Package ubic.gemma.core.visualization

Class ExpressionDataHeatmap

java.lang.Object

ubic.gemma.core.visualization.ExpressionDataHeatmap

All Implemented Interfaces:

Serializable, Heatmap

public class ExpressionDataHeatmap
extends Object
implements Heatmap

Expression data heatmap for experiments and subsets.

There is also an implementation of this in JavaScript

Author:

poirigui

See Also:

• Serialized Form

Field Summary

Fields inherited from interface ubic.gemma.core.visualization.Heatmap

GEMMA_PAINT_SCALE

Method Summary

Modifier and Type	Method	Description
BufferedImage	createImage(int cellSize)	Render a heatmap image.
static ExpressionDataHeatmap	fromDesignElements(ExpressionExperiment ee, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes)	Create a heatmap for a given set of design elements.
static ExpressionDataHeatmap	fromDesignElements(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<CompositeSequence> designElements, List<Gene> genes)	Create a heatmap for a subset using design elements.
static ExpressionDataHeatmap	fromVectors(ExpressionExperiment ee, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a given set of vectors.
static ExpressionDataHeatmap	fromVectors(ExpressionExperimentSubSet subSet, BioAssayDimension dimension, Slice<? extends BulkExpressionDataVector> vectors, List<Gene> genes)	Create a heatmap for a subset.
int[]	getAssayIndex()
List<BioAssay>	getAssays()
BioAssaySet	getBioAssaySet()
CellLevelCharacteristics	getCellLevelCharacteristics()
int	getCellSize()	Get the size of a cell in pixels.
Slice<CompositeSequence>	getDesignElements()
BioAssayDimension	getDimension()
Characteristic	getFocusedCellLevelCharacteristic()
List<Gene>	getGenes()	List of genes to use for display purposes.
QuantitationType	getSingleCellQuantitationType()	Quantitation type of the single-cell data this heatmap was generated from, if applicable.
Slice<? extends BulkExpressionDataVector>	getVectors()
List<String>	getXLabels()
List<String>	getYLabels()
boolean	isTranspose()	Indicate if this heatmap is transposed.
void	setCellLevelCharacteristics(CellLevelCharacteristics cellLevelCharacteristics)
void	setCellSize(int cellSize)
void	setFocusedCellLevelCharacteristic(Characteristic focusedCellLevelCharacteristic)
void	setSingleCellQuantitationType(QuantitationType singleCellQuantitationType)	Quantitation type of the single-cell data this heatmap was generated from, if applicable.
void	setTranspose(boolean transpose)

Methods inherited from class java.lang.Object

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

Methods inherited from interface ubic.gemma.core.visualization.Heatmap

createImage

Method Details

fromVectors

public static ExpressionDataHeatmap fromVectors(ExpressionExperiment ee,
 BioAssayDimension dimension,
 Slice<? extends BulkExpressionDataVector> vectors,
 @Nullable
 List<Gene> genes)

Create a heatmap for a given set of vectors.

Parameters:

ee - experiment from which the data originates

dimension - dimension to render

vectors - vectors to display

genes - genes to display as row labels (must match the number of vectors)

fromVectors

public static ExpressionDataHeatmap fromVectors(ExpressionExperimentSubSet subSet,
 BioAssayDimension dimension,
 Slice<? extends BulkExpressionDataVector> vectors,
 @Nullable
 List<Gene> genes)

Create a heatmap for a subset.

Parameters:

subSet - subset from which the data originates

dimension - dimension encompassing the subset, only the assays from the subset will be displayed

See Also:

• fromVectors(ExpressionExperiment, BioAssayDimension, Slice, List)

fromDesignElements

public static ExpressionDataHeatmap fromDesignElements(ExpressionExperiment ee,
 BioAssayDimension dimension,
 Slice<CompositeSequence> designElements,
 @Nullable
 List<Gene> genes)

Create a heatmap for a given set of design elements.

in this mode, no image can be generated, but labels are available.

See Also:

• fromVectors(ExpressionExperiment, BioAssayDimension, Slice, List)

fromDesignElements

public static ExpressionDataHeatmap fromDesignElements(ExpressionExperimentSubSet subSet,
 BioAssayDimension dimension,
 Slice<CompositeSequence> designElements,
 @Nullable
 List<Gene> genes)

Create a heatmap for a subset using design elements. Create a heatmap for a subset.

See Also:

• fromVectors(ExpressionExperimentSubSet, BioAssayDimension, Slice, List)

createImage

public BufferedImage createImage(int cellSize)

Description copied from interface: Heatmap

Render a heatmap image.

Specified by:

createImage in interface Heatmap

Parameters:

cellSize - size in pixel to use for individual cells in the heatmap

getXLabels

public List<String> getXLabels()

Specified by:

getXLabels in interface Heatmap

getYLabels

public List<String> getYLabels()

Specified by:

getYLabels in interface Heatmap

getBioAssaySet

public BioAssaySet getBioAssaySet()

getDimension

public BioAssayDimension getDimension()

getAssays

public List<BioAssay> getAssays()

getAssayIndex

public int[] getAssayIndex()

getVectors

@Nullable
public Slice<? extends BulkExpressionDataVector> getVectors()

getDesignElements

@Nullable
public Slice<CompositeSequence> getDesignElements()

getGenes

@Nullable
public List<Gene> getGenes()

List of genes to use for display purposes.

getSingleCellQuantitationType

@Nullable
public QuantitationType getSingleCellQuantitationType()

Quantitation type of the single-cell data this heatmap was generated from, if applicable.

getCellLevelCharacteristics

@Nullable
public CellLevelCharacteristics getCellLevelCharacteristics()

getFocusedCellLevelCharacteristic

@Nullable
public Characteristic getFocusedCellLevelCharacteristic()

getCellSize

public int getCellSize()

Description copied from interface: Heatmap

Get the size of a cell in pixels.

Use this to adjust how labels are displayed.

Specified by:

getCellSize in interface Heatmap

isTranspose

public boolean isTranspose()

Description copied from interface: Heatmap

Indicate if this heatmap is transposed.

Specified by:

isTranspose in interface Heatmap

setSingleCellQuantitationType

public void setSingleCellQuantitationType(@Nullable
 QuantitationType singleCellQuantitationType)

Quantitation type of the single-cell data this heatmap was generated from, if applicable.

setCellLevelCharacteristics

public void setCellLevelCharacteristics(@Nullable
 CellLevelCharacteristics cellLevelCharacteristics)

setFocusedCellLevelCharacteristic

public void setFocusedCellLevelCharacteristic(@Nullable
 Characteristic focusedCellLevelCharacteristic)

setCellSize

public void setCellSize(int cellSize)

setTranspose

public void setTranspose(boolean transpose)