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---
layout: layout.njk
permalink: "{{ page.filePathStem }}.html"
---
{% include "toc.njk" %}
<div class="col-md-9 col-md-pull-3">
<h1 id="visualization-top" class="title">Data Visualization</h1>
<p>A picture is worth a thousand words. In machine learning, we usually handle
high-dimensional data, which is impossible to draw on display directly. But
a variety of statistical plots are tremendously valuable for us to grasp
the characteristics of many data points. Smile provides data visualization tools
such as plots and maps for researchers to understand information more easily and quickly.</p>
<h2 id="scatter" class="title">Scatter Plot</h2>
<p>A scatter plot displays data as a collection of points. The points can be color-coded,
which is very useful for classification tasks.
The user can use <code>plot</code> functions to draw scatter plot easily.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_1" data-toggle="tab">Scala</a></li>
<li><a href="#java_1" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_1">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def plot(x: Array[Array[Double]], mark: Char = '*', color: Color = Color.BLACK): Canvas
def plot(x: Array[Array[Double]], y: Array[String], mark: Char): Canvas
def plot(x: Array[Array[Double]], y: Array[Int], mark: Char): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_1">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class ScatterPlot {
public static ScatterPlot of(double[][] points, char mark, Color color);
public static ScatterPlot of(double[][] x, String[] y, char mark);
public static ScatterPlot of(double[][] x, int[] y, char mark);
}
</code></pre>
</div>
</div>
</div>
<p>The legends are as follows.</p>
<ul>
<li> <code>.</code> : dot
<li> <code>+</code> : +
<li> <code>-</code> : -
<li> <code>|</code> : |
<li> <code>*</code> : star
<li> <code>x</code> : x
<li> <code>o</code> : circle
<li> <code>O</code> : large circle
<li> <code>@</code> : solid circle
<li> <code>#</code> : large solid circle
<li> <code>s</code> : square
<li> <code>S</code> : large square
<li> <code>q</code> : solid square
<li> <code>Q</code> : large solid square
</ul>
<p>For any other char, the data point will be drawn as a dot.</p>
<p>The functions return a Canvas, which can be used to control the plot
programmatically. The user can also use the popup context menu by right
mouse click to print, change the title, axis labels, and font, etc. To
display the canvas on desktop, call <code>show(canvas)</code>, which
will render the plot properly with an implicit renderer engine.</p>
<p>For both 2D and 3D plot, the user can zoom in/out by mouse wheel. For 2D plot,
the user can shift the coordinates by moving mouse after double click. The
user can also select an area by mouse for detailed view. For 3D plot, the user
can rotate the view by dragging mouse.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_2" data-toggle="tab">Scala</a></li>
<li><a href="#java_2" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_2">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val iris = read.arff("data/weka/iris.arff")
val canvas = plot(iris, "sepallength", "sepalwidth", "class", '*')
canvas.setAxisLabels("sepallength", "sepalwidth")
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_2">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
import java.awt.Color;
import smile.io.*;
import smile.plot.swing.*;
import smile.stat.distribution.*;
import smile.math.matrix.*;
var iris = Read.arff("data/weka/iris.arff");
var canvas = ScatterPlot.of(iris, "sepallength", "sepalwidth", "class", '*').canvas();
canvas.setAxisLabels("sepallength", "sepalwidth");
canvas.window();
</code></pre>
</div>
</div>
</div>
<p>In this example, we plot the first two columns of Iris data. We use the class
label for legend and color coding.</p>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/iris2d.png" class="enlarge" style="width: 480px;" />
<div class="caption" style="min-width: 480px;">Iris 2D Scatter Plot</div>
</div>
<p>It is also easy to draw a 3D plot.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_3" data-toggle="tab">Scala</a></li>
<li><a href="#java_3" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_3">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val canvas = plot(iris, "sepallength", "sepalwidth", "petallength", "class", '*')
canvas.setAxisLabels("sepallength", "sepalwidth", "petallength")
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_3">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var canvas = ScatterPlot.of(iris, "sepallength", "sepalwidth", "petallength", "class", '*').canvas();
canvas.setAxisLabels("sepallength", "sepalwidth", "petallength");
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/iris3d.png" class="enlarge" style="width: 480px;" />
<div class="caption" style="min-width: 480px;">Iris 3D Scatter Plot</div>
</div>
<p>However, the Iris data has four attributes. So even 3D plot is not sufficient to see the
whole picture. A general practice is plot all the attribute pairs. For example,</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_4" data-toggle="tab">Scala</a></li>
<li><a href="#java_4" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_4">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
show(plot(iris, "class", '*'))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_4">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var canvas = PlotGrid.of(iris, "class", '*');
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/iris.png" class="enlarge" style="width: 480px;" />
<div class="caption" style="min-width: 480px;">Iris Plot of All Attribute Pairs</div>
</div>
<h2 id="line" class="title">Line Chart</h2>
<p>A line chart connects points by straight lines.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_5" data-toggle="tab">Scala</a></li>
<li><a href="#java_5" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_5">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def line(data: Array[Array[Double]], style: Line.Style = Line.Style.SOLID, color: Color = Color.BLACK, mark: Char = ' ', label: String = null): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_5">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class LinePlot {
public static LinePlot of(double[][] data, Line.Style style, Color color);
public static LinePlot of(double[] y, Line.Style style, Color color);
}
</code></pre>
</div>
</div>
</div>
<p>Let's draw a heart with it!</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_6" data-toggle="tab">Scala</a></li>
<li><a href="#java_6" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_6">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val heart = -314 to 314 map { i =>
val t = i / 100.0
val x = 16 * pow(sin(t), 3)
val y = 13 * cos(t) - 5 * cos(2*t) - 2 * cos(3*t) - cos(4*t)
Array(x, y)
}
show(line(heart.toArray, color = RED))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_6">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
import static java.lang.Math.*;
double[][] heart = new double[200][2];
for (int i = 0; i < 200; i++) {
double t = PI * (i - 100) / 100;
heart[i][0] = 16 * pow(sin(t), 3);
heart[i][1] = 13 * cos(t) - 5 * cos(2*t) - 2 * cos(3*t) - cos(4*t);
}
var canvas = LinePlot.of(heart, Color.RED);
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/heart.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="box" class="title">Box Plot</h2>
<p>The box plot is a standardized way of displaying the distribution of data
based on the five number summary: minimum, first quartile, median,
third quartile, and maximum.</p>
<p>Box plots can be useful to display differences between populations without
making any assumptions of the underlying statistical distribution: they are
non-parametric. The spacings between the different parts of the box help
indicate the degree of dispersion (spread) and skewness in the data, and
identify outliers.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_7" data-toggle="tab">Scala</a></li>
<li><a href="#java_7" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_7">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def boxplot(data: Array[Double]*): Canvas
def boxplot(data: Array[Array[Double]], labels: Array[String]): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_7">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class BoxPlot {
public BoxPlot(double[][] data, String[] labels);
public static BoxPlot of(double[]... data);
}
</code></pre>
</div>
</div>
</div>
<p>Note that the parameter <code>data</code> is a matrix of which each row to
create a box plot.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_8" data-toggle="tab">Scala</a></li>
<li><a href="#java_8" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_8">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val groups = (iris("sepallength").toDoubleArray zip iris("class").toStringArray).groupBy(_._2)
val labels = groups.keys.toArray
val data = groups.values.map { a => a.map(_._1) }.toArray
val canvas = boxplot(data, labels)
canvas.setAxisLabels("", "sepallength")
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_8">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
String[] labels = ((smile.data.measure.NominalScale) iris.schema().field("class").measure).levels();
double[][] data = new double[labels.length][];
for (int i = 0; i < data.length; i++) {
var label = labels[i];
data[i] = iris.stream().
filter(row -> row.getString("class").equals(label)).
mapToDouble(row -> row.getFloat("sepallength")).
toArray();
}
var canvas = new BoxPlot(data, labels).canvas();
canvas.setAxisLabels("", "sepallength");
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/iris-boxplot.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="historgram" class="title">Histogram</h2>
<p>A histogram is a graphical representation of the distribution of numerical data.
The range of values is divided into a series of consecutive, non-overlapping intervals/bins.
The bins must be adjacent, and are usually equal size.</p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_9" data-toggle="tab">Scala</a></li>
<li><a href="#java_9" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_9">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def hist(data: Array[Double], k: Int = 10, prob: Boolean = false, color: Color = Color.BLUE): Canvas
def hist(data: Array[Double], breaks: Array[Double], prob: Boolean, color: Color): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_9">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class Histogram {
public static BarPlot of(double[] data);
public static BarPlot of(double[] data, int k, boolean prob);
public static BarPlot of(double[] data, int k, boolean prob, Color color);
public static BarPlot of(double[] data, double[] breaks, boolean prob);
public static BarPlot of(double[] data, double[] breaks, boolean prob, Color color);
}
</code></pre>
</div>
</div>
</div>
<p>where <code>k</code> is the number of bins (10 by default), or you can
also specify an array of the breakpoints between bins.</p>
<p>Let's apply the histogram to an interesting data: the wisdom of crowds.
The original experiment took place about a hundred years ago at a county fair in England.
The fair had a guess the weight of the ox contest. Francis Galton calculated the average
of all guesses, which is right to within one pound.</p>
<p>Recently, NPR Planet Money ran the experiment again. NPR posted a couple of pictures of a cow
(named Penelope) and asked people to guess her weight. They got over 17,000 responses. The average
of guesses was 1,287 pounds, which is pretty close to Penelope's weight 1,355 pounds. </p>
<ul class="nav nav-tabs">
<li class="active"><a href="#scala_10" data-toggle="tab">Scala</a></li>
<li><a href="#java_10" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_10">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val cow = read.csv("data/npr/cow.txt", header=false)("V1").toDoubleArray
val canvas = hist(cow, 50)
canvas.setAxisLabels("Weight", "Probability")
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_10">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var cow = Read.csv("data/npr/cow.txt").column("V1").toDoubleArray();
var canvas = Histogram.of(cow, 50, true).canvas();
canvas.setAxisLabels("Weight", "Probability");
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/penelope.png" class="enlarge" style="width: 480px;" />
</div>
<p>The histogram gives a rough sense of the distribution of crowd guess, which has a long tail.
Filter out the weights over 3500 pounds, the histogram shows more details.</p>
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</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_11">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val canvas = hist(cow.filter(_ <= 3500), 50)
canvas.setAxisLabels("Weight", "Probability")
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_11">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var canvas = Histogram.of(Arrays.stream(cow).filter(w -> w <= 3500).toArray(), 50, true).canvas();
canvas.setAxisLabels("Weight", "Probability");
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/penelope3500.png" class="enlarge" style="width: 480px;" />
</div>
<p>Smile also supports histograms that display the distribution of 2-dimensional data.</p>
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<li class="active"><a href="#scala_12" data-toggle="tab">Scala</a></li>
<li><a href="#java_12" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_12">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def hist3(data: Array[Array[Double]], xbins: Int = 10, ybins: Int = 10, prob: Boolean = false, palette: Array[Color] = Palette.jet(16)): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_12">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class Histogram3D {
public static Histogram3D of(double[][] data);
public static Histogram3D of(double[][] data, int nbins, Color[] palette);
public static Histogram3D of(double[][] data, int nbins, boolean prob);
public static Histogram3D of(double[][] data, int nbins, boolean prob, Color[] palette);
}
</code></pre>
</div>
</div>
</div>
<p>Here we generate a data set from a 2-dimensional Gaussian distribution.</p>
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<div class="tab-pane active" id="scala_13">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val gauss = new MultivariateGaussianDistribution(Array(0.0, 0.0), Matrix.of(Array(Array(1.0, 0.6), Array(0.6, 2.0))))
val data = (0 until 10000) map { i: Int => gauss.rand }
show(hist3(data.toArray, 50, 50))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_13">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
double[] mu = {0.0, 0.0};
double[][] v = { {1.0, 0.6}, {0.6, 2.0} };
var gauss = new MultivariateGaussianDistribution(mu, Matrix.of(v));
var data = Stream.generate(gauss::rand).limit(10000).toArray(double[][]::new);
Histogram3D.of(data, 50, false).canvas().window();
</code></pre>
</div>
</div>
</div>
<p>The corresponding histogram looks like</p>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/histogram3d.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="qq" class="title">Q-Q Plot</h2>
<p>A Q–Q plot ("Q" stands for quantile) is a probability plot for comparing two probability distributions
by plotting their quantiles against each other. A point (x, y) on the plot corresponds to one of
the quantiles of the second distribution (y-coordinate) plotted against the same quantile of
the first distribution (x-coordinate).</p>
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</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_14">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def qqplot(x: Array[Double]): Canvas
def qqplot(x: Array[Double], d: Distribution): Canvas
def qqplot(x: Array[Double], y: Array[Double]): Canvas
def qqplot(x: Array[Int], d: DiscreteDistribution): Canvas
def qqplot(x: Array[Int], y: Array[Int]): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_14">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class QQPlot {
public static QQPlot of(double[] x);
public static QQPlot of(double[] x, Distribution d);
public static QQPlot of(double[] x, double[] y);
public static QQPlot of(int[] x, DiscreteDistribution d);
public static QQPlot of(int[] x, int[] y);
}
</code></pre>
</div>
</div>
</div>
<p>Smile supports the Q-Q plot of samples to a given distribution and also of two sample sets.
The second distribution/samples is optional. If missing, we assume it the standard Gaussian distribution.</p>
<p>In what follows, we generate a random sample set from standard Gaussian distribution and draw its Q-Q plot.</p>
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<li class="active"><a href="#scala_15" data-toggle="tab">Scala</a></li>
<li><a href="#java_15" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_15">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val gauss = new GaussianDistribution(0.0, 1.0)
val data = (0 until 1000) map { i: Int => gauss.rand }
show(qqplot(data.toArray))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_15">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var gauss = new GaussianDistribution(0.0, 1.0);
var data = DoubleStream.generate(gauss::rand).limit(1000).toArray();
QQPlot.of(data).canvas().window();
</code></pre>
</div>
</div>
</div>
<p>In fact, this is also a good visual way to verify the quality of our random number generator.</p>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/qqplot.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="heatmap" class="title">Heatmap</h2>
<p>A heat map is a graphical representation of data where the values in a matrix are represented as colors.
In cluster analysis, researchers often employs the heat map by permuting the rows and the columns
of a matrix to place similar values near each other according to the clustering.</p>
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<li class="active"><a href="#scala_16" data-toggle="tab">Scala</a></li>
<li><a href="#java_16" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_16">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def heatmap(z: Array[Array[Double]], palette: Array[Color] = Palette.jet(16)): Canvas
def heatmap(x: Array[Double], y: Array[Double], z: Array[Array[Double]], palette: Array[Color]): Canvas
def heatmap(rowLabels: Array[String], columnLabels: Array[String], z: Array[Array[Double]], palette: Array[Color]): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_16">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class Heatmap {
public static Heatmap of(double[][] z);
public static Heatmap of(double[][] z, int k);
public static Heatmap of(double[] x, double[] y, double[][] z);
public static Heatmap of(double[] x, double[] y, double[][] z, int k);
public static Heatmap of(String[] rowLabels, String[] columnLabels, double[][] z);
public static Heatmap of(String[] rowLabels, String[] columnLabels, double[][] z, int k);
}
</code></pre>
</div>
</div>
</div>
<p>where <code>z</code> is the matrix to display and the optional parameters <code>x</code> and <code>y</code>
are the coordinates of data matrix cells, which must be in ascending order. Alternatively, one can also
provide labels as the coordinates, which is a common practice in cluster analysis.</p>
<p>In what follows, we display the heat map of a matrix. We starts with a small <code>4 x 4</code> matrix and
enlarge it with bicubic interpolation. We also use the helper class <code>Palette</code> to generate the color
scheme. This class provides many other color schemes.</p>
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<li class="active"><a href="#scala_17" data-toggle="tab">Scala</a></li>
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</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_17">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
// the matrix to display
val z = Array(
Array(1.0, 2.0, 4.0, 1.0),
Array(6.0, 3.0, 5.0, 2.0),
Array(4.0, 2.0, 1.0, 5.0),
Array(5.0, 4.0, 2.0, 3.0)
)
// make the matrix larger with bicubic interpolation
val x = Array(0.0, 1.0, 2.0, 3.0)
val y = Array(0.0, 1.0, 2.0, 3.0)
val bicubic = new BicubicInterpolation(x, y, z)
val Z = Array.ofDim[Double](101, 101)
for (i <- 0 to 100) {
for (j <- 0 to 100)
Z(i)(j) = bicubic.interpolate(i * 0.03, j * 0.03)
}
show(heatmap(Z, Palette.jet(256)))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_17">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
// the matrix to display
double[][] z = {
{1.0, 2.0, 4.0, 1.0},
{6.0, 3.0, 5.0, 2.0},
{4.0, 2.0, 1.0, 5.0},
{5.0, 4.0, 2.0, 3.0}
};
// make the matrix larger with bicubic interpolation
double[] x = {0.0, 1.0, 2.0, 3.0};
double[] y = {0.0, 1.0, 2.0, 3.0};
var bicubic = new BicubicInterpolation(x, y, z);
var Z = new double[101][101];
for (int i = 0; i <= 100; i++) {
for (int j = 0; j <= 100; j++)
Z[i][j] = bicubic.interpolate(i * 0.03, j * 0.03);
}
Heatmap.of(Z, Palette.jet(256)).canvas().window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/heatmap.png" class="enlarge" style="width: 480px;" />
</div>
<p>A special case of heat map is to draw the sparsity pattern of a matrix.</p>
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<li class="active"><a href="#scala_18" data-toggle="tab">Scala</a></li>
<li><a href="#java_18" data-toggle="tab">Java</a></li>
</ul>
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<div class="tab-pane active" id="scala_18">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def spy(matrix: SparseMatrix, k: Int = 1): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_18">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class SparseMatrixPlot {
public static SparseMatrixPlot of(SparseMatrix sparse);
public static SparseMatrixPlot of(SparseMatrix sparse, int k);
}
</code></pre>
</div>
</div>
</div>
<p>The structure of sparse matrix is critical in solving linear systems.</p>
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<li class="active"><a href="#scala_19" data-toggle="tab">Scala</a></li>
<li><a href="#java_19" data-toggle="tab">Java</a></li>
</ul>
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<div class="tab-pane active" id="scala_19">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val sparse = SparseMatrix.text(java.nio.file.Paths.get("data/matrix/mesh2em5.txt"))
val canvas = spy(sparse)
canvas.setTitle("mesh2em5")
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_19">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var sparse = SparseMatrix.text(java.nio.file.Paths.get("data/matrix/mesh2em5.txt"));
var canvas = SparseMatrixPlot.of(sparse).canvas();
canvas.setTitle("mesh2em5");
canvas.window();
</code></pre>
</div>
</div>
</div>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/mesh2em5.png" class="enlarge" style="width: 480px;" />
</div>
<p>Another variant is the hex map where hexagon cells replace rectangle cells.</p>
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<li class="active"><a href="#scala_20" data-toggle="tab">Scala</a></li>
<li><a href="#java_20" data-toggle="tab">Java</a></li>
</ul>
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<div class="tab-pane active" id="scala_20">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def hexmap(z: Array[Array[Double]], palette: Array[Color] = Palette.jet(16)): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_20">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class Hexmap {
public static Hexmap of(double[][] z);
public static Hexmap of(double[][] z, int k);
public static Hexmap of(double[][] z, Color[] palette);
} </code></pre>
</div>
</div>
</div>
<p>In machine learning, the hex map is often used to visualize self-organized map (SOM).
An SOM is a type of artificial neural network that is trained using unsupervised learning to
produce a low-dimensional (typically two-dimensional), discretized representation of
the input space of the training samples. An SOM consists of components called nodes or neurons.
Associated with each node are a weight vector of the same dimension as the input data vectors,
and a position in the map space. The U-Matrix value of a particular node is the average distance
between the node's weight vector and that of its closest neighbors. In practice, researchers
often use the hex map to visualize the U-Matrix.</p>
<p>In the following example, we train and visualize a SOM on the USPS training data set with <code>30 x 30</code>
nodes.</p>
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</ul>
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<div class="tab-pane active" id="scala_21">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val zip = read.csv("data/usps/zip.train", delimiter = ' ', header = false)
val x = zip.drop(0).toArray
val lattice = SOM.lattice(30, 30, x)
val som = new SOM(lattice,
TimeFunction.constant(0.1),
Neighborhood.Gaussian(1, x.length * 10 / 4))
for (i <- 0 until 10) {
MathEx.permutate(x.length).foreach { j =>
som.update(x(j))
}
}
show(hexmap(som.umatrix, Palette.heat(256)))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_21">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var zip = Read.csv("data/usps/zip.train", CSVFormat.DEFAULT.withDelimiter(' '));
var x = zip.drop(0).toArray();
var lattice = SOM.lattice(30, 30, x);
var som = new SOM(lattice,
TimeFunction.constant(0.1),
Neighborhood.Gaussian(1, x.length * 10 / 4));
for (int i = 0; i < 10; i++) {
for (int j : MathEx.permutate(x.length)) {
som.update(x[j]);
}
}
Hexmap.of(som.umatrix(), Palette.heat(256)).canvas().window()
</code></pre>
</div>
</div>
</div>
<p>In the hex map, areas of low neighbour distance indicate groups of nodes that are similar.
Areas with large distances indicate the nodes are much more dissimilar, and indicate
natural boundaries between node clusters.</p>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/hexmap.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="contour" class="title">Contour</h2>
<p>A contour plot represents a 3-dimensional surface by plotting constant <code>z</code> slices, called contours,
on a 2-dimensional format. That is, given a value for <code>z</code>, lines are drawn for connecting the
<code>(x, y)</code> coordinates where that z value occurs.</p>
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</ul>
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<div class="tab-pane active" id="scala_22">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def contour(z: Array[Array[Double]]): Canvas
def contour(z: Array[Array[Double]], levels: Array[Double]): Canvas
def contour(x: Array[Double], y: Array[Double], z: Array[Array[Double]]): Canvas
def contour(x: Array[Double], y: Array[Double], z: Array[Array[Double]], levels: Array[Double]): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_22">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class Contour {
public static Contour of(double[][] z);
public static Contour of(double[][] z, int numLevels);
public static Contour of(double[] x, double[] y, double[][] z);
public static Contour of(double[] x, double[] y, double[][] z, int numLevels);
}
</code></pre>
</div>
</div>
</div>
<p>Similar to <code>heatmap</code>, the parameters <code>x</code> and <code>y</code>
are the coordinates of data matrix cells, which must be in ascending order.
The slice values can be automatically determined from the data, or provided through
the parameter <code>levels</code>.</p>
<p>Contours are often jointly used with the heat map. In the following example, we add the contour lines to
the previous heat map exampl.</p>
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<li class="active"><a href="#scala_23" data-toggle="tab">Scala</a></li>
<li><a href="#java_23" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_23">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
val canvas = heatmap(Z, Palette.jet(256))
canvas.add(Contour.of(Z))
show(canvas)
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_23">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
var canvas = Heatmap.of(Z, 256).canvas();
canvas.add(Contour.of(Z));
canvas.window();
</code></pre>
</div>
</div>
</div>
<p>This example also shows how to mix multiple plots together. Besides using the plot functions directly,
one can also construct plots with Java classes and add them to existing a plot canvas.</p>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/contour.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="surface" class="title">Surface</h2>
<p>Besides heat map and contour, we can also visualize a matrix with the three-dimensional shaded surface.</p>
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<li class="active"><a href="#scala_24" data-toggle="tab">Scala</a></li>
<li><a href="#java_24" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_24">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def surface(z: Array[Array[Double]], palette: Array[Color] = Palette.jet(16)): Canvas
def surface(x: Array[Double], y: Array[Double], z: Array[Array[Double]], palette: Array[Color]): Canvas
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_24">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
public class Surface {
public static Surface of(double[][] z);
public static Surface of(double[][] z, Color[] palette);
public static Surface of(double[] x, double[] y, double[][] z);
public static Surface of(double[] x, double[] y, double[][] z, Color[] palette);
}
</code></pre>
</div>
</div>
</div>
<p>The usage is similar with <code>heatmap</code> and <code>contour</code> functions.</p>
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<li class="active"><a href="#scala_25" data-toggle="tab">Scala</a></li>
<li><a href="#java_25" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_25">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
show(surface(Z, Palette.jet(256, 1.0f)))
</code></pre>
</div>
</div>
<div class="tab-pane" id="java_25">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-java"><code>
Surface.of(Z, Palette.jet(256, 1.0f)).canvas().window();
</code></pre>
</div>
</div>
</div>
<p>The surface of same example data is shown as</p>
<div style="width: 100%; display: inline-block; text-align: center;">
<img src="images/surface.png" class="enlarge" style="width: 480px;" />
</div>
<h2 id="wireframe" class="title">Wireframe</h2>
<p>The wireframe model is a visual presentation of a three-dimensional physical object.
A wireframe model consists of two tables,
the vertex table and the edge table. Each entry of the vertex table records a vertex and its coordinate values,
while each entry of the edge table has two components giving the two incident vertices of that edge.</p>
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<li><a href="#java_26" data-toggle="tab">Java</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane active" id="scala_26">
<div class="code" style="text-align: left;">
<pre class="prettyprint lang-scala"><code>
def wireframe(vertices: Array[Array[Double]], edges: Array[Array[Int]]): Canvas
</code></pre>