split CompositePlotCLI to create script class

For the purpose of building out a GUI for the composite plot image generating tool (#96), the CLI class is broken up in this commit to separate out the input data parsing and chart building from command line parsing and input validation components in the CLI class. The new class organization further added minor adjustments to script behavior:
- the default filepath suffix is now "_plot.png"
- color defaults are determined by a null input and n>2 condition uses YEP color palette instead of Kelly colors
- data parsing issues throw Exceptions rather than print statements
- input/output extensions no longer restricted

The new ColorSeries class saves color palettes and can be reused and expanded upon for future tools.

Author: owlang

src/cli/Figure_Generation/CompositePlotCLI.java

@@ -5,29 +5,21 @@
 import picocli.CommandLine.Parameters;
 
 import java.awt.Color;
-import java.lang.NullPointerException;
 import java.io.File;
 import java.io.IOException;
-import java.io.OutputStream;
-import java.io.FileOutputStream;
-import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.Scanner;
 import java.util.concurrent.Callable;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 
-import org.jfree.chart.JFreeChart;
-import org.jfree.chart.ChartUtils;
-import org.jfree.data.xy.XYSeriesCollection;
-import org.jfree.data.xy.XYSeries;
-
-import charts.CompositePlot;
 import objects.ToolDescriptions;
-import util.ExtensionFileFilter;
+import scripts.Figure_Generation.PlotComposite;
 
 /**
- * Figure_GenerationCLI/CompositePlotCLI
+ * Command line interface class for scripts.Figure_Generation.PlotComposite to create line plot images based on the output files of scripts.Figure_Generation.TagPileup.
+ * @author Olivia Lang
+ * @see scripts.Figure_Generation.PlotComposite
+ * @see scripts.Figure_Generation.TagPileup
  */
 @Command(name = "composite-plot", mixinStandardHelpOptions = true,
 	description = ToolDescriptions.composite_description,
@@ -38,10 +30,9 @@
 public class CompositePlotCLI implements Callable<Integer> {
 
 	@Parameters(index = "0", description = "Composite data to plot. (formatted like TagPileup composite output)")
-	private File compositeData;
+	private File inputComposite;
 
-	@Option(names = { "-o",
-			"--output" }, description = "specify output filename, please use PNG extension\n(default=Input filename with \"_compositePlot.png\" appended to the name in working directory of ScriptManager")
+	@Option(names = { "-o", "--output" }, description = "specify output filename, please use PNG extension\n(default=Input filename with \"_compositePlot.png\" appended to the name in working directory of ScriptManager")
 	private File output = null;
 	@Option(names = { "-t", "--title" }, description = "set title (default=<composite-file-name>)")
 	private String title = null;
@@ -55,37 +46,11 @@ public class CompositePlotCLI implements Callable<Integer> {
 			"--custom-colors" }, description = "indicate colors to use for each series. Must indicate a number of colors that matches number of dataseries\n"
 					+ "default behavior:\n" + "if one series input, use black\n"
 					+ "if two series input, use blue(sense) and red(anti)\n"
-					+ "if greater than two series, cycle through a set of 20 preset colors.", arity = "1..")
+					+ "if greater than two series, cycle through a set of 10 preset colors based on Rossi et al, 2021 (PMID:33692541).", arity = "1..")
 	private String[] colors = null;
 
-	XYSeriesCollection xydata = null;
 	private ArrayList<Color> COLORS = new ArrayList<Color>();
 
-	// Colors copied from response on StackOverflow:
-	// https://stackoverflow.com/questions/470690/how-to-automatically-generate-n-distinct-colors
-	String[] KELLY_COLORS_HEX = { "0xFFB300", // Vivid Yellow
-			"0x803E75", // Strong Purple
-			"0xFF6800", // Vivid Orange
-			"0xA6BDD7", // Very Light Blue
-			"0xC10020", // Vivid Red
-			"0xCEA262", // Grayish Yellow
-			"0x817066", // Medium Gray
-			// The following don't work well for people with defective color vision
-			"0x007D34", // Vivid Green
-			"0xF6768E", // Strong Purplish Pink
-			"0x00538A", // Strong Blue
-			"0xFF7A5C", // Strong Yellowish Pink
-			"0x53377A", // Strong Violet
-			"0xFF8E00", // Vivid Orange Yellow
-			"0xB32851", // Strong Purplish Red
-			"0xF4C800", // Vivid Greenish Yellow
-			"0x7F180D", // Strong Reddish Brown
-			"0x93AA00", // Vivid Yellowish Green
-			"0x593315", // Deep Yellowish Brown
-			"0xF13A13", // Vivid Reddish Orange
-			"0x232C16", // Dark Olive Green
-	};
-
 	@Override
 	public Integer call() throws Exception {
 		System.err.println(">CompositePlotCLI.call()");
@@ -97,98 +62,52 @@ public Integer call() throws Exception {
 		}
 
 		// Generate Composite Plot
-		JFreeChart chart = CompositePlot.createChart(xydata, title, COLORS, legend);
-		// Save Composite Plot
-		OutputStream OUT = new FileOutputStream(output);
-		ChartUtils.writeChartAsPNG(OUT, chart, pixelWidth, pixelHeight);
+		PlotComposite.plotCompositeFile(inputComposite, output, true, title, COLORS, legend, pixelWidth, pixelHeight);
 
 		System.err.println("Image Generated.");
 		return (0);
 	}
 
+	/**
+	 * Validate input values and create user-readable error messages.
+	 * @return
+	 * @throws IOException
+	 */
 	private String validateInput() throws IOException {
 		String r = "";
 
-		// check inputs exist
-		if (!compositeData.exists()) {
-			r += "(!)Composite Data file does not exist: " + compositeData.getName() + "\n";
-			return (r);
-		}
-		// check input extensions
-		if (!"out".equals(ExtensionFileFilter.getExtension(compositeData))) {
-			r += "(!)Is this a \".out\" file? Check extension: " + compositeData.getName() + "\n";
+		// Input file check
+		if (!inputComposite.exists()) {
+			r += "(!)Composite Data file does not exist: " + inputComposite.getName() + "\n";
+		} else if (inputComposite.isDirectory()) {
+			r += "(!)Composite Data file is a directory: " + inputComposite.getName() + "\n";
 		}
-		// set default output filename
-		if (output == null) {
-			output = new File(ExtensionFileFilter.stripExtension(compositeData) + "_compositePlot.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: "
-						+ ExtensionFileFilter.stripExtension(output) + ".png\n";
-			}
-			// check directory
+		
+		// Output file check
+		if (output != null) {
 			if (output.getParent() == null) {
 // 				System.err.println("default to current directory");
 			} else if (!new File(output.getParent()).exists()) {
 				r += "(!)Check output directory exists: " + output.getParent() + "\n";
 			}
 		}
 
-		// check pixel ranges are valid
+		// Pixel ranges must be valid
 		if (pixelHeight <= 0) {
 			r += "(!)Cell height must be a positive integer value! check \"-y\" flag.\"";
 		}
 		if (pixelWidth <= 0) {
 			r += "(!)Cell width must be a positive integer value! check \"-x\" flag.\"";
 		}
 
-		// Parse Datafile
-		try {
-			xydata = parseData();
-			if (xydata == null) {
-				r += "(!)The number of y-values don't match the number of x-values";
-			}
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-		}
-
-		// Set Color
-		if (colors == null) { // set defaults based on number of dataseries (n=1 -> black, n=2 -> blue,red,
-								// n=3 -> cycle through kelly colors)
-			if (xydata.getSeriesCount() == 1) {
-				// set color to black default unless otherwise indicated
-				COLORS.add(Color.BLACK);
-			} else if (xydata.getSeriesCount() == 2) {
-				// set colors to blue and red default unless otherwise indicated
-				COLORS.add(Color.BLUE);
-				COLORS.add(Color.RED);
-			} else if (xydata.getSeriesCount() > 2) {
-				// assign a diverse set of colors (as many as there are series)
-				for (int i = 0; i < xydata.getSeriesCount(); i++) {
-					int index = i % KELLY_COLORS_HEX.length;
-					COLORS.add(Color.decode(KELLY_COLORS_HEX[index]));
-				}
-			}
-		} else { // set user specified values and check they match number of data series
-			// assert custom colors have been assigned and length matches number of series
-			if (colors.length != xydata.getSeriesCount()) {
-				r += "(!)Number of colors specified(" + colors.length + ") must match number of dataseries("
-						+ xydata.getSeriesCount() + ")\n";
-			}
+		// Set Colors (customized)
+		if (colors != null) {
 			// check color input format and decode
 			Pattern hexColorPat = Pattern.compile("[0-9A-Fa-f]{6}");
 			for (int i = 0; i < colors.length; i++) {
 				Matcher m = hexColorPat.matcher(colors[i]);
 				if (!m.matches()) {
-					r += "(!)Color(" + colors[i]
-							+ ") must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"\n";
+					r += "(!)Color(" + colors[i] + ") must be formatted as a hexidecimal String!\n\tExpected input string format: \"[0-9A-Fa-f]{6}\"\n";
 				} else {
 					System.err.println("Decoding color: 0x" + colors[i]);
 					COLORS.add(Color.decode("0x" + colors[i]));
@@ -197,55 +116,4 @@ private String validateInput() throws IOException {
 		}
 		return (r);
 	}
-
-	public XYSeriesCollection parseData() throws FileNotFoundException {
-		// parse input into XYDataset obj
-		XYSeriesCollection dataset = new XYSeriesCollection();
-		Scanner scan = new Scanner(compositeData);
-		// parse x values
-		String[] tokens = scan.nextLine().split("\t");
-		if (!tokens[0].equals("")) {
-			scan.close();
-			System.err.println("(!) First row of input file must have an empty first column (as x-values)");
-			return null;
-		}
-		double[] x = new double[tokens.length - 1];
-		for (int i = 1; i < tokens.length; i++) {
-			x[i - 1] = Double.parseDouble(tokens[i]);
-		}
-
-		XYSeries s;
-		// line-by-line through file
-		while (scan.hasNextLine()) {
-			tokens = scan.nextLine().split("\t");
-			// check for format consistency: number of x-values matches y-values
-			if (tokens.length - 1 != x.length) {
-				System.err.println("(!) Check number of x-values matches number of y-values");
-				scan.close();
-				return null;
-			}
-			// skip any rows with blank labels
-			if (tokens[0].equals("")) {
-				for (int i = 1; i < tokens.length; i++) {
-					if (x[i - 1] != Double.parseDouble(tokens[i])) {
-						System.err.println(x[i - 1]);
-						System.err.println(tokens[i]);
-						System.err.println("(!) Check dataseries based on same x-scale file");
-						scan.close();
-						return null;
-					}
-				}
-				continue;
-			}
-			// initialize series based on rowname column of input file
-			s = new XYSeries(tokens[0]);
-			// parse y-values of current row
-			for (int i = 1; i < tokens.length; i++) {
-				s.add(x[i - 1], Double.parseDouble(tokens[i]));
-			}
-			dataset.addSeries(s);
-		}
-		scan.close();
-		return (dataset);
-	}
 }

src/scripts/Figure_Generation/PlotComposite.java

@@ -0,0 +1,120 @@
+package scripts.Figure_Generation;
+
+import java.awt.Color;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Scanner;
+
+import org.jfree.chart.ChartUtils;
+import org.jfree.chart.JFreeChart;
+import org.jfree.data.xy.XYSeries;
+import org.jfree.data.xy.XYSeriesCollection;
+
+import charts.CompositePlot;
+import util.ColorSeries;
+import util.ExtensionFileFilter;
+
+/**
+ * The script class to create/display line plot images based on the output files of scripts.Figure_Generation.TagPileup.
+ * @author Olivia Lang
+ * @see util.ColorSeries
+ * @see charts.CompositePlot
+ * @see cli.Figure_Generation.CompositePlotCLI
+ */
+public class PlotComposite {
+
+	/**
+	 * Static method that parses the input composite data (formatted like output of TagPileup), determines the default color palette if none specified, and plots the line chart, saving the image file to the appropriate output if indicated.
+	 * @param input a tab-delimited file containing the composite information in the format of scripts.Figure_Generation.TagPileup's output
+	 * @param OUT_PATH filepath to save composite image to. if null, defaults to <InputWithoutExtension>_plot.png.
+	 * @param outputImage to save image (true) or not (false)
+	 * @param title the string to include at the top of the line chart
+	 * @param COLORS the color palette list of colors to plot. If null, then a different color palette is chosen based on the number of lines parsed from the composite input file: if n=1, then black is used, if n=2, then the first plot is blue and the second is red, if n>2, then the YEP color pallete is used.
+	 * @param legend to include the legend in the chart (true) or not (false)
+	 * @param pxHeight height of image to save
+	 * @param pxWidth width of image to save
+	 * @return
+	 * @throws IOException
+	 * @throws IllegalArgumentException
+	 * @throws FileNotFoundException 
+	 */
+	public static JFreeChart plotCompositeFile(File input, File OUT_PATH, boolean outputImage, String title, ArrayList<Color> COLORS, boolean legend, int pxHeight, int pxWidth) throws IOException, IllegalArgumentException, FileNotFoundException {
+		Scanner scan = new Scanner(input);
+		// parse x values
+		String[] tokens = scan.nextLine().split("\t");
+		if (!tokens[0].equals("")) {
+			scan.close();
+			throw new IllegalArgumentException("(!) First row of input file must have an empty first column (as x-values)");
+		}
+		double[] x = new double[tokens.length - 1];
+		for (int i = 1; i < tokens.length; i++) {
+			x[i - 1] = Double.parseDouble(tokens[i]);
+		}
+
+		// parse input into XYDataset obj
+		XYSeriesCollection dataset = new XYSeriesCollection();
+
+		XYSeries s;
+		// line-by-line through file
+		while (scan.hasNextLine()) {
+			tokens = scan.nextLine().split("\t");
+			// check for format consistency: number of x-values matches y-values
+			if (tokens.length - 1 != x.length) {
+				scan.close();
+				throw new IllegalArgumentException("(!) Check number of x-values matches number of y-values");
+			}
+			// skip any rows with blank labels
+			if (tokens[0].equals("")) {
+				for (int i = 1; i < tokens.length; i++) {
+					if (x[i - 1] != Double.parseDouble(tokens[i])) {
+						System.err.println(x[i - 1]);
+						System.err.println(tokens[i]);
+						scan.close();
+						throw new IllegalArgumentException("(!) Check dataseries based on same x-scale file");
+					}
+				}
+				continue;
+			}
+			// initialize series based on rowname column of input file
+			s = new XYSeries(tokens[0]);
+			// parse y-values of current row
+			for (int i = 1; i < tokens.length; i++) {
+				s.add(x[i - 1], Double.parseDouble(tokens[i]));
+			}
+			dataset.addSeries(s);
+		}
+		scan.close();
+
+		// Set-up colors
+		if (COLORS==null) {
+			COLORS = new ArrayList<Color>(2);
+			if (dataset.getSeriesCount() == 1) { // n=1, default to black
+				COLORS.add(Color.BLACK);
+			} else if (dataset.getSeriesCount() == 2) { // n=2, default to red & blue  XO colors
+				COLORS = ColorSeries.InitializeXOColors();
+			} else if (dataset.getSeriesCount() > 2) { // n>2, default to yep colors
+				COLORS = ColorSeries.InitializeYEPColors();
+			}
+		// assert custom colors have been assigned and length matches number of series
+		} else if (COLORS.size() != dataset.getSeriesCount()) {
+			System.err.println("(Caution!) Number of colors specified(" + COLORS.size() + ") doesnt match number of dataseries(" + dataset.getSeriesCount() + ")\n");
+		}
+		
+		// Make chart
+		JFreeChart chart = CompositePlot.createChart(dataset, title, COLORS, legend);
+
+		// Save Composite Plot
+		if (outputImage) {
+			// set default output filename
+			if (OUT_PATH == null) {
+				OUT_PATH = new File(ExtensionFileFilter.stripExtension(input) + "_plot.png");
+			}
+			ChartUtils.writeChartAsPNG(new FileOutputStream(OUT_PATH), chart, pxWidth, pxHeight);
+		}
+				
+		return (chart);
+	}
+}