Java tutorial
/************************************************************************* * * * This file is part of the 20n/act project. * * 20n/act enables DNA prediction for synthetic biology/bioengineering. * * Copyright (C) 2017 20n Labs, Inc. * * * * Please direct all queries to act@20n.com. * * * * This program is free software: you can redistribute it and/or modify * * it under the terms of the GNU General Public License as published by * * the Free Software Foundation, either version 3 of the License, or * * (at your option) any later version. * * * * This program is distributed in the hope that it will be useful, * * but WITHOUT ANY WARRANTY; without even the implied warranty of * * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * * GNU General Public License for more details. * * * * You should have received a copy of the GNU General Public License * * along with this program. If not, see <http://www.gnu.org/licenses/>. * * * *************************************************************************/ package com.act.lcms.plotter; import com.act.utils.TSVWriter; import com.act.lcms.Gnuplotter; import com.act.lcms.MS1; import com.act.lcms.XZ; import com.act.lcms.db.analysis.PathwayProductAnalysis; import com.act.lcms.db.analysis.ScanData; import com.act.lcms.db.model.LCMSWell; import com.act.lcms.db.model.MS1ScanForWellAndMassCharge; import org.apache.commons.lang3.tuple.Pair; import java.io.FileOutputStream; import java.io.IOException; import java.io.OutputStream; import java.io.PrintStream; import java.util.ArrayList; import java.util.HashMap; import java.util.List; import java.util.Map; import java.util.Set; public class WriteAndPlotMS1Results { public void plotTIC(List<XZ> tic, String outPrefix, String fmt) throws IOException { String outImg = outPrefix + "." + fmt; String outData = outPrefix + ".data"; // Write data output to outfile try (PrintStream out = new PrintStream(new FileOutputStream(outData))) { // print each time point + intensity to outDATA for (XZ xz : tic) { out.format("%.4f\t%.4f\n", xz.getTime(), xz.getIntensity()); out.flush(); } } // render outDATA to outPDF using gnuplot new Gnuplotter().plot2D(outData, outImg, new String[] { "TIC" }, "time", null, "intensity", fmt); } public void plotScan(List<MS1.YZ> scan, String outPrefix, String fmt) throws IOException { String outPDF = outPrefix + "." + fmt; String outDATA = outPrefix + ".data"; // Write data output to outfile PrintStream out = new PrintStream(new FileOutputStream(outDATA)); // print out the spectra to outDATA for (MS1.YZ yz : scan) { out.format("%.4f\t%.4f\n", yz.getMZ(), yz.getIntensity()); out.flush(); } // close the .data out.close(); // render outDATA to outPDF using gnuplot new Gnuplotter().plot2DImpulsesWithLabels(outDATA, outPDF, new String[] { "mz distribution at TIC max" }, null, "mz", null, "intensity", fmt); } private List<String> writeFeedMS1Values(List<Pair<Double, List<XZ>>> ms1s, Double maxIntensity, OutputStream os) throws IOException { // Write data output to outfile PrintStream out = new PrintStream(os); List<String> plotID = new ArrayList<>(ms1s.size()); for (Pair<Double, List<XZ>> ms1ForFeed : ms1s) { Double feedingConcentration = ms1ForFeed.getLeft(); List<XZ> ms1 = ms1ForFeed.getRight(); plotID.add(String.format("concentration: %5e", feedingConcentration)); // print out the spectra to outDATA for (XZ xz : ms1) { out.format("%.4f\t%.4f\n", xz.getTime(), xz.getIntensity()); out.flush(); } // delimit this dataset from the rest out.print("\n\n"); } return plotID; } private void writeFeedMS1Values(List<Pair<Double, Double>> concentrationIntensity, OutputStream os) throws IOException { PrintStream out = new PrintStream(os); for (Pair<Double, Double> ci : concentrationIntensity) { out.format("%f\t%f\n", ci.getLeft(), ci.getRight()); } out.flush(); } // input: list sorted on first field of pair of (concentration, ms1 spectra) // the ion of relevance to compare across different spectra // outPrefix for pdfs and data, and fmt (pdf or png) of output public void plotFeedings(List<Pair<Double, MS1ScanForWellAndMassCharge>> feedings, String ion, String outPrefix, String fmt, String gnuplotFile) throws IOException { String outSpectraImg = outPrefix + "." + fmt; String outSpectraData = outPrefix + ".data"; String outFeedingImg = outPrefix + ".fed." + fmt; String outFeedingData = outPrefix + ".fed.data"; String feedingGnuplotFile = gnuplotFile + ".fed"; boolean useMaxPeak = true; // maps that hold the values for across different concentrations List<Pair<Double, List<XZ>>> concSpectra = new ArrayList<>(); List<Pair<Double, Double>> concAreaUnderSpectra = new ArrayList<>(); List<Pair<Double, Double>> concMaxPeak = new ArrayList<>(); // we will compute a running max of the intensity in the plot, and integral Double maxIntensity = 0.0d, maxAreaUnder = 0.0d; // now compute the maps { conc -> spectra } and { conc -> area under spectra } for (Pair<Double, MS1ScanForWellAndMassCharge> feedExpr : feedings) { Double concentration = feedExpr.getLeft(); MS1ScanForWellAndMassCharge scan = feedExpr.getRight(); // get the ms1 spectra for the selected ion, and the max for it as well List<XZ> ms1 = scan.getIonsToSpectra().get(ion); Double maxInThisSpectra = scan.getMaxIntensityForIon(ion); Double areaUnderSpectra = scan.getIntegralForIon(ion); // update the max intensity over all different spectra maxIntensity = Math.max(maxIntensity, maxInThisSpectra); maxAreaUnder = Math.max(maxAreaUnder, areaUnderSpectra); // install this concentration and spectra in map, to be dumped to file later concSpectra.add(Pair.of(concentration, ms1)); concAreaUnderSpectra.add(Pair.of(concentration, areaUnderSpectra)); concMaxPeak.add(Pair.of(concentration, maxInThisSpectra)); } // Write data output to outfiles List<String> plotID = null; try (FileOutputStream outSpectra = new FileOutputStream(outSpectraData)) { plotID = writeFeedMS1Values(concSpectra, maxIntensity, outSpectra); } try (FileOutputStream outFeeding = new FileOutputStream(outFeedingData)) { writeFeedMS1Values(useMaxPeak ? concMaxPeak : concAreaUnderSpectra, outFeeding); } // render outDATA to outPDF using gnuplot Gnuplotter gp = new Gnuplotter(); String[] plotNames = plotID.toArray(new String[plotID.size()]); gp.plotOverlayed2D(outSpectraData, outSpectraImg, plotNames, "time", maxIntensity, "intensity", fmt, gnuplotFile); gp.plot2D(outFeedingData, outFeedingImg, new String[] { "feeding ramp" }, "concentration", useMaxPeak ? maxIntensity : maxAreaUnder, "integrated area under spectra", fmt, null, null, null, feedingGnuplotFile); } private List<Pair<String, String>> writeMS1Values(Map<String, List<XZ>> ms1s, Double maxIntensity, Map<String, Double> metlinMzs, OutputStream os, boolean heatmap) throws IOException { return writeMS1Values(ms1s, maxIntensity, metlinMzs, os, heatmap, true, null); } public List<Pair<String, String>> writeMS1Values(Map<String, List<XZ>> ms1s, Double maxIntensity, Map<String, Double> metlinMzs, OutputStream os, boolean heatmap, boolean applyThreshold, Set<String> ionsToWrite) throws IOException { // Write data output to outfile PrintStream out = new PrintStream(os); List<Pair<String, String>> plotID = new ArrayList<>(ms1s.size()); for (Map.Entry<String, List<XZ>> ms1ForIon : ms1s.entrySet()) { String ion = ms1ForIon.getKey(); // Skip ions not in the ionsToWrite set if that set is defined. if (ionsToWrite != null && !ionsToWrite.contains(ion)) { continue; } List<XZ> ms1 = ms1ForIon.getValue(); String plotName = String.format("ion: %s, mz: %.5f", ion, metlinMzs.get(ion)); plotID.add(Pair.of(ion, plotName)); // print out the spectra to outDATA for (XZ xz : ms1) { if (heatmap) { /* * When we are building heatmaps, we use gnuplots pm3d package * along with `dgrid3d 2000,2` (which averages data into grids * that are 2000 on the time axis and 2 in the y axis), and * `view map` that flattens a 3D graphs into a 2D view. * We want time to be on the x-axis and intensity on the z-axis * (because that is the one that is mapped to heat colors) * but then we need an artificial y-axis. We create proxy y=1 * and y=2 datapoints, and then dgrid3d averaging over 2 creates * a vertical "strip". */ out.format("%.4f\t1\t%.4f\n", xz.getTime(), xz.getIntensity()); out.format("%.4f\t2\t%.4f\n", xz.getTime(), xz.getIntensity()); } else { out.format("%.4f\t%.4f\n", xz.getTime(), xz.getIntensity()); } out.flush(); } // delimit this dataset from the rest out.print("\n\n"); } return plotID; } public void plotSpectra(Map<String, List<XZ>> ms1s, Double maxIntensity, Map<String, Double> individualMaxIntensities, Map<String, Double> metlinMzs, String outPrefix, String fmt, boolean makeHeatmap, boolean overlayPlots) throws IOException { String outImg = outPrefix + "." + fmt; String outData = outPrefix + ".data"; // Write data output to outfile try (FileOutputStream out = new FileOutputStream(outData)) { List<Pair<String, String>> ionAndplotID = writeMS1Values(ms1s, maxIntensity, metlinMzs, out, makeHeatmap); // writeMS1Values picks an ordering of the plots. // create two new sets plotID and yMaxes that have the matching ordering // and contain plotNames, and yRanges respectively List<Double> yMaxesInSameOrderAsPlots = new ArrayList<>(); List<String> plotID = new ArrayList<>(); for (Pair<String, String> plot : ionAndplotID) { String ion = plot.getLeft(); Double yMax = individualMaxIntensities.get(ion); yMaxesInSameOrderAsPlots.add(yMax); plotID.add(plot.getRight()); } Double[] yMaxes = yMaxesInSameOrderAsPlots.toArray(new Double[yMaxesInSameOrderAsPlots.size()]); // render outDATA to outPDF using gnuplot Gnuplotter gp = new Gnuplotter(); String[] plotNames = plotID.toArray(new String[plotID.size()]); if (makeHeatmap) { gp.plotHeatmap(outData, outImg, plotNames, maxIntensity, fmt); } else { if (!overlayPlots) { gp.plot2D(outData, outImg, plotNames, "time", maxIntensity, "intensity", fmt, null, null, yMaxes, outImg + ".gnuplot"); } else { gp.plotOverlayed2D(outData, outImg, plotNames, "time", maxIntensity, "intensity", fmt, outImg + ".gnuplot"); } } } } /** * This function writes the pathway product results to an analysis file * @param writer This is a handle to the tsv writer * @param chemicalName The name of the primary chemical of inspection * @param positiveAndNegativeWells This is a list of positive and negative control well samples * @param pathwayStepIon This is the metlin ion which usually is the best metlin ion based on standard ion analysis * @param wellsToBestPeaks This is a map of well to the best peak positions in the spectral charts * @throws IOException */ public static void writePathwayProductOutput(TSVWriter<String, String> writer, String chemicalName, List<ScanData<LCMSWell>> positiveAndNegativeWells, String pathwayStepIon, Map<ScanData<LCMSWell>, XZ> wellsToBestPeaks) throws IOException { for (ScanData<LCMSWell> well : positiveAndNegativeWells) { String fedChemical = well.getWell().getChemical() == null || well.getWell().getChemical().isEmpty() ? "nothing" : well.getWell().getChemical(); String pelletOrSupernatant = well.getPlate().getDescription().contains("pellet") ? "pellet" : "supernatant"; String detected; String intensity; String time; if (wellsToBestPeaks.get(well) != null) { detected = "YES"; intensity = String.format("%.4f", wellsToBestPeaks.get(well).getIntensity()); time = String.format("%.4f", wellsToBestPeaks.get(well).getTime()); } else { detected = "NO"; intensity = "-"; time = "-"; } Map<String, String> row = new HashMap<>(); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.TARGET_CHEMICAL.name(), chemicalName); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.TYPE.name(), pelletOrSupernatant); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.FED_CHEMICAL.name(), fedChemical); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.DETECTED.name(), detected); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.INTENSITY.name(), intensity); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.TIME.name(), time); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.PLATE_BARCODE.name(), well.getPlate().getBarcode()); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.MODE.name(), well.getScanFile().getMode().toString().toLowerCase()); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.WELL_COORDINATES.name(), well.getWell().getCoordinatesString()); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.MSID.name(), well.getWell().getMsid()); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.CONSTRUCT_ID.name(), well.getWell().getComposition()); row.put(PathwayProductAnalysis.PATHWAY_PRODUCT_HEADER_FIELDS.METLIN_ION.name(), pathwayStepIon); writer.append(row); writer.flush(); } } }