan);
 		}
+		// check that Alpha channel/transparency values are formatted properly and decode/assign colors
+		if (alpha.max<0 || alpha.max>255) { r += "(!)Alpha/transparency value for higher values (max) must be a numeric 0 to 255\n"; }
+		else { CMAX = new Color(CMAX.getRed(), CMAX.getGreen(), CMAX.getBlue(), alpha.max); }
+		if (alpha.mid<0 || alpha.mid>255) { r += "(!)Alpha/transparency value for middling values (mid) must be a numeric 0 to 255\n"; }
+		else { CMID = new Color(CMID.getRed(), CMID.getGreen(), CMID.getBlue(), alpha.mid); }
+		if (alpha.min<0 || alpha.min>255) { r += "(!)Alpha/transparency value for lower values(min) must be a numeric 0 to 255\n"; }
+		else { CMIN = new Color(CMIN.getRed(), CMIN.getGreen(), CMIN.getBlue(), alpha.min); }
+		if (alpha.nan<0 || alpha.nan>255) { r += "(!)Alpha/transparency value for invalid/non-numeric values(NaN) must be a numeric 0 to 255\n"; }
+		else { CNAN = new Color(CNAN.getRed(), CNAN.getGreen(), CNAN.getBlue(), alpha.nan); }
+
 		// assign vals for contrast thresholds and set bools
 		if(maxGroup.percentile!=null) {
 			MAX = maxGroup.percentile;

src/cli/Figure_Generation/TwoColorHeatMapCLI.java

@@ -56,7 +56,6 @@ public class TwoColorHeatMapCLI implements Callable<Integer> {
 
 	@ArgGroup(exclusive = true, multiplicity = "0..1", heading = "%nSelect heatmap color:%n\t@|fg(red) (select no more than one of these options)|@%n")
 	private ColorGroup color = new ColorGroup();
-
 	static class ColorGroup {
 		@Option(names = { "--black" }, description = "Use the color black for generating the heatmap (default)")
 		private boolean black = false;
@@ -68,6 +67,12 @@ static class ColorGroup {
 				"--color" }, description = "For custom color: type hexadecimal string to represent colors (e.g. \"FF0000\" is hexadecimal for red).\n See <http://www.javascripter.net/faq/rgbtohex.htm> for some color options with their corresponding hex strings.\n")
 		private String custom = null;
 	}
+	@Option(names = { "-t", "--transparent" }, description = "Value indicating transparency of heatmap, 0 to 255  (default=255)\n")
+	private int alpha = 255;
+
+	@Option(names = { "-b", "--background" }, description = "Set a transparent background for the heatmap minimum values (default=white)\n")
+	private boolean transparentBackground = false;
+
 
 	String scaleType = "treeview";
 	Color MAXCOLOR = Color.BLACK;
@@ -84,7 +89,7 @@ public Integer call() throws Exception {
 
 		// Generate HeatMap
 		TwoColorHeatMap script_object = new TwoColorHeatMap(CDT, MAXCOLOR, startROW, startCOL, pixelHeight, pixelWidth,
-				scaleType, absolute, percentile, output, true);
+				scaleType, absolute, percentile, output, true, transparentBackground);
 		script_object.run();
 
 		System.err.println("Image Generated.");
@@ -108,26 +113,12 @@ private String validateInput() throws IOException {
 			r += "(!)CDT file does not exist: " + CDT.getName() + "\n";
 			return (r);
 		}
-		// check input extensions
-		if (!"cdt".equals(ExtensionFileFilter.getExtension(CDT))) {
-			r += "(!)Is this a CDT file? Check extension: " + CDT.getName() + "\n";
-		}
 		// set default output filename
 		if (output == null) {
 			String NAME = ExtensionFileFilter.stripExtension(CDT);
 			output = new File(NAME + "_" + scaleType + ".png");
 			// check output filename is valid
 		} else {
-			// check ext
-			try {
-				if (!"png".equals(ExtensionFileFilter.getExtension(output))) {
-					r += "(!)Use PNG extension for output filename. Try: " + ExtensionFileFilter.stripExtension(output)
-							+ ".png\n";
-				}
-			} catch (NullPointerException e) {
-				r += "(!)Output filename must have extension: use PNG extension for output filename. Try: " + output
-						+ ".png\n";
-			}
 			// check directory
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");
@@ -140,14 +131,7 @@ private String validateInput() throws IOException {
 		if (compression < 1 || compression > 4) {
 			r += "(!)Compression must be integer 1-4. Please select from the available compression types.";
 		}
-		// check that hex string is formatted properly
-		if (color.custom != null) {
-			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
-			Matcher m = hexColorPat.matcher(color.custom);
-			if (!m.matches()) {
-				r += "(!)Color must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"";
-			}
-		}
+
 		// check scaling is valid input
 		if (absolute == -999 && percentile == -999) {
 			absolute = 10;
@@ -169,8 +153,16 @@ private String validateInput() throws IOException {
 			MAXCOLOR = Color.BLUE;
 		} else if (color.custom != null) {
 			System.err.println("Decoding color: 0x" + color.custom);
-			MAXCOLOR = Color.decode("0x" + color.custom);
+			// check that hex string is formatted properly
+			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
+			Matcher m = hexColorPat.matcher(color.custom);
+			if (!m.matches()) {
+				r += "(!)Color must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"";
+			} else { MAXCOLOR = Color.decode("0x" + color.custom); }
 		}
+		// check that Alpha channel/transparency values are formatted properly and decode/assign colors
+		if (alpha<0 || alpha>255) { r += "(!)Alpha/transparency value for higher values (max) must be a numeric 0 to 255\n"; }
+		else { MAXCOLOR = new Color(MAXCOLOR.getRed(), MAXCOLOR.getGreen(), MAXCOLOR.getBlue(), alpha); }
 
 		return (r);
 	}

src/scripts/Figure_Generation/ThreeColorHeatMap.java

@@ -175,7 +175,7 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 		BufferedImage im = new BufferedImage(pixwidth, pixheight, BufferedImage.TYPE_INT_ARGB);
 		Graphics g = im.getGraphics();
 		Graphics2D g2 = (Graphics2D) g;
-		g2.setColor(new Color(255, 255, 255));
+		g2.setColor(new Color(255, 255, 255, 0));
 		g2.fillRect(0, 0, pixwidth, pixheight);
 
 		int count = 0;
@@ -196,7 +196,8 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 					int red = (int) (MAXCOLOR.getRed() * sVal + MIDCOLOR.getRed() * (1 - sVal));
 					int green = (int) (MAXCOLOR.getGreen() * sVal + MIDCOLOR.getGreen() * (1 - sVal));
 					int blue = (int) (MAXCOLOR.getBlue() * sVal + MIDCOLOR.getBlue() * (1 - sVal));
-					g.setColor(new Color(red, green, blue));
+					int alpha = (int) (MAXCOLOR.getAlpha() * sVal + MIDCOLOR.getAlpha() * (1 - sVal));
+					g.setColor(new Color(red, green, blue, alpha));
 				} else if (IDj < MIDVAL) {
 					double v = (MIDVAL - IDj) / LOWER_RATIO;
 					double sVal = v > 1 ? 1 : v;
@@ -206,7 +207,8 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 					int red = (int) (MINCOLOR.getRed() * sVal + MIDCOLOR.getRed() * (1 - sVal));
 					int green = (int) (MINCOLOR.getGreen() * sVal + MIDCOLOR.getGreen() * (1 - sVal));
 					int blue = (int) (MINCOLOR.getBlue() * sVal + MIDCOLOR.getBlue() * (1 - sVal));
-					g.setColor(new Color(red, green, blue));
+					int alpha = (int) (MINCOLOR.getAlpha() * sVal + MIDCOLOR.getAlpha() * (1 - sVal));
+					g.setColor(new Color(red, green, blue, alpha));
 				} else {
 					g.setColor(MIDCOLOR);
 				}

src/scripts/Figure_Generation/TwoColorHeatMap.java

@@ -47,7 +47,7 @@ public class TwoColorHeatMap {
 	private JLabel picLabel = null;
 
 	public TwoColorHeatMap(File in, Color c, int startR, int startC, int pHeight, int pWidth, String scale, double abs,
-			double quant, File output, boolean outstatus) {
+			double quant, File output, boolean outstatus, boolean trans) {
 
 		SAMPLE = in;
 		MAXCOLOR = c;
@@ -62,6 +62,10 @@ public TwoColorHeatMap(File in, Color c, int startR, int startC, int pHeight, in
 
 		OUTFILE = output;
 		OUTPUTSTATUS = outstatus;
+		MINCOLOR = new Color(255, 255, 255, 255);
+		if (trans) {
+			MINCOLOR = new Color(MAXCOLOR.getRed(), MAXCOLOR.getGreen(), MAXCOLOR.getBlue(), 0);
+		}
 	}
 
 	public void run() throws IOException {
@@ -120,7 +124,7 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 		BufferedImage im = new BufferedImage(pixwidth, pixheight, BufferedImage.TYPE_INT_ARGB);
 		Graphics g = im.getGraphics();
 		Graphics2D g2 = (Graphics2D) g;
-		g2.setColor(new Color(255, 255, 255));
+		g2.setColor(MINCOLOR);
 		g2.fillRect(0, 0, pixwidth, pixheight);
 
 		int count = 0;
@@ -134,9 +138,10 @@ public static BufferedImage generateHeatMap(ArrayList<double[]> matrix) throws F
 					int red = (int) (MAXCOLOR.getRed() * sVal + MINCOLOR.getRed() * (1 - sVal));
 					int green = (int) (MAXCOLOR.getGreen() * sVal + MINCOLOR.getGreen() * (1 - sVal));
 					int blue = (int) (MAXCOLOR.getBlue() * sVal + MINCOLOR.getBlue() * (1 - sVal));
-					g.setColor(new Color(red, green, blue));
+					int alpha = (int) (MAXCOLOR.getAlpha() * sVal + MINCOLOR.getAlpha() * (1 - sVal));
+					g.setColor(new Color(red, green, blue, alpha));
 				} else {
-					g.setColor(Color.WHITE);
+					g.setColor(MINCOLOR);
 				}
 				g.fillRect(j * width, count * height, width, height);
 			}
@@ -352,7 +357,7 @@ public static double getQuantile(ArrayList<double[]> matrix, double percent) {
 		ArrayList<Double> nonZero = new ArrayList<Double>();
 		for (int x = 0; x < matrix.size(); x++) {
 			for (int y = 0; y < matrix.get(x).length; y++) {
-				if (matrix.get(x)[y] != 0) {
+				if (matrix.get(x)[y] != 0 && !Double.isNaN(matrix.get(x)[y])) {
 					nonZero.add(Double.valueOf(matrix.get(x)[y]));
 				}
 			}

src/window_interface/Figure_Generation/TwoColorHeatMapOutput.java

@@ -28,8 +28,8 @@ public class TwoColorHeatMapOutput extends JFrame {
 	protected static double quantile = 0.9;
 	protected static double absolute = -999;
 
-	public static Color MINCOLOR = new Color(255, 255, 255);
 	public static Color MAXCOLOR = new Color(255, 0, 0);
+	public boolean transparentBackground = false;
 
 	protected static boolean OUTPUTSTATUS = false;
 	protected static File OUT_DIR = null;
@@ -39,7 +39,7 @@ public class TwoColorHeatMapOutput extends JFrame {
 	JTabbedPane newpane;
 
 	public TwoColorHeatMapOutput(ArrayList<File> in, Color c, int startR, int startC, int pHeight, int pWidth,
-			String scale, double abs, double quant, File out_dir, boolean outstatus) {
+			String scale, double abs, double quant, File out_dir, boolean outstatus, boolean trans) {
 		setTitle("Heatmap");
 		setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
 		setBounds(150, 150, 600, 800);
@@ -49,6 +49,7 @@ public TwoColorHeatMapOutput(ArrayList<File> in, Color c, int startR, int startC
 
 		SAMPLE = in;
 		MAXCOLOR = c;
+		transparentBackground = trans;
 		startROW = startR;
 		startCOL = startC;
 		pixelHeight = pHeight;
@@ -60,7 +61,6 @@ public TwoColorHeatMapOutput(ArrayList<File> in, Color c, int startR, int startC
 
 		OUT_DIR = out_dir;
 		OUTPUTSTATUS = outstatus;
-		System.out.println(OUTPUTSTATUS);
 	}
 
 	public void run() throws IOException {
@@ -72,7 +72,7 @@ public void run() throws IOException {
 
 			// Execute script
 			TwoColorHeatMap script_object = new TwoColorHeatMap(SAMPLE.get(x), MAXCOLOR, startROW, startCOL,
-					pixelHeight, pixelWidth, scaleType, absolute, quantile, OUTPUT, OUTPUTSTATUS);
+					pixelHeight, pixelWidth, scaleType, absolute, quantile, OUTPUT, OUTPUTSTATUS, transparentBackground);
 			script_object.run();
 			JLabel picLabel = script_object.getImg();
 

src/window_interface/Figure_Generation/TwoColorHeatMapWindow.java

@@ -60,6 +60,7 @@ public class TwoColorHeatMapWindow extends JFrame implements ActionListener, Pro
 	private JTextField txtHeight;
 	private JTextField txtWidth;
 	private JButton btnColor;
+	private JCheckBox chckbxTransparentBackground;
 	private JRadioButton rdbtnAbsoluteValue;
 	private JRadioButton rdbtnPercentileValue;
 	private JRadioButton rdbtnTreeview;
@@ -125,7 +126,7 @@ public Void doInBackground() throws IOException {
 				double quantile = Double.parseDouble(txtPercent.getText());
 
 				TwoColorHeatMapOutput heat = new TwoColorHeatMapOutput(txtFiles, COLOR, startR, startC, pHeight, pWidth,
-						scaletype, absolute, quantile, OUT_DIR, chckbxOutputHeatmap.isSelected());
+						scaletype, absolute, quantile, OUT_DIR, chckbxOutputHeatmap.isSelected(), chckbxTransparentBackground.isSelected());
 
 				heat.addPropertyChangeListener("heat", new PropertyChangeListener() {
 					public void propertyChange(PropertyChangeEvent propertyChangeEvent) {
@@ -333,9 +334,14 @@ public void itemStateChanged(ItemEvent e) {
 			}
 		});
 
+		chckbxTransparentBackground = new JCheckBox("Use transparent background");
+		sl_contentPane.putConstraint(SpringLayout.NORTH, chckbxTransparentBackground, 8, SpringLayout.SOUTH, lblSelectColor);
+		sl_contentPane.putConstraint(SpringLayout.WEST, chckbxTransparentBackground, 10, SpringLayout.WEST, lblSelectColor);
+		contentPane.add(chckbxTransparentBackground);
+
 		JLabel lblPixelHeight = new JLabel("Image Height:");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, lblPixelHeight, 20, SpringLayout.SOUTH, btnColor);
-		sl_contentPane.putConstraint(SpringLayout.WEST, lblPixelHeight, 0, SpringLayout.WEST, lblSelectColor);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, lblPixelHeight, 8, SpringLayout.SOUTH, chckbxTransparentBackground);
+		sl_contentPane.putConstraint(SpringLayout.WEST, lblPixelHeight, 15, SpringLayout.WEST, contentPane);
 		contentPane.add(lblPixelHeight);
 
 		JLabel lblPixelWidth = new JLabel("Image Width:");
@@ -425,7 +431,7 @@ public void itemStateChanged(ItemEvent e) {
 		});
 
 		JLabel lblImageCompression = new JLabel("Image Compression:");
-		sl_contentPane.putConstraint(SpringLayout.NORTH, lblImageCompression, 10, SpringLayout.SOUTH, txtAbsolute);
+		sl_contentPane.putConstraint(SpringLayout.NORTH, lblImageCompression, 5, SpringLayout.SOUTH, txtAbsolute);
 		sl_contentPane.putConstraint(SpringLayout.WEST, lblImageCompression, 10, SpringLayout.WEST, contentPane);
 		contentPane.add(lblImageCompression);