de.unihalle.informatik.MiToBo.visualization.plots

Class BoxWhiskerChartPlotter

java.lang.Object

de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.MiToBo.core.operator.MTBOperator

de.unihalle.informatik.MiToBo.visualization.plots.BoxWhiskerChartPlotter

All Implemented Interfaces:

de.unihalle.informatik.Alida.datatypes.ALDConfigurationValidator, de.unihalle.informatik.Alida.operator.events.ALDOperatorExecutionProgressEventListener, EventListener

@ALDAOperator(genericExecutionMode=NONE,
              level=STANDARD,
              allowBatchMode=false)
public class BoxWhiskerChartPlotter
extends MTBOperator

Operator that generates box-whisker plots using JFreeChart.

For details on the library take a look here: http://www.jfree.org/jfreechart/

The operator takes input data and generates a box-whisker plot of the data, optionally grouping the boxes into different categories. In addition, the operator provides various parameters to adjust the plot's appearance, like title of the plot, axes labels, or the font size of the tick labels on the axes.

As input data the operator takes a hash map which should contain a key for each category to be displayed, i.e., each group of boxes to appear in the plot, and as values the corresponding data. The data is also expected to be arranged in a hash map where the key string indicates the name of the variable or indicator, and the values are given in terms of a list of doubles.

For an example how the data should look like, consider the following: assume that we are given two groups of cells, i.e., two categories g1 and g2, and each group contains 30 elements. For each element two measurements (or 'indicators' in this context) are given, denoted m1 and m2. We would like to visualize for each group the distribution of the two measurements, i.e., get a box plot with two categories and two boxes in each category. Consequently, we have to pass a hash map to the operator containing two key-value pairs, one for each category or group, respectively:
[g1, hash_1] , [g2, hash_2]
In each group hash, key-value pairs are expected where the key refers to the indicator and the value, given in terms of a list, contains the measurements of the indicator for the elements of that group. In this example each hash, thus, contains two key-value pairs where the keys are given by m1 and m2, and each value is given by a list of 30 double entries:
[m1, [v1, ..., v30] ] , [m2, [v1, ..., v30] ]

For more details on box-whisker plots in JFreeChart, e.g., refer to
http://www.jfree.org/jfreechart/api/javadoc/org/jfree/chart/renderer/category/BoxAndWhiskerRenderer.html

Author:

moeller

Nested Class Summary

Nested classes/interfaces inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

de.unihalle.informatik.Alida.operator.ALDOperator.HidingMode, de.unihalle.informatik.Alida.operator.ALDOperator.HistoryConstructionMode

Field Summary

Fields

Modifier and Type	Field and Description
protected org.jfree.chart.JFreeChart	boxWhiskerChart Resulting box-whisker chart.
protected Color[]	categoryColors Color map for category colors in plot.
private int	categoryCount Local variable to store number of categories.
protected String	chartTitle Title of the chart.
protected HashMap<String,HashMap<String,LinkedList<Double>>>	data Data to display.
protected int	tickLabelSize Size of axes' tick labels.
protected String	xLabel Label of the x-axis.
protected String	yLabel Label of the y-axis.

Fields inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

completeDAG, name, operatorExecutionEventlistenerList, portHashAccess, verbose, versionProvider

Constructor Summary

Constructors

Constructor and Description
BoxWhiskerChartPlotter() Default constructor.

Method Summary

Modifier and Type	Method and Description
private org.jfree.chart.JFreeChart	createChart(org.jfree.data.category.CategoryDataset dataset) Creates the chart.
private org.jfree.data.statistics.BoxAndWhiskerCategoryDataset	createDataset() Create the dataset from the given input data.
org.jfree.chart.JFreeChart	getChart() Get reference to resulting chart.
protected void	operate()
void	setCategoryColors(Color[] colors) Specify colors for different categories.
void	setData(HashMap<String,HashMap<String,LinkedList<Double>>> d) Set the data to plot.
void	setTickLabelSize(int size) Set size of tick labels on both axes.
void	setTitle(String title) Set title of chart plot.
void	setXAxisLabel(String xlabel) Set label of x-axis.
void	setYAxisLabel(String ylabel) Set label of y-axis.
private LinkedList<String>	sortStringSet(Set<String> input) Helper method to sort set of strings alphabetically in ascending order.

Methods inherited from class de.unihalle.informatik.MiToBo.core.operator.MTBOperator

readResolve

Methods inherited from class de.unihalle.informatik.Alida.operator.ALDOperator

addOperatorExecutionProgressEventListener, addParameter, addParameter, addParameterUnconditioned, fieldContained, fireOperatorExecutionProgressEvent, getALDPortHashAccessKey, getConstructionMode, getDocumentation, getHidingMode, getInactiveParameterNames, getInInoutNames, getInInoutNames, getInNames, getInOutNames, getMissingRequiredInputs, getName, getNumParameters, getOutInoutNames, getOutNames, getParameter, getParameterDescriptor, getParameterDescriptorUnconditioned, getParameterNames, getParameterUnconditioned, getSupplementalNames, getVerbose, getVersion, handleOperatorExecutionProgressEvent, hasInOutParameters, hasParameter, isAnnotatedParameter, isConfigured, print, print, print, printInterface, printInterface, readHistory, reinitializeParameterDescriptors, removeOperatorExecutionProgressEventListener, removeParameter, runOp, runOp, runOp, setConstructionMode, setConstructionMode, setConstructionMode, setHidingMode, setName, setParameter, setParameterUnconditioned, setVerbose, toStringVerbose, unconfiguredItems, validate, validateCustom, validateGeneric, writeHistory, writeHistory, writeHistory

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

data

@Parameter(label="Data",
           required=true,
           dataIOOrder=-1,
           direction=IN,
           description="Data.",
           mode=STANDARD)
protected HashMap<String,HashMap<String,LinkedList<Double>>> data

Data to display.

chartTitle

@Parameter(label="Chart title",
           required=false,
           dataIOOrder=1,
           direction=IN,
           description="Chart title.",
           mode=STANDARD)
protected String chartTitle

Title of the chart.

xLabel

@Parameter(label="X-axis label",
           required=false,
           dataIOOrder=2,
           direction=IN,
           description="Label of x-axis.",
           mode=STANDARD)
protected String xLabel

Label of the x-axis.

yLabel

@Parameter(label="Y-axis label",
           required=false,
           dataIOOrder=3,
           direction=IN,
           description="Label of y-axis.",
           mode=STANDARD)
protected String yLabel

Label of the y-axis.

tickLabelSize

@Parameter(label="Tick label size",
           required=false,
           dataIOOrder=4,
           direction=IN,
           mode=STANDARD,
           description="Size of tick labels on both axes.")
protected int tickLabelSize

Size of axes' tick labels.

categoryColors

@Parameter(label="Category colors",
           required=false,
           dataIOOrder=5,
           direction=IN,
           mode=STANDARD,
           description="List of colors for categories.")
protected Color[] categoryColors

Color map for category colors in plot.

boxWhiskerChart

@Parameter(label="Box-whisker chart plot",
           dataIOOrder=1,
           direction=OUT,
           description="Resulting plot.",
           mode=STANDARD)
protected org.jfree.chart.JFreeChart boxWhiskerChart

Resulting box-whisker chart.

categoryCount

private int categoryCount

Local variable to store number of categories.

Constructor Detail

BoxWhiskerChartPlotter

public BoxWhiskerChartPlotter()
                       throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Default constructor.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

Method Detail

setData

public void setData(HashMap<String,HashMap<String,LinkedList<Double>>> d)

Set the data to plot.

Parameters:

d - Data to plot.

setTitle

public void setTitle(String title)

Set title of chart plot.

Parameters:

title - Title string.

setXAxisLabel

public void setXAxisLabel(String xlabel)

Set label of x-axis.

Parameters:

xlabel - Label string.

setYAxisLabel

public void setYAxisLabel(String ylabel)

Set label of y-axis.

Parameters:

ylabel - Label string.

setTickLabelSize

public void setTickLabelSize(int size)

Set size of tick labels on both axes.

Parameters:

size - Size of tick labels.

setCategoryColors

public void setCategoryColors(Color[] colors)

Specify colors for different categories.

Parameters:

colors - List of colors to use for categories.

getChart

public org.jfree.chart.JFreeChart getChart()

Get reference to resulting chart.

Returns:

Generated chart plot.

operate

protected void operate()
                throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                       de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Specified by:

operate in class de.unihalle.informatik.Alida.operator.ALDOperator

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

createDataset

private org.jfree.data.statistics.BoxAndWhiskerCategoryDataset createDataset()

Create the dataset from the given input data.

Returns:

Resulting dataset.

createChart

private org.jfree.chart.JFreeChart createChart(org.jfree.data.category.CategoryDataset dataset)
                                        throws de.unihalle.informatik.Alida.exceptions.ALDOperatorException,
                                               de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

Creates the chart.

Parameters:

dataset - The dataset for the chart.

Returns:

Resulting chart.

Throws:

de.unihalle.informatik.Alida.exceptions.ALDOperatorException

de.unihalle.informatik.Alida.exceptions.ALDProcessingDAGException

sortStringSet

private LinkedList<String> sortStringSet(Set<String> input)

Helper method to sort set of strings alphabetically in ascending order.

Parameters:

input - Set of strings to sort.

Returns:

Sorted list.