Merge pull request #119 from CEGRcode/working-dev

Rework TagPileup Window Graphics

Author: WilliamKMLai

singularity/README.md

@@ -0,0 +1,17 @@
+## Singularity
+
+### Build Singularity Image
+```
+$ cd scriptmanager
+$ singularity build --fakeroot scriptmanager.sif scriptmanager.def
+```
+
+### Run from Singularity Image
+```
+$ singularity exec scriptmanager.sif scriptmanager ${command}
+```
+
+**Example:**
+```
+$ singularity exec scriptmanager.sif scriptmanager coordinate-manipulation bed-to-gff BEDFILE.bed -o OUTPUT.gff
+```

scriptmanager.def singularity/scriptmanager.defscriptmanager.def renamed to singularity/scriptmanager.def

@@ -16,12 +16,31 @@
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
 
+/**
+ * Collection of static methods for plotting lines of sense {@literal &}
+ * antisense or combined composite plots with customizable titles, colors, and
+ * legends.
+ * 
+ * @author William KM Lai
+ * @see scriptmanager.scripts.Sequence_Analysis.DNAShapefromBED
+ * @see scriptmanager.scripts.Sequence_Analysis.DNAShapefromFASTA
+ * @see scriptmanager.window_interface.Read_Analysis.TagPileupOutput
+ */
 public class CompositePlot {
 
-	public CompositePlot() {
-		
-	}
-	
+	/**
+	 * Create a two-line plot (sense and antisense composites) with a title and
+	 * custom colors. There are no checks on input array lengths (line plot
+	 * determined by length of domain array).
+	 * 
+	 * @param x      the domain values array
+	 * @param y1     "Sense Strand" values array
+	 * @param y2     "Anti Strand" values array
+	 * @param name   title of the plot
+	 * @param COLORS a 2-element array of colors of the sense and antisense lines
+	 *               (first color = sense, second color = anti)
+	 * @return the line plot for display
+	 */
 	public static ChartPanel createCompositePlot(double[] x, double[] y1, double[] y2, String name, ArrayList<Color> COLORS){
 		final XYSeriesCollection dataset = new XYSeriesCollection();
 		final XYSeries seriesF = new XYSeries("Sense Strand");
@@ -39,7 +58,19 @@ public static ChartPanel createCompositePlot(double[] x, double[] y1, double[] y
 		chartPanel.setPreferredSize(new java.awt.Dimension(500, 270));
 		return chartPanel;
 	}
-	
+
+	/**
+	 * Create a one-line plot (combined composites) with a title and custom color.
+	 * There are no checks on input array lengths (line plot determined by length of
+	 * domain array).
+	 * 
+	 * @param x      the domain values array
+	 * @param y1     "Combined" values array
+	 * @param name   title of the plot
+	 * @param COLORS a 1-element array of colors of the sense and antisense lines
+	 *               (first color = sense, second color = anti)
+	 * @return the line plot for display
+	 */
 	public static Component createCompositePlot(double[] x, double[] y1, String name, ArrayList<Color> COLORS){
 		final XYSeriesCollection dataset = new XYSeriesCollection();
 		final XYSeries seriesC = new XYSeries("Data");
@@ -53,17 +84,45 @@ public static Component createCompositePlot(double[] x, double[] y1, String name
 		chartPanel.setPreferredSize(new java.awt.Dimension(500, 270));
 		return chartPanel;
 	}
-	
+
+	/**
+	 * Create a one-line plot (combined composites) with a title using a black line.
+	 * There are no checks on input array lengths (line plot determined by length of
+	 * domain array).
+	 * 
+	 * @param x    the domain values array
+	 * @param y1   "Combined" values array
+	 * @param name title of the plot
+	 * @return the line plot for display
+	 */
 	public static Component createCompositePlot(double[] x, double[] y1, String name){
 		ArrayList<Color> COLORS = new ArrayList<Color>();
 		COLORS.add(Color.BLACK);
 		return(createCompositePlot(x, y1, name, COLORS));
 	}
-		
+
+	/**
+	 * Create line chart with a legend
+	 * 
+	 * @param dataset the (x,y) values (agnostic to number of series)
+	 * @param TITLE   title of the plot
+	 * @param COLORS  colors to use for each data series (depends on dataset)
+	 * @return the line plot
+	 */
+
 	public static JFreeChart createChart(final XYDataset dataset, String TITLE, ArrayList<Color> COLORS) {
 		return(createChart(dataset, TITLE, COLORS, true));
 	}
-	
+
+	/**
+	 * Create line chart with an optional legend
+	 * 
+	 * @param dataset the (x,y) values (agnostic to number of series)
+	 * @param TITLE   title of the plot
+	 * @param COLORS  colors to use for each dataseries (depends on dataset)
+	 * @param legend  to print legend describing series
+	 * @return the line plot
+	 */
 	public static JFreeChart createChart(final XYDataset dataset, String TITLE, ArrayList<Color> COLORS, boolean legend) {
 		//Call Chart
 		final JFreeChart chart = ChartFactory.createXYLineChart(

src/main/java/scriptmanager/charts/CompositePlot.java

@@ -18,15 +18,59 @@
 import org.jfree.chart.ui.RectangleEdge;
 import org.jfree.chart.ui.RectangleInsets;
 
+/**
+ * Collection of static methods for formatting and plotting data into heatmaps
+ * of matrix values
+ * 
+ * @author William KM Lai
+ * @see scriptmanager.scripts.BAM_Statistics.BAMGenomeCorrelation
+ */
 public class HeatMap {
-	
-	public HeatMap() {
-		
-	}
-	
-	public static ChartPanel createCorrelationHeatmap(String[] labels, double[][] MATRIX, File output) {
-        // create a paint-scale and a legend showing it
-        LookupPaintScale paintScale = new LookupPaintScale(0, 1, Color.black);       
+
+    /**
+     * Constant value encoding the blue to white to red color scale. (0)
+     */
+    public final static short BLUEWHITERED = 0;
+    /**
+     * Constant value encoding the jet-like color scale. (0)
+     */
+    public final static short JETLIKE = 1;
+
+    /**
+     * Create a multi-color color scale inspired by Matplotlib's "jet" color scheme.
+     * 15 starting colors are set to 15 values.
+     * 
+     * @return jet-like paintscale
+     */
+    private static LookupPaintScale getJetLikeScale() {
+        LookupPaintScale paintScale = new LookupPaintScale(0, 1, Color.black);
+        paintScale.add(0.938, Color.decode("#75140C"));    //dark blue
+        paintScale.add(0.871, Color.decode("#C0281B"));
+        paintScale.add(0.804, Color.decode("#EB4826"));
+        paintScale.add(0.737, Color.decode("#FF7500"));
+        paintScale.add(0.670, Color.decode("#F4BC41"));
+        paintScale.add(0.603, Color.decode("#F3FC53"));
+        paintScale.add(0.536, Color.decode("#C6FD64"));
+        paintScale.add(0.469, Color.decode("#9EFC8A"));
+        paintScale.add(0.402, Color.decode("#81FBBB"));
+        paintScale.add(0.335, Color.decode("#6DE9EF"));
+        paintScale.add(0.268, Color.decode("#08A3FF"));
+        paintScale.add(0.201, Color.decode("#255AF6"));
+        paintScale.add(0.134, Color.decode("#0912F5"));
+        paintScale.add(0.134, Color.decode("#0912F5"));
+        paintScale.add(0.067, Color.decode("#0600C9"));
+        paintScale.add(0.000, Color.decode("#020080"));    //dark red
+        return paintScale;
+    }
+
+    /**
+	 * Create a paint scale using original BAM Genome Correlation color scale scheme:
+	 * blue (low) to white (mid) to red (high).
+	 * 
+	 * @return original blue-white-red paintscale
+	 */
+    private static LookupPaintScale getBlueWhiteRedScale() {
+        LookupPaintScale paintScale = new LookupPaintScale(0, 1, Color.black);
         paintScale.add(0.0, new Color(0, 0, 255));
         paintScale.add(0.11, new Color(63, 63, 255));
         paintScale.add(0.22, new Color(126, 126, 255));
@@ -36,11 +80,39 @@ public static ChartPanel createCorrelationHeatmap(String[] labels, double[][] MA
         paintScale.add(0.66, new Color(255, 126, 126));
         paintScale.add(0.77, new Color(255, 63, 63));
         paintScale.add(0.88, new Color(255, 0, 0));
-		
-		NumberAxis xAxis = new NumberAxis(null);
-		xAxis.setVisible(false);
-		String[] reverselabels = new String[labels.length];
-		for(int x = 0; x < labels.length; x++) { reverselabels[labels.length - x - 1]  = labels[x]; }
+        return paintScale;
+    }
+
+	/**
+	 * Get paint scale based on scale encoding value.
+	 * 
+	 * @param type scale encoding for one of the preset paint scales (e.g.
+	 *             REDWHITEBLUE, JETLIKE).
+	 * @return paintscale for the given encoding
+	 */
+    public static LookupPaintScale getPresetPaintscale(short type) {
+        if (type == BLUEWHITERED) { return getBlueWhiteRedScale(); }
+        else if (type == JETLIKE) { return getJetLikeScale(); }
+        // Use original red-white-blue paintscale as default
+        return getBlueWhiteRedScale();
+    }
+
+    /**
+	 * Create a correlation heatmap plot based on a square matrix of inputs with a
+	 * strict percentile-based blue-to-red paint scale (9 levels).
+	 * 
+	 * @param labels (sample names) for labeling the y-axis (symmetrical plot so
+	 *               x-axis labels are implied)
+	 * @param MATRIX the symmetrical 2D array of values
+	 * @param output the file to write the PNG chart to. File not written if this
+	 *               value is null.
+	 * @return the resulting correlation heatmap chart
+	 */
+    public static ChartPanel createCorrelationHeatmap(String[] labels, double[][] MATRIX, File output, LookupPaintScale paintScale) {
+        NumberAxis xAxis = new NumberAxis(null);
+        xAxis.setVisible(false);
+        String[] reverselabels = new String[labels.length];
+        for(int x = 0; x < labels.length; x++) { reverselabels[labels.length - x - 1]  = labels[x]; }
         SymbolAxis yAxis = new SymbolAxis("Experiments", reverselabels);
         XYPlot plot = new XYPlot(createDataset(MATRIX), xAxis, yAxis, null);
         XYBlockRenderer r = new XYBlockRenderer();
@@ -52,7 +124,7 @@ public static ChartPanel createCorrelationHeatmap(String[] labels, double[][] MA
         JFreeChart chart = new JFreeChart("Correlation Matrix", JFreeChart.DEFAULT_TITLE_FONT, plot, false);
         NumberAxis scaleAxis = new NumberAxis("Scale");
         scaleAxis.setAxisLinePaint(Color.white);
-        scaleAxis.setTickMarkPaint(Color.white);        
+        scaleAxis.setTickMarkPaint(Color.white);
         PaintScaleLegend legend = new PaintScaleLegend(paintScale, scaleAxis);
         legend.setSubdivisionCount(128);
         legend.setAxisLocation(AxisLocation.TOP_OR_RIGHT);
@@ -64,19 +136,28 @@ public static ChartPanel createCorrelationHeatmap(String[] labels, double[][] MA
         chart.addSubtitle(legend);
         chart.setBackgroundPaint(Color.white);
 
-        if(output!=null){
-			int width = 640;
-			int height = 480;
-			try{ ChartUtils.saveChartAsPNG(output, chart, width, height); }
-			catch( IOException e ){ e.printStackTrace(); }
+        // Save PNG if output filepath given
+        if (output!=null) {
+            int width = 640;
+            int height = 480;
+            try{ ChartUtils.saveChartAsPNG(output, chart, width, height); }
+            catch( IOException ioe ){ ioe.printStackTrace(); }
+            catch( Exception e ){ e.printStackTrace(); }
         }
-        
+
         return new ChartPanel(chart);
     }
-	
+
+
+	/**
+	 * Helper method for formatting data into the XYZDatset type
+	 * 
+	 * @param MATRIX the 2-d array of values to convert
+	 * @return the formatted data series
+	 */
     private static XYZDataset createDataset(double[][] MATRIX) {
-    	//The heatmap is based on a standard XY scatterplot as as such, is built with 0,0 in the lower left
-    	//The matrix must be rotated such that the final output is consistent
+        //The heatmap is based on a standard XY scatterplot as as such, is built with 0,0 in the lower left
+        //The matrix must be rotated such that the final output is consistent
         DefaultXYZDataset dataset = new DefaultXYZDataset();
         int N = MATRIX.length;
         for (int i = 0; i < N; i++) {

src/main/java/scriptmanager/charts/HeatMap.java

@@ -16,33 +16,54 @@
 import org.jfree.data.xy.XYSeries;
 import org.jfree.data.xy.XYSeriesCollection;
 
+/**
+ * Collection of static methods for plotting interactive histograms.
+ * 
+ * @author William KM Lai
+ * @see scriptmanager.scripts.BAM_Statistics.PEStats
+ */
 public class Histogram {
-	
-	public Histogram() {
 
-	}
-			
+	/**
+	 * Plot a set of bar-style plots using the frequencies (y) of values (x)
+	 * parallel input arrays.
+	 * 
+	 * @param y the list of frequencies
+	 * @param x the list of values that have frequencies (same len as y)
+	 * @return the bar-style histogram chart
+	 * @throws IOException
+	 */
 	public static ChartPanel createBarChart(double[] y, int[] x) throws IOException {
 		final XYSeries series = new XYSeries("Frequency");
 		for(int i = 0; i < x.length; i++) {
 			series.add((double)x[i], (double)y[i]);
 		}
 		final XYSeriesCollection dataset = new XYSeriesCollection(series);
 
-        JFreeChart chart = createChart(dataset);
+		JFreeChart chart = createChart(dataset);
 		final ChartPanel chartPanel = new ChartPanel(chart);
 		chartPanel.setPreferredSize(new java.awt.Dimension(500, 270));
-		return chartPanel;				
+		return chartPanel;
 	}
-	
+
+	/**
+	 * Plot a set of bar-style plots using the frequencies (y) of values (x)
+	 * parallel input arrays and save the chart as a PNG.
+	 * 
+	 * @param y the list of frequencies
+	 * @param x the list of values that have frequencies (same len as y)
+	 * @param output the path of the PNG file to save the chart image to
+	 * @return the bar-style histogram chart
+	 * @throws IOException
+	 */
 	public static ChartPanel createBarChart(double[] y, int[] x, File output) throws IOException {
 		final XYSeries series = new XYSeries("Frequency");
 		for(int i = 0; i < x.length; i++) {
 			series.add((double)x[i], (double)y[i]);
 		}
 		final XYSeriesCollection dataset = new XYSeriesCollection(series);
 
-        JFreeChart chart = createChart(dataset);
+		JFreeChart chart = createChart(dataset);
 		final ChartPanel chartPanel = new ChartPanel(chart);
 		chartPanel.setPreferredSize(new java.awt.Dimension(500, 270));
 
@@ -51,9 +72,18 @@ public static ChartPanel createBarChart(double[] y, int[] x, File output) throws
 			int height = 480;
 			ChartUtils.saveChartAsPNG(output, chart, width, height);
 		}
-		return chartPanel;				
+		return chartPanel;
 	}
-	
+
+	/**
+	 * Helper method to turn a formatted dataset into a standard chart with specific
+	 * look configurations including hard coded titles, axis labels, orientation,
+	 * legend, tooltips, grid colors, etc).
+	 * 
+	 * @param dataset the formatted dataset to plot
+	 * @return the formatted and configured histogram chart
+	 * @throws IOException
+	 */
 	private static JFreeChart createChart(IntervalXYDataset dataset) throws IOException {
         final JFreeChart chart = ChartFactory.createXYBarChart(
         		"Paired-End Insert Size Frequency Histogram",      // chart title
@@ -88,6 +118,6 @@ private static JFreeChart createChart(IntervalXYDataset dataset) throws IOExcept
         //target.setPaint(new Color(222, 222, 255, 128));
         //plot.addRangeMarker(target, Layer.BACKGROUND);
 
-        return chart;    
+        return chart;
     }
 }