Examples with NumberAxis javafx.scene.chart.NumberAxis used on opensource projects

Example 26 with NumberAxis

use of javafx.scene.chart.NumberAxis in project jvarkit by lindenb.

the class GenotypeTypeChartFactory method build.

@Override
public Chart build() {
    final CategoryAxis xAxis = new CategoryAxis();
    xAxis.setLabel("Sample");
    final NumberAxis yAxis = new NumberAxis();
    yAxis.setLabel("Count");
    final List<XYChart.Series<String, Number>> gtype2count = new ArrayList<>(GenotypeType.values().length);
    for (final GenotypeType genotypeType : GenotypeType.values()) {
        final XYChart.Series<String, Number> serie = new XYChart.Series<String, Number>();
        serie.setName(genotypeType.name());
        gtype2count.add(serie);
        for (final String sampleName : this.sample2count.keySet()) {
            serie.getData().add(new XYChart.Data<String, Number>(sampleName, this.sample2count.get(sampleName).count(genotypeType)));
        }
    }
    final StackedBarChart<String, Number> sbc = new StackedBarChart<String, Number>(xAxis, yAxis);
    sbc.setTitle(this.getName());
    sbc.getData().addAll(gtype2count);
    sbc.setCategoryGap(0.2);
    return sbc;
}

Example 27 with NumberAxis

use of javafx.scene.chart.NumberAxis in project jvarkit by lindenb.

the class QualityPerPositionChartFactory method build.

public LineChart<Number, Number> build() {
    final NumberAxis xAxis = new NumberAxis();
    xAxis.setLabel("Position in Read");
    final NumberAxis yAxis = new NumberAxis();
    yAxis.setLabel("Read Quality");
    final XYChart.Series<Number, Number> serie_mean = new XYChart.Series<Number, Number>();
    serie_mean.setName("Mean Quality");
    final XYChart.Series<Number, Number> serie_min = new XYChart.Series<Number, Number>();
    serie_min.setName("Min Quality");
    final XYChart.Series<Number, Number> serie_max = new XYChart.Series<Number, Number>();
    serie_max.setName("Max Quality");
    for (int x = 0; x < this.pos2qual.size(); ++x) {
        final QualData q = this.pos2qual.get(x);
        serie_mean.getData().add(new XYChart.Data<Number, Number>((x + 1), q.get()));
        serie_min.getData().add(new XYChart.Data<Number, Number>((x + 1), q.min()));
        serie_max.getData().add(new XYChart.Data<Number, Number>((x + 1), q.max()));
    }
    final LineChart<Number, Number> sbc = new LineChart<Number, Number>(xAxis, yAxis);
    sbc.setTitle("Position/Quality");
    sbc.getData().add(serie_min);
    sbc.getData().add(serie_mean);
    sbc.getData().add(serie_max);
    sbc.setCreateSymbols(false);
    return sbc;
}

Example 28 with NumberAxis

use of javafx.scene.chart.NumberAxis in project jvarkit by lindenb.

the class ReadLengthChartFactory method build.

@Override
public StackedBarChart<String, Number> build() {
    final CategoryAxis xAxis = new CategoryAxis();
    xAxis.setLabel("Length");
    final NumberAxis yAxis = new NumberAxis();
    yAxis.setLabel("Count");
    final XYChart.Series<String, Number> serie = new XYChart.Series<String, Number>();
    serie.setName("Length");
    for (final Integer L : new TreeSet<Integer>(this.length2count.keySet())) {
        serie.getData().add(new XYChart.Data<String, Number>(String.valueOf(L), this.length2count.count(L)));
    }
    final StackedBarChart<String, Number> sbc = new StackedBarChart<String, Number>(xAxis, yAxis);
    sbc.setTitle("Reads Lengths");
    sbc.getData().add(serie);
    sbc.setCategoryGap(0.2);
    sbc.setLegendVisible(false);
    return sbc;
}

Example 29 with NumberAxis

use of javafx.scene.chart.NumberAxis in project jvarkit by lindenb.

the class SamFlagsChartFactory method build.

@Override
public StackedBarChart<String, Number> build() {
    final CategoryAxis xAxis = new CategoryAxis();
    xAxis.setLabel("Flags");
    final NumberAxis yAxis = new NumberAxis();
    yAxis.setLabel("Count");
    final XYChart.Series<String, Number> serie = new XYChart.Series<String, Number>();
    serie.setName("Flags");
    for (final Integer L : new TreeSet<Integer>(this.flags2count.keySet())) {
        serie.getData().add(new XYChart.Data<String, Number>(String.valueOf(L), this.flags2count.count(L)));
    }
    final StackedBarChart<String, Number> sbc = new StackedBarChart<String, Number>(xAxis, yAxis);
    sbc.setTitle("SAM Flags");
    sbc.getData().add(serie);
    sbc.setCategoryGap(0.2);
    sbc.setLegendVisible(false);
    return sbc;
}

Example 30 with NumberAxis

use of javafx.scene.chart.NumberAxis in project jvarkit by lindenb.

the class CaseControlJfx method doWork.

@Override
public int doWork(final Stage primaryStage, final List<String> args) {
    final VariantPartition partition;
    Pedigree pedigree = null;
    VcfIterator in = null;
    try {
        switch(this.partitionType) {
            case variantType:
                partition = new VariantTypePartition();
                break;
            case chromosome:
                partition = new ChromosomePartition();
                break;
            case autosomes:
                partition = new SexualContigPartition();
                break;
            case qual:
                partition = new QualPartition();
                break;
            case vqslod:
                partition = new VQSLODPartition();
                break;
            case typeFilter:
                partition = new TypeAndFilterPartiton();
                break;
            case distance:
                partition = new DisanceToDiagonalPartiton();
                break;
            case n_alts:
                partition = new NAltsPartition();
                break;
            default:
                throw new IllegalStateException(this.partitionType.name());
        }
        if (args.isEmpty()) {
            in = VCFUtils.createVcfIteratorStdin();
            primaryStage.setTitle(CaseControlJfx.class.getSimpleName());
        } else if (args.size() == 1) {
            in = VCFUtils.createVcfIterator(args.get(0));
            primaryStage.setTitle(args.get(0));
        } else {
            LOG.error("Illegal Number of arguments: " + args);
            return -1;
        }
        if (this.pedigreeFile != null) {
            pedigree = Pedigree.newParser().parse(this.pedigreeFile);
        } else {
            pedigree = Pedigree.newParser().parse(in.getHeader());
        }
        if (this.controlTag != null) {
            final VCFInfoHeaderLine infoHeaderLine = in.getHeader().getInfoHeaderLine(this.controlTag);
            if (infoHeaderLine == null) {
                LOG.error("No such attribute in the VCF header: " + this.controlTag);
                return -1;
            }
        }
        int count = 0;
        final SAMSequenceDictionaryProgress progress = new SAMSequenceDictionaryProgress(in.getHeader());
        while (in.hasNext() && (this.limit_to_N_variants < 0 || count < this.limit_to_N_variants)) {
            final VariantContext ctx = progress.watch(in.next());
            if (this.ignore_ctx_filtered && ctx.isFiltered())
                continue;
            ++count;
            final List<Allele> alternates = ctx.getAlternateAlleles();
            for (int alt_idx = 0; alt_idx < alternates.size(); ++alt_idx) {
                final Allele alt = alternates.get(alt_idx);
                final Double[] mafs = { null, null };
                for (int i = 0; i < 2; ++i) {
                    if (i == 1 && this.controlTag != null) {
                        if (ctx.hasAttribute(this.controlTag)) {
                            try {
                                final List<Double> dvals = ctx.getAttributeAsDoubleList(this.controlTag, Double.NaN);
                                if (alt_idx < dvals.size() && dvals.get(alt_idx) != null) {
                                    final double d = dvals.get(alt_idx);
                                    if (!Double.isNaN(d) && d >= 0 && d <= 1.0)
                                        mafs[1] = d;
                                }
                            } catch (NumberFormatException err) {
                            }
                        }
                    } else {
                        final MafCalculator mafCalculator = new MafCalculator(alt, ctx.getContig());
                        mafCalculator.setNoCallIsHomRef(no_call_is_homref);
                        for (Pedigree.Person person : (i == 0 ? pedigree.getAffected() : pedigree.getUnaffected())) {
                            if (selectSamples.equals(SelectSamples.males) && !person.isMale())
                                continue;
                            if (selectSamples.equals(SelectSamples.females) && !person.isFemale())
                                continue;
                            final Genotype genotype = ctx.getGenotype(person.getId());
                            if (genotype == null)
                                continue;
                            if (ignore_gt_filtered && genotype.isFiltered())
                                continue;
                            mafCalculator.add(genotype, person.isMale());
                        }
                        if (!mafCalculator.isEmpty()) {
                            mafs[i] = mafCalculator.getMaf();
                        }
                    }
                }
                if (mafs[0] == null || mafs[1] == null)
                    continue;
                final XYChart.Data<Number, Number> data = new XYChart.Data<Number, Number>(mafs[0], mafs[1]);
                if (this.add_tooltip && this.outputFile == null) {
                    data.setExtraValue(ctx.getContig() + ":" + ctx.getStart());
                }
                partition.add(ctx, pedigree, data);
            }
        }
        progress.finish();
        in.close();
        in = null;
    } catch (final Exception err) {
        LOG.error(err);
        return -1;
    } finally {
        CloserUtil.close(in);
    }
    final NumberAxis xAxis = new NumberAxis(0.0, 1.0, 0.1);
    xAxis.setLabel("Cases");
    final NumberAxis yAxis = new NumberAxis(0.0, 1.0, 0.1);
    yAxis.setLabel("Controls" + (this.controlTag == null ? "" : "[" + this.controlTag + "]"));
    final ScatterChart<Number, Number> chart = new ScatterChart<>(xAxis, yAxis);
    for (final XYChart.Series<Number, Number> series : partition.getSeries()) {
        chart.getData().add(series);
    }
    String title = "Case/Control";
    if (!args.isEmpty()) {
        title = args.get(0);
        int slash = title.lastIndexOf("/");
        if (slash != -1)
            title = title.substring(slash + 1);
        if (title.endsWith(".vcf.gz"))
            title = title.substring(0, title.length() - 7);
        if (title.endsWith(".vcf"))
            title = title.substring(0, title.length() - 4);
    }
    if (userTitle != null)
        title = userTitle;
    chart.setTitle(title);
    chart.setAnimated(false);
    chart.setLegendSide(this.legendSide);
    final VBox root = new VBox();
    MenuBar menuBar = new MenuBar();
    Menu menu = new Menu("File");
    MenuItem item = new MenuItem("Save image as...");
    item.setOnAction(AE -> {
        doMenuSave(chart);
    });
    menu.getItems().add(item);
    menu.getItems().add(new SeparatorMenuItem());
    item = new MenuItem("Quit");
    item.setOnAction(AE -> {
        Platform.exit();
    });
    menu.getItems().add(item);
    menuBar.getMenus().add(menu);
    root.getChildren().add(menuBar);
    final BorderPane contentPane = new BorderPane();
    contentPane.setCenter(chart);
    root.getChildren().add(contentPane);
    Rectangle2D screen = Screen.getPrimary().getVisualBounds();
    double minw = Math.max(Math.min(screen.getWidth(), screen.getHeight()) - 50, 50);
    chart.setPrefSize(minw, minw);
    final Scene scene = new Scene(root, minw, minw);
    primaryStage.setScene(scene);
    if (this.outputFile != null) {
        primaryStage.setOnShown(WE -> {
            LOG.info("saving as " + this.outputFile);
            try {
                saveImageAs(chart, this.outputFile);
            } catch (IOException err) {
                LOG.error(err);
                System.exit(-1);
            }
            Platform.exit();
        });
    }
    primaryStage.show();
    if (this.outputFile == null) {
        // http://stackoverflow.com/questions/14117867
        for (final XYChart.Series<Number, Number> series : partition.getSeries()) {
            for (XYChart.Data<Number, Number> d : series.getData()) {
                if (dataOpacity >= 0 && dataOpacity < 1.0) {
                    d.getNode().setStyle(d.getNode().getStyle() + "-fx-opacity:0.3;");
                }
                if (this.add_tooltip) {
                    final Tooltip tooltip = new Tooltip();
                    tooltip.setText(String.format("%s (%f / %f)", String.valueOf(d.getExtraValue()), d.getXValue().doubleValue(), d.getYValue().doubleValue()));
                    Tooltip.install(d.getNode(), tooltip);
                }
            }
        }
    }
    return 0;
}