List of usage examples for com.lowagie.text Table addCell
public void addCell(String content) throws BadElementException
Cell to the Table. From source file:jp.ac.utokyo.rcast.karkinos.graph.GetCNVCharts.java
License:Apache License
private static Object cnvSummaryTable(DataSet dataset, int dispFlg) { Table table; try {//ww w . j a v a 2s. c o m if (dispFlg == 1) { table = new Table(8); } else { table = new Table(6); } // header table.addCell("chr"); table.addCell("start"); table.addCell("end"); table.addCell("copy number"); table.addCell("gain/loss"); table.addCell("num hetro SNP"); if (dispFlg == 1) { table.addCell("AAF"); table.addCell("BAF"); } // table.addCell("SNP ratio correl"); // table.addCell("rejected"); for (CopyNumberInterval cni : dataset.getCopyNumberIntervalList(9)) { if (cni.getCopynumber() == dataset.getBaseploidy()) { if (cni.getAaf() == dataset.getBaseploidy() / 2) { continue; } } if (dispFlg == 1) { if (cni.isAllelic()) continue; // if (cni.getCopynumber() == 0) // continue; // if (cni.getCopynumber() >= 4) // continue; } else if (dispFlg == 2) { if (!cni.isAllelic()) continue; if (cni.getCopynumber() == 0) continue; if (cni.isHdeletion()) continue; } else { if (1 <= cni.getCopynumber() && !cni.isHdeletion()) { continue; } if (cni.getCopynumber() != 0 && cni.isHdeletion()) { continue; } } table.addCell(cni.getChr()); table.addCell(format(cni.getStart()) + ""); table.addCell(format(cni.getEnd()) + ""); table.addCell("n=" + cni.getCopynumber()); String s = cni.getCopynumber() < 2 ? "loss" : "gain"; table.addCell(s); table.addCell(format(cni.getNoSNP()) + ""); if (dispFlg == 1) { table.addCell(cni.getAaf() + ""); table.addCell(cni.getBaf() + ""); } // table.addCell(format(cni.getSnpclrrel())+""); // table.addCell(cni.getRejected()+""); } return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetReadsStatsChart.java
License:Apache License
private static Object getCaptureCoveageTable(ReadsSummary readsSummary) { Table table; try {//from ww w . j av a 2 s . c o m table = new Table(5); // row1 table.addCell("coveage"); table.addCell("normal count"); table.addCell("normal %"); table.addCell("tumor count"); table.addCell("tumor %"); DepthCounter nd = readsSummary.getNormalDepth(); long normaltotal = nd.getTotal(); Map<Integer, CounterA> mn = nd.getMap(); DepthCounter td = readsSummary.getTumorDepth(); long tumortotal = td.getTotal(); Map<Integer, CounterA> mt = td.getMap(); Set<Integer> keySet = new TreeSet<Integer>(); keySet.addAll(mn.keySet()); keySet.addAll(mt.keySet()); for (Integer key : keySet) { int countNormal = 0; float normalP = 0; int countTumor = 0; float tumorP = 0; String s; int n = key; if (n >= 1000) { s = "1000 -"; // } else if (n >= 300) { // s = "" + n + "-" + (n + 99); } else if (n >= 10) { s = "" + n + "-" + (n + 9); } else if (n >= 1) { s = "" + n + "-" + (n + 8); } else { s = "" + n; } CounterA normal = mn.get(key); if (normal != null) { countNormal = normal.getCnt(); } CounterA tumor = mt.get(key); if (tumor != null) { countTumor = tumor.getCnt(); } normalP = (float) (((double) countNormal / (double) normaltotal) * 100); tumorP = (float) (((double) countTumor / (double) tumortotal) * 100); table.addCell(s); table.addCell(format(countNormal)); table.addCell(format(normalP) + "%"); table.addCell(format(countTumor)); table.addCell(format(tumorP) + "%"); } return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetReadsStatsChart.java
License:Apache License
private static Object getLibrarySizeTable(ReadsSummary readsSummary) { Table table; try {/*w w w. j a v a2 s . c o m*/ table = new Table(6); // row1 table.addCell("Library size"); table.addCell("normal"); table.addCell("tumor"); table.addCell(""); table.addCell(format(readsSummary.getNormalCounter().getMeanInsertSize())); table.addCell(format(readsSummary.getTumorCounter().getMeanInsertSize())); return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetReadsStatsChart.java
License:Apache License
private static Object getChrSummaryTable(ReadsCounter totalc, Map<String, ReadsCounter> datamap) { Table table; try {//from w ww . ja va 2 s . com table = new Table(6); // row1 table.addCell("chr/"); table.addCell("on target"); table.addCell("out of target"); table.addCell("on tag unique"); table.addCell("outoftag unique"); table.addCell("ontag %"); for (Entry<String, ReadsCounter> entry : datamap.entrySet()) { String chrom = entry.getKey(); // boolean usualchrom = usualChrom(chrom); ReadsCounter rc = entry.getValue(); int target = rc.getTotalOnTarget(); int total = rc.getTotalmap(); int outoftarget = total - target; int totalu = rc.getTotalunique(); int uniqueoutoftarget = totalu - rc.getTotalUniqueOntarget(); table.addCell(chrom); table.addCell(format(target)); table.addCell(format(outoftarget)); table.addCell(format(rc.getTotalUniqueOntarget())); table.addCell(format(uniqueoutoftarget)); table.addCell(format(rc.onTargetParcent()) + "%"); } // write total table.addCell("Total"); ReadsCounter rc = totalc; int target = rc.getTotalOnTarget(); int total = rc.getTotalmap(); int outoftarget = total - target; int totalu = rc.getTotalunique(); int uniqueoutoftarget = totalu - rc.getTotalUniqueOntarget(); table.addCell(format(target)); table.addCell(format(outoftarget)); table.addCell(format(rc.getTotalUniqueOntarget())); table.addCell(format(uniqueoutoftarget)); table.addCell(format(rc.onTargetParcent()) + "%"); return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetReadsStatsChart.java
License:Apache License
private static Object getSummaryTable(ReadsSummary readsSummary, String readsStat) { try {//from w w w.j a v a 2 s . c om ReadsCounter normal = readsSummary.getNormalCounter(); ReadsCounter tumor = readsSummary.getTumorCounter(); Table table = new Table(3); int[] width = new int[] { 60, 20, 20 }; table.setWidths(width); // row1 table.addCell("reads stats/"); table.addCell("normal"); table.addCell("tumor"); // // row if (readsStat != null) { String[] sa = readsStat.split(","); String normalfile = sa[0]; Properties np = getProp(normalfile); String tumorfile = sa[1]; Properties tp = getProp(tumorfile); // datamap.put("total", total); // datamap.put("passfilter", passfilter); // datamap.put("mapped", mapped); // datamap.put("nonduplicate", nonduplicate); // datamap.put("duplicate", duplicate); // //datamap.put("identityLow", identityLow); // datamap.put("unique", unique); // datamap.put("proper", proper); // datamap.put("properOrunique", properOrunique); // datamap.put("bincount", 1l); // datamap.put("afterrealgin", afterrealgin); // datamap.put("identityLow", identityLow); String[] keys = new String[] { "total", "passfilter", "mapped", "nonduplicate", "duplicate", "unique", "proper", "properOrunique", "afterrealgin", "identityLow" }; for (String key : keys) { if (np.containsKey(key)) { // row2 String kyeDisp = key.replaceAll("Or", " or "); table.addCell(kyeDisp + " tags"); table.addCell(format(np.getProperty(key))); table.addCell(format(tp.getProperty(key))); if (key.equals("duplicate")) { try { // row 13 table.addCell("duplicate (%)"); table.addCell( format(getParcent(np.getProperty(key), np.getProperty("nonduplicate"))) + "%"); table.addCell( format(getParcent(tp.getProperty(key), tp.getProperty("nonduplicate"))) + "%"); } catch (Exception ex) { } } } } } // row table.addCell("Total used tags"); table.addCell(format(normal.getTotalmap())); table.addCell(format(tumor.getTotalmap())); // row4 table.addCell("Target tags"); table.addCell(format(normal.getTotalOnTarget())); table.addCell(format(tumor.getTotalOnTarget())); // row5 table.addCell("Target unique tags"); table.addCell(format(normal.getTotalUniqueOntarget())); table.addCell(format(tumor.getTotalUniqueOntarget())); if (readsSummary.isPairStats()) { // row6 table.addCell("First reads"); table.addCell(format(normal.getFirstReads())); table.addCell(format(tumor.getFirstReads())); // row7 table.addCell("Second reads"); table.addCell(format(normal.getSecondReads())); table.addCell(format(tumor.getSecondReads())); // row8 table.addCell("Both mapped"); table.addCell(format(normal.getBothmap())); table.addCell(format(tumor.getBothmap())); // row9 table.addCell("Proper reads"); table.addCell(format(normal.getPropermap())); table.addCell(format(tumor.getPropermap())); // row10 table.addCell("mean library size"); table.addCell(format(normal.getMeanInsertSize())); table.addCell(format(tumor.getMeanInsertSize())); } // // row11 // row 12 table.addCell("mean depth"); table.addCell(format(readsSummary.getNormalDepth().getMeanDepth())); table.addCell(format(readsSummary.getTumorDepth().getMeanDepth())); table.addCell("total covered region"); table.addCell(format(readsSummary.getNormalDepth().getTotal())); table.addCell(format(readsSummary.getTumorDepth().getTotal())); // row 13 table.addCell("On target(%)"); table.addCell(format(normal.onTargetParcent()) + "%"); table.addCell(format(tumor.onTargetParcent()) + "%"); table.addCell("more than X20(%)"); table.addCell(format(getX20percent(readsSummary.getNormalDepth())) + "%"); table.addCell(format(getX20percent(readsSummary.getTumorDepth())) + "%"); table.addCell("mean depth CDS"); table.addCell(format(readsSummary.getNormalDepth().getMeanCDSDepth())); table.addCell(format(readsSummary.getTumorDepth().getMeanCDSDepth())); table.addCell("more than X10(%) CDS"); table.addCell(format(readsSummary.getNormalDepth().getOver10X()) + "%"); table.addCell(format(readsSummary.getTumorDepth().getOver10X()) + "%"); table.addCell("more than X20(%) CDS"); table.addCell(format(readsSummary.getNormalDepth().getOver20X()) + "%"); table.addCell(format(readsSummary.getTumorDepth().getOver20X()) + "%"); return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetSNVChart.java
License:Apache License
private static List[] getFilterStatsTables(DataSet dataset) { List olist = new ArrayList(); List olistG = new ArrayList(); Map<Integer, CounterA> sm = new LinkedHashMap<Integer, CounterA>(); Map<Integer, CounterA> ti = new LinkedHashMap<Integer, CounterA>(); Map<Integer, CounterA> smsolo = new LinkedHashMap<Integer, CounterA>(); Map<Integer, CounterA> tisolo = new LinkedHashMap<Integer, CounterA>(); ////from ww w . java 2 s.com int insersion = 0; int delation = 0; int totalmutaion = 0; // Map<String, MutationCounter> mutationCounter = new TreeMap<String, MutationCounter>(); Map<String, SNPDepthCounter> mutationCounterNormalSNP = new TreeMap<String, SNPDepthCounter>(); Map<String, SNPDepthCounter> normalmutationCounter = new TreeMap<String, SNPDepthCounter>(); Map<String, CounterA> chrCounts = new LinkedHashMap<String, CounterA>(); // String keys[] = new String[] { "AtoT", "AtoG", "AtoC", "TtoA", "TtoG", // "TtoC", "CtoA", "CtoT", "CtoG", "GtoA", "GtoT", "GtoC" }; for (String key : GenotypeKeyUtils.keys1) { mutationCounter.put(key, new MutationCounter()); mutationCounterNormalSNP.put(key, new SNPDepthCounter()); normalmutationCounter.put(key, new SNPDepthCounter()); } int mutationfilterout = 0; int indelfilterout = 0; for (SNVHolder snv : dataset.getSnvlist()) { int flg = snv.getFlg(); if (flg == PileUP.NormalSNP || flg == PileUP.REGBOTH) { char ref = snv.getNormal().getGenomeR(); char alt = snv.getNormal().getALT(); String key = ref + "to" + alt; key = GenotypeKeyUtils.aggrigateKeys(key); SNPDepthCounter counter = null; if (normalmutationCounter.containsKey(key)) { counter = normalmutationCounter.get(key); counter.reg(snv.getNormal().getTotalcnt()); } } if (flg == PileUP.NormalSNP) { // char ref = snv.getNormal().getGenomeR(); char alt = snv.getNormal().getALT(); String key = ref + "to" + alt; key = GenotypeKeyUtils.aggrigateKeys(key); SNPDepthCounter counter = null; boolean hetroSNP = snv.getNormal().getRatio() < 0.6; if (hetroSNP && mutationCounterNormalSNP.containsKey(key)) { counter = mutationCounterNormalSNP.get(key); counter.reg(snv.getNormal().getTotalcnt()); } } else if ((flg == PileUP.SomaticMutation) || (flg == PileUP.TumorINDEL)) { if (null != snv.getFilterResult()) { if (snv.getChr().equals("chr1")) { if (snv.getPos() == 13645209) { System.out.println("here"); } } Set<Integer> filterflgs = snv.getFilterResult().getPassFilterFlg(); Set<Integer> infoflgs = snv.getFilterResult().getInfoFlg(); Map<Integer, CounterA> map = (flg == PileUP.SomaticMutation) ? sm : ti; Map<Integer, CounterA> mapsolo = (flg == PileUP.SomaticMutation) ? smsolo : tisolo; CounterA ca = null; if (snv.getFilterResult().isPassFilter()) { if (map.containsKey(PASS_FILTER)) { ca = map.get(PASS_FILTER); } else { ca = new CounterA(); map.put(PASS_FILTER, ca); } ca.inc(); if (CalcUtils.pass2(snv.getFilterResult())) { addchrCounts(chrCounts, snv.getChr()); // CounterA caf = null; if (map.containsKey(PASS_FILTERFinal)) { caf = map.get(PASS_FILTERFinal); } else { caf = new CounterA(); map.put(PASS_FILTERFinal, caf); } caf.inc(); } else { for (int filterflg : infoflgs) { if (map.containsKey(filterflg)) { ca = map.get(filterflg); } else { ca = new CounterA(); map.put(filterflg, ca); } ca.inc(); } // filtered by this property only if (infoflgs.size() == 1) { int filterflg = infoflgs.iterator().next(); CounterA counter2 = null; if (mapsolo.containsKey(filterflg)) { counter2 = mapsolo.get(filterflg); } else { counter2 = new CounterA(); mapsolo.put(filterflg, counter2); } counter2.inc(); } } if (flg == PileUP.TumorINDEL) { if (snv.getTumor().isInsersion()) { insersion++; } else { delation++; } } else { char ref = snv.getTumor().getGenomeR(); char alt = snv.getTumor().getALT(); String key = ref + "to" + alt; key = GenotypeKeyUtils.aggrigateKeys(key); MutationCounter counter = null; if (mutationCounter.containsKey(key)) { counter = mutationCounter.get(key); int copynumber = (int) (snv.getCi().getVaridateVal() * 2); PileUPResult pir = snv.getTumor(); float ratio = pir.getRatio(); float fpval = (float) snv.getPvalFisher(); float normallogodd = snv.getNormal().getRefLogLikeHood(); float adgustedmutateodds = (float) snv.getFilterResult().getLogtAjusted(); if (fpval == 0) { fpval = 0.0000000000000001f; } float logp = (float) (-1 * Math.log10(fpval)); int depth = pir.getTotalcnt(); counter.regStat(copynumber, ratio, logp, depth); if (CalcUtils.pass2(snv.getFilterResult())) { counter.regStat2(depth); } totalmutaion++; } // / } } else { // filter out if (flg == PileUP.TumorINDEL) { indelfilterout++; } else { mutationfilterout++; } for (int filterflg : filterflgs) { if (map.containsKey(filterflg)) { ca = map.get(filterflg); } else { ca = new CounterA(); map.put(filterflg, ca); } ca.inc(); } // filtered by this property only if (filterflgs.size() == 1) { int filterflg = filterflgs.iterator().next(); CounterA counter2 = null; if (mapsolo.containsKey(filterflg)) { counter2 = mapsolo.get(filterflg); } else { counter2 = new CounterA(); mapsolo.put(filterflg, counter2); } counter2.inc(); } } } } } try { Table table1 = summarytable(sm, ti, smsolo, tisolo, mutationfilterout, indelfilterout); olist.add(table1); // // ////////////////// // mutation stat Table tablemutation = new Table(3); tablemutation.addCell("mutation type"); tablemutation.addCell("counts"); tablemutation.addCell("%"); Set<Entry<String, MutationCounter>> s = mutationCounter.entrySet(); for (Entry<String, MutationCounter> e : s) { tablemutation.addCell(GenotypeKeyUtils.toDispKey(e.getKey())); MutationCounter mc = e.getValue(); int cnt = mc.getTotal(); float parcent = (float) ((double) cnt * 100 / (double) totalmutaion); tablemutation.addCell(String.valueOf(cnt)); tablemutation.addCell(String.valueOf(parcent) + "%"); } tablemutation.addCell("delation"); tablemutation.addCell(String.valueOf(delation)); tablemutation.addCell("-"); tablemutation.addCell("insertion"); tablemutation.addCell(String.valueOf(insersion)); tablemutation.addCell("-"); olist.add(tablemutation); ///chr table // Table tablechr = new Table(2); tablechr.addCell("chr"); tablechr.addCell("final candidates"); Set<Entry<String, CounterA>> chrs = chrCounts.entrySet(); for (Entry<String, CounterA> e : chrs) { tablechr.addCell(e.getKey()); tablechr.addCell("" + e.getValue().getCnt()); } olist.add(tablechr); // mutation stat Table tableallele = new Table(13); tableallele.addCell("type"); tableallele.addCell("counts(n=1)"); tableallele.addCell("ratio mean(n=1)"); tableallele.addCell("ratio sd(n=1)"); tableallele.addCell("counts(n=2)"); tableallele.addCell("ratio mean(n=2)"); tableallele.addCell("ratio sd(n=2)"); tableallele.addCell("counts(n=3)"); tableallele.addCell("ratio mean(n=3)"); tableallele.addCell("ratio sd(n=3)"); tableallele.addCell("counts(n=4)"); tableallele.addCell("ratio mean(n=4)"); tableallele.addCell("ratio sd(n=4)"); // for (Entry<String, MutationCounter> e : s) { MutationCounter mc = e.getValue(); // int cnt = mc.getTotal(); tableallele.addCell(GenotypeKeyUtils.toDispKey(e.getKey())); for (int n = 1; n <= 4; n++) { SummaryStatsHolder ssh = mc.getSummaryStatsHolder(n); if (null != ssh) { tableallele.addCell(ssh.getRatio().getN() + ""); tableallele.addCell(format(ssh.getRatio().getMean())); tableallele.addCell(format(ssh.getRatio().getStandardDeviation())); } else { tableallele.addCell("-"); tableallele.addCell("-"); tableallele.addCell("-"); } } } olist.add(tableallele); // mutation stat Table tableallelep = new Table(13); tableallelep.addCell("type"); tableallelep.addCell("counts(n=1)"); tableallelep.addCell("log(p val) mean(n=1)"); tableallelep.addCell("log(p val) sd(n=1)"); tableallelep.addCell("counts(n=2)"); tableallelep.addCell("log(p val) mean(n=2)"); tableallelep.addCell("log(p val) sd(n=2)"); tableallelep.addCell("counts(n=3)"); tableallelep.addCell("log(p val) mean(n=3)"); tableallelep.addCell("log(p val) sd(n=3)"); tableallelep.addCell("counts(n=4)"); tableallelep.addCell("log(p val) mean(n=4)"); tableallelep.addCell("log(p val) sd(n=4)"); // for (Entry<String, MutationCounter> e : s) { MutationCounter mc = e.getValue(); // int cnt = mc.getTotal(); tableallelep.addCell(GenotypeKeyUtils.toDispKey(e.getKey())); for (int n = 1; n <= 4; n++) { SummaryStatsHolder ssh = mc.getSummaryStatsHolder(n); if (null != ssh) { tableallelep.addCell(ssh.getOddsratio().getN() + ""); tableallelep.addCell(format(ssh.getOddsratio().getMean())); tableallelep.addCell(format(ssh.getOddsratio().getStandardDeviation())); } else { tableallelep.addCell("-"); tableallelep.addCell("-"); tableallelep.addCell("-"); } } } olist.add(tableallelep); Set<Entry<String, SNPDepthCounter>> sNormal = normalmutationCounter.entrySet(); DefaultCategoryDataset cdatasetNormal = new DefaultCategoryDataset(); for (Entry<String, SNPDepthCounter> e : sNormal) { SNPDepthCounter sc = e.getValue(); int lowcnt = sc.getLowdepthcnt(); cdatasetNormal.addValue(lowcnt, "x1-x2(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x2count = sc.getX2count(); cdatasetNormal.addValue(x2count, "x2-x3(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x3count = sc.getX3count(); cdatasetNormal.addValue(x3count, "x3-x4(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x4count = sc.getX2count(); cdatasetNormal.addValue(x4count, "x4-x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int highdepth = sc.getHighdepthcnt(); cdatasetNormal.addValue(highdepth, "< x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); } JFreeChart jfcNormal = ChartFactory.createStackedBarChart("normal mutation frequency", "mutation", "counts", cdatasetNormal, PlotOrientation.VERTICAL, true, false, false); jfcNormal.getPlot().setBackgroundPaint(Color.WHITE); setSeriespaint(jfcNormal); olistG.add(jfcNormal); // Set<Entry<String, SNPDepthCounter>> sSNP = mutationCounterNormalSNP.entrySet(); DefaultCategoryDataset cdatasetSNP = new DefaultCategoryDataset(); for (Entry<String, SNPDepthCounter> e : sSNP) { SNPDepthCounter sc = e.getValue(); int lowcnt = sc.getLowdepthcnt(); cdatasetSNP.addValue(lowcnt, "x1-x2(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x2count = sc.getX2count(); cdatasetSNP.addValue(x2count, "x2-x3(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x3count = sc.getX3count(); cdatasetSNP.addValue(x3count, "x3-x4(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x4count = sc.getX2count(); cdatasetSNP.addValue(x4count, "x4-x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int highdepth = sc.getHighdepthcnt(); cdatasetSNP.addValue(highdepth, "< x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); } JFreeChart jfcSNP = ChartFactory.createStackedBarChart("normal SNP frequency", "mutation", "counts", cdatasetSNP, PlotOrientation.VERTICAL, true, false, false); jfcSNP.getPlot().setBackgroundPaint(Color.WHITE); setSeriespaint(jfcSNP); olistG.add(jfcSNP); // DefaultCategoryDataset cdataset = new DefaultCategoryDataset(); for (Entry<String, MutationCounter> e : s) { MutationCounter mc = e.getValue(); int lowcnt = mc.getLowdepthcnt(); cdataset.addValue(lowcnt, "x1-x2(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x2count = mc.getX2count(); cdataset.addValue(x2count, "x2-x3(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x3count = mc.getX3count(); cdataset.addValue(x3count, "x3-x4(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x4count = mc.getX2count(); cdataset.addValue(x4count, "x4-x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int highdepth = mc.getHighdepthcnt(); cdataset.addValue(highdepth, "< x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); } JFreeChart jfc = ChartFactory.createStackedBarChart("mutation frequency", "mutation", "counts", cdataset, PlotOrientation.VERTICAL, true, false, false); jfc.getPlot().setBackgroundPaint(Color.WHITE); setSeriespaint(jfc); olistG.add(jfc); // DefaultCategoryDataset cdataset2 = new DefaultCategoryDataset(); for (Entry<String, MutationCounter> e : s) { MutationCounter mc = e.getValue(); int lowcnt = mc.getLowdepthcntH(); cdataset2.addValue(lowcnt, "x1-x2(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x2count = mc.getX2countH(); cdataset2.addValue(x2count, "x2-x3(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x3count = mc.getX3countH(); cdataset2.addValue(x3count, "x3-x4(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int x4count = mc.getX2countH(); cdataset2.addValue(x4count, "x4-x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); int highdepth = mc.getHighdepthcntH(); cdataset2.addValue(highdepth, "< x5(" + KarkinosProp.mindepth + ")", GenotypeKeyUtils.toDispKey(e.getKey())); } JFreeChart jfc2 = ChartFactory.createStackedBarChart("mutation frequency filter2", "mutation", "counts", cdataset2, PlotOrientation.VERTICAL, true, false, false); jfc2.getPlot().setBackgroundPaint(Color.WHITE); setSeriespaint(jfc2); olistG.add(jfc2); return new List[] { olist, olistG }; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetSNVChart.java
License:Apache License
private static Table summarytable(Map<Integer, CounterA> sm, Map<Integer, CounterA> ti, Map<Integer, CounterA> smsolo, Map<Integer, CounterA> tisolo, int mutationfilterout, int indelfilterout) throws BadElementException { Table table = new Table(3); ////from ww w . ja v a 2s. c o m // row1 table.addCell("filter type"); table.addCell("somatic mutation"); table.addCell("somatic indel"); // public static final int SNP = 1; // public static final int Low_mappability = 5; // public static final int Low_complexty = 6; // public static final int Low_SNPQual = 7; // public static final int Basian_Filteling = 9; // public static final int SUPPORTED_READSNG = 19; // public static final int SUPPORTED_BY_ONEDirection = 11; // public static final int CONTAIN_Reccurent_MISMATCH = 12; // public static final int READSENDSONLY = 13; // public static final int TooManyMismatchReads = 14; // public static final int MutationAtSameCycle = 15; // table.addCell("Pass filter Filter2"); table.addCell(getContStr(sm, PASS_FILTERFinal)); table.addCell(getContStr(ti, PASS_FILTERFinal)); table.addCell("Pass filter Filter1"); table.addCell(getContStr(sm, FilterResult.PASS_FILTER)); table.addCell(getContStr(ti, FilterResult.PASS_FILTER)); table.addCell("Filtered out total"); table.addCell(String.valueOf(mutationfilterout)); table.addCell(String.valueOf(indelfilterout)); // table.addCell("High normal TC adjuated ratio"); // table.addCell(getContStr(sm, smsolo, FilterResult.High_normal_adjustedRatio)); // table.addCell(getContStr(ti, tisolo, FilterResult.High_normal_adjustedRatio)); // table.addCell("Bayesian filter for normal"); table.addCell(getContStr(sm, smsolo, FilterResult.INFO_LOW_refOddsRatio)); table.addCell(getContStr(ti, tisolo, FilterResult.INFO_LOW_refOddsRatio)); table.addCell("Bayesian filter for tumor"); table.addCell(getContStr(sm, smsolo, FilterResult.INFO_LOW_tumorOddsRatio)); table.addCell(getContStr(ti, tisolo, FilterResult.INFO_LOW_tumorOddsRatio)); table.addCell("Low adjuated allele ratio"); table.addCell(getContStr(sm, smsolo, FilterResult.INFO_adjustAlleleFreq)); table.addCell(getContStr(ti, tisolo, FilterResult.INFO_adjustAlleleFreq)); table.addCell("Low support reads for TP rescued candidate"); table.addCell(getContStr(sm, smsolo, FilterResult.INFO_adjustLowdepth)); table.addCell(getContStr(ti, tisolo, FilterResult.INFO_adjustLowdepth)); table.addCell("min support reads for non cosmic sites"); table.addCell(getContStr(sm, smsolo, FilterResult.INFO_minimumSupportReads)); table.addCell(getContStr(ti, tisolo, FilterResult.INFO_minimumSupportReads)); table.addCell("Low TC adjuated ratio"); table.addCell(getContStr(sm, smsolo, FilterResult.Low_tumor_adjustedRatio)); table.addCell(getContStr(ti, tisolo, FilterResult.Low_tumor_adjustedRatio)); table.addCell("Low AF in AF depth matrix"); table.addCell(getContStr(sm, smsolo, FilterResult.Low_tumor_adjustedReads)); table.addCell(getContStr(ti, tisolo, FilterResult.Low_tumor_adjustedReads)); table.addCell("High low base quality reads ratio"); table.addCell(getContStr(sm, smsolo, FilterResult.HighLowQualReads)); table.addCell(getContStr(ti, tisolo, FilterResult.HighLowQualReads)); table.addCell("dbSNP"); table.addCell(getContStr(sm, smsolo, FilterResult.SNP)); table.addCell(getContStr(ti, tisolo, FilterResult.SNP)); // table.addCell("Supported by only one directional reads"); table.addCell(getContStr(sm, smsolo, SUPPORTED_BY_ONEDirection)); table.addCell(getContStr(ti, tisolo, FilterResult.SUPPORTED_BY_ONEDirection)); // table.addCell("Support reads contain another recurrent mismatch"); table.addCell(getContStr(sm, smsolo, FilterResult.CONTAIN_Reccurent_MISMATCH)); table.addCell(getContStr(ti, tisolo, FilterResult.CONTAIN_Reccurent_MISMATCH)); table.addCell("Support reads allelic inblance"); table.addCell(getContStr(sm, smsolo, FilterResult.noStrandSpecific)); table.addCell(getContStr(ti, tisolo, FilterResult.noStrandSpecific)); table.addCell("Support reads contain toomany mismatch"); table.addCell(getContStr(sm, smsolo, FilterResult.TooManyMismatchReads)); table.addCell(getContStr(ti, tisolo, FilterResult.TooManyMismatchReads)); // table.addCell("Low Mappability "); table.addCell(getContStr(sm, smsolo, FilterResult.Low_mappability)); table.addCell(getContStr(ti, tisolo, FilterResult.Low_mappability)); table.addCell("Low Map Quality "); table.addCell(getContStr(sm, smsolo, FilterResult.Low_MapQuality)); table.addCell(getContStr(ti, tisolo, FilterResult.Low_MapQuality)); table.addCell("Low sequence complexty"); table.addCell(getContStr(sm, smsolo, FilterResult.Low_complexty)); table.addCell(getContStr(ti, tisolo, FilterResult.Low_complexty)); table.addCell("illumina Sys Error"); table.addCell(getContStr(sm, smsolo, FilterResult.illuminaSpecific)); table.addCell(getContStr(ti, tisolo, FilterResult.illuminaSpecific)); table.addCell("only softClip support"); table.addCell(getContStr(sm, smsolo, FilterResult.softClip)); table.addCell(getContStr(ti, tisolo, FilterResult.softClip)); table.addCell("Mutation at same Cycle"); table.addCell(getContStr(sm, smsolo, FilterResult.MutationAtSameCycle)); table.addCell(getContStr(ti, tisolo, FilterResult.MutationAtSameCycle)); table.addCell("Fisher test fail p > " + (float) KarkinosProp.Fisher_Thres_For_SNV_Detection); table.addCell(getContStr(sm, smsolo, FilterResult.FisherTestFail)); table.addCell(getContStr(ti, tisolo, FilterResult.FisherTestFail)); table.addCell("SNV near Indel"); table.addCell(getContStr(sm, smsolo, FilterResult.NEARINDEL)); table.addCell(getContStr(ti, tisolo, FilterResult.NEARINDEL)); return table; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.GetSNVChart.java
License:Apache License
private static Object getTRTable(DataSet dataset, PeaksInfo pi) { AnalyseDist analyseDist = dataset.getAnalyseDist(); try {// w ww .j a v a2s.co m Table table = new Table(6); // row1 table.addCell("source"); table.addCell("tumor purity"); table.addCell("s.d."); table.addCell("#total SNP"); table.addCell("correl"); table.addCell("method"); // row2 table.addCell("n=1"); table.addCell(format(analyseDist.getTumorratioFromLOH().getTumorratio())); table.addCell(format(analyseDist.getTumorratioFromLOH().getSd() * 0.01)); table.addCell(format(analyseDist.getTumorratioFromLOH().getNumber())); table.addCell(format(analyseDist.getTumorratioFromLOH().getCorrel())); table.addCell(analyseDist.getTumorratioFromLOH().getModeStr()); // row2 table.addCell("n=3"); table.addCell(format(analyseDist.getTumorratioFromGAIN().getTumorratio())); table.addCell(format(analyseDist.getTumorratioFromGAIN().getSd() * 0.01)); table.addCell(format(analyseDist.getTumorratioFromGAIN().getNumber())); table.addCell(format(analyseDist.getTumorratioFromGAIN().getCorrel())); table.addCell(analyseDist.getTumorratioFromGAIN().getModeStr()); // row2 table.addCell("somatic"); table.addCell(format(analyseDist.getTumorratioFromSomatic().getTumorratio())); table.addCell(format(analyseDist.getTumorratioFromSomatic().getSd() * 0.01)); table.addCell(format(analyseDist.getTumorratioFromSomatic().getNumber())); table.addCell(format(analyseDist.getTumorratioFromSomatic().getCorrel())); table.addCell("from distribution of somatic mutations"); table.addCell("tumor purity from ploidy matrix"); table.addCell(format(dataset.getTumorratioFiitiingMatrix())); table.addCell(""); table.addCell(""); table.addCell(""); table.addCell(""); table.addCell("tumor purity from ploidy matrix"); table.addCell(format(dataset.getTumorratioFiitiingMatrix())); table.addCell(""); table.addCell(""); table.addCell(""); table.addCell(""); table.addCell("ploidy"); table.addCell(format(pi.getPloidy())); table.addCell(""); table.addCell(""); table.addCell(""); table.addCell(""); table.addCell("tumor purity used"); table.addCell(format(dataset.getTumorRatio())); // return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:jp.ac.utokyo.rcast.karkinos.graph.SNPGraph.java
License:Apache License
private static Object getTable(long snpRecurrent, long snpDiff) { Table table; try {/* w ww .java 2 s . com*/ table = new Table(4); // row1 table.addCell("total dbSNP detected in 2n"); table.addCell("recurrent SNP"); table.addCell("different SNP"); table.addCell("% diffrerence SNP"); table.addCell(format(snpRecurrent + snpDiff)); table.addCell(format(snpRecurrent)); table.addCell(format(snpDiff)); double ratio = ((double) snpDiff / (double) (snpRecurrent + snpDiff)) * 100; table.addCell(format(ratio) + "%"); return table; } catch (Exception e) { // TODO Auto-generated catch block e.printStackTrace(); } return null; }
From source file:net.bull.javamelody.swing.print.MPdfWriter.java
License:Apache License
/** * Effectue le rendu des headers./*from ww w .j a v a 2s . c om*/ * * @param table * MBasicTable * @param datatable * Table * @throws BadElementException * e */ protected void renderHeaders(final MBasicTable table, final Table datatable) throws BadElementException { final int columnCount = table.getColumnCount(); final TableColumnModel columnModel = table.getColumnModel(); // size of columns float totalWidth = 0; for (int i = 0; i < columnCount; i++) { totalWidth += columnModel.getColumn(i).getWidth(); } final float[] headerwidths = new float[columnCount]; for (int i = 0; i < columnCount; i++) { headerwidths[i] = 100f * columnModel.getColumn(i).getWidth() / totalWidth; } datatable.setWidths(headerwidths); datatable.setWidth(100f); // table header final com.lowagie.text.Font font = FontFactory.getFont(FontFactory.HELVETICA, 12, Font.BOLD); datatable.getDefaultCell().setBorderWidth(2); datatable.getDefaultCell().setHorizontalAlignment(Element.ALIGN_CENTER); // datatable.setDefaultCellGrayFill(0.75f); String text; Object value; for (int i = 0; i < columnCount; i++) { value = columnModel.getColumn(i).getHeaderValue(); text = value != null ? value.toString() : ""; datatable.addCell(new Phrase(text, font)); } // end of the table header datatable.endHeaders(); }