Look at the attached movie.

I set Xaxis to be at the left, and Yaxis to be at the bottom, and got the confused chart. If it is not a permissed action, it must at least not to affect.

Code:

import java.util.Arrays;
import java.util.Comparator;
import java.util.Random;
import javafx.application.Application;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.geometry.Side;
import javafx.scene.Scene;
import javafx.scene.chart.LineChart;
import javafx.scene.chart.NumberAxis;
import javafx.scene.chart.XYChart;
import javafx.scene.control.ComboBox;
import javafx.scene.control.Label;
import javafx.scene.layout.Pane;
import javafx.scene.layout.VBox;
import javafx.stage.Stage;

public class JavaCharts extends Application {

    public static void main(String[] args) {
        launch(args);
    }
    NumberAxis axis1 = new NumberAxis(0, 100, 10);
    NumberAxis axis2 = new NumberAxis(0, 100, 10);
    LineChart testedLineChart = new LineChart(axis1, axis2);
    VBox vb = new VBox();

    @Override
    public void start(Stage stage) throws Exception {
        testedLineChart.setTitle("LineChart");
        testedLineChart.setStyle("-fx-border-color: darkgray;");

        ObservableList list = FXCollections.observableArrayList();
        int max = 100;
        int min = 30;

        for (int i = 0; i < 30; i++) {
            XYChart.Data newData = new XYChart.Data();
            newData.setXValue(new Random().nextDouble() * (max - min) + min);
            newData.setYValue(new Random().nextDouble() * (max - min) + min);
            list.add(newData);
        }
        Object[] array = list.toArray();
        Arrays.sort(array, new Comparator() {

            @Override
            public int compare(Object t, Object t1) {
                return (int) Math.round(((Double) ((XYChart.Data) t).getXValue()) - ((Double) ((XYChart.Data) t1).getXValue()));
            }
        });

        XYChart.Series serie = new XYChart.Series("serie", FXCollections.observableArrayList(array));

        testedLineChart.getData().add(serie);

        Pane pane = new Pane();
        pane.setPrefSize(600, 600);

        ComboBox cb1 = new ComboBox();
        cb1.getItems().addAll(Side.values());
        cb1.valueProperty().bindBidirectional(axis1.sideProperty());

        ComboBox cb2 = new ComboBox();
        cb2.getItems().addAll(Side.values());
        cb2.valueProperty().bindBidirectional(axis2.sideProperty());

        pane.setPrefSize(600, 600);
        pane.getChildren().add(testedLineChart);

        vb.getChildren().addAll(pane, new Label("X-axis"), cb1, new Label("Y-axis"), cb2);

        Scene scene = new Scene(vb, 700, 700);
        stage.setScene(scene);
        stage.show();
    }
}