I am trying to perform PCA, TSne or some other sort of dimensionality reduction technique to get a visualisation of cluster assignments from a text file in the following format (where the first column shown is the instance number and the second column shown is what cluster that instance belongs to. Can this be done? Any suggestions as to how I would do this would be great.
0 1
1 0
2 1
3 0
4 0
5 0
6 1
7 0
8 1
9 0
10 1
11 1
12 1
13 1
14 1
15 0
my first Answer on stackoverflow (ahhh ^^')
for PCA-implementation see here: PCA Implementation in Java
for easy plotting of any kind in Java I recommend JavaFX (https://openjfx.io/)
here is some sample code to create plots using JavaFX:
import javafx.application.Application;
import javafx.collections.FXCollections;
import javafx.collections.ObservableList;
import javafx.geometry.Rectangle2D;
import javafx.scene.Parent;
import javafx.scene.Scene;
import javafx.scene.chart.BarChart;
import javafx.scene.chart.CategoryAxis;
import javafx.scene.chart.LineChart;
import javafx.scene.chart.NumberAxis;
import javafx.scene.chart.PieChart;
import javafx.scene.chart.XYChart;
import javafx.scene.layout.HBox;
import javafx.scene.layout.Pane;
import javafx.scene.layout.VBox;
import javafx.stage.Screen;
import javafx.stage.Stage;
/*
* DIFFERENT CHART TYPES IN JAVA FX:
*
* JavaFX PieChart
JavaFX LineChart
JavaFX Area Chart
JavaFX BubbleChart
JavaFX BarChart
JavaFX ScatterChart
*
*/
public class MyCharts extends Application {
private double screenFac = 1.25;
private Rectangle2D screenSize;
private double width;
private double height;
private Pane root;
private Parent showMyCharts() {
root = createRoot();
/* we have to use NEW NumberAxis-Objects
* for each BarChart
* it is not possible to share the same NumberAxis-Object
* with different Bar charts
*/
final NumberAxis xAxis1 = new NumberAxis();
final NumberAxis xAxis2 = new NumberAxis();
final NumberAxis xAxis3 = new NumberAxis();
final CategoryAxis yAxis1 = new CategoryAxis();
final CategoryAxis yAxis2 = new CategoryAxis();
final CategoryAxis yAxis3 = new CategoryAxis();
final BarChart<Number, String> bc1 = new BarChart<Number, String>(xAxis1, yAxis1);
// here use other NumberAxis-Object
// final BarChart<Number, String> bc2 = new BarChart<Number, String>(xAxis2, yAxis2);
LineChart<Number, String> l1 = new LineChart<>(xAxis2, yAxis2);
// define BarChart settings
bc1.setTitle("myBarChart");
xAxis1.setLabel("Value");
xAxis1.setTickLabelRotation(90);
yAxis1.setLabel("Item");
l1.setTitle("myLineChart");
xAxis2.setLabel("Value");
// create some Data series
XYChart.Series<Number, String> series1 = new XYChart.Series<>();
final String itemA = "A";
final String itemB = "B";
final String itemC = "F";
series1.setName("2005");
series1.getData().add(new XYChart.Data<Number, String>(45.0D, itemA));
series1.getData().add(new XYChart.Data<Number, String>(55.0D, itemB));
series1.getData().add(new XYChart.Data<Number, String>(75.0D, itemC));
// series1.getData().add(new XYChart.Data(44, itemB));
// series1.getData().add(new XYChart.Data(18, itemC));
bc1.getData().add(series1);
// also XYChart.Series cannot be shared; we have to create a new Object for the line chart
XYChart.Series<Number, String> series2 = new XYChart.Series<>();
series2.setName("2005");
series2.getData().add(new XYChart.Data<Number, String>(45.0D, itemA));
series2.getData().add(new XYChart.Data<Number, String>(55.0D, itemB));
series2.getData().add(new XYChart.Data<Number, String>(75.0D, itemC));
l1.getData().add(series2);
/* piechart seems to be a bit special; you cann add the observeabel list directly if you create
* the piechart or you have to create PieChart.Data(..) if you want to add the data after creating the piechart-object
*/
ObservableList<PieChart.Data> pieChartData =
FXCollections.observableArrayList(
new PieChart.Data("Grapefruit", 13),
new PieChart.Data("Oranges", 25),
new PieChart.Data("Plums", 10),
new PieChart.Data("Pears", 22),
new PieChart.Data("Apples", 30));
PieChart p2 = new PieChart(pieChartData);
PieChart p1 = new PieChart();
PieChart.Data slice1 = new PieChart.Data("Desktop", 213);
PieChart.Data slice2 = new PieChart.Data("Phone" , 67);
PieChart.Data slice3 = new PieChart.Data("Tablet" , 36);
p1.getData().add(slice1);
p1.getData().add(slice2);
p1.getData().add(slice3);
HBox hbox = new HBox();
VBox vBox1 = new VBox();
VBox vBox2 = new VBox();
vBox1.getChildren().addAll(l1, bc1);
vBox2.getChildren().addAll(p1, p2);
hbox.getChildren().addAll(vBox1, vBox2);
// bc.getData().addAll(series1, series2, series3);
// XYChart<>.Series series1 = new XYChart.Series();
// series1.setName("2003");
// series1.getData().add(new XYChart.Data(2, itemA));
// series1.getData().add(new XYChart.Data(20, itemB));
// series1.getData().add(new XYChart.Data(10, itemC));
//
root.getChildren().add(hbox);
return root;
}
private Pane createRoot() {
screenSize = Screen.getPrimary().getBounds();
width = screenSize.getWidth();
height = screenSize.getHeight();
root = new Pane(); // Pane is a layout without any grid o.s.e.
root.setPrefSize(width / screenFac, height / screenFac);
return root;
}
@Override
public void start(Stage stage) throws Exception {
Scene scene = new Scene(showMyCharts());
stage.setScene(scene);
stage.show();
}
public static void main(String[] charts) {
launch(charts);
}
}
