Package ubic.gemma.core.visualization

Class SingleCellSparsityHeatmap

java.lang.Object

ubic.gemma.core.visualization.SingleCellSparsityHeatmap

All Implemented Interfaces:

Serializable, Heatmap

public class SingleCellSparsityHeatmap
extends Object
implements Heatmap

Heatmap that displays the sparsity of single-cell data.

Author:

poirigui

See Also:

• Serialized Form

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	SingleCellSparsityHeatmap.SingleCellHeatmapType

Field Summary

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

GEMMA_PAINT_SCALE

Constructor Summary

Constructors

Constructor	Description
SingleCellSparsityHeatmap(ExpressionExperiment expressionExperiment, SingleCellDimension singleCellDimension, BioAssayDimension dimension, Collection<ExpressionExperimentSubSet> subSets, Map<BioAssay,Long> designElementsPerSample, SingleCellSparsityHeatmap.SingleCellHeatmapType type)

Method Summary

Modifier and Type	Method	Description
BufferedImage	createAggregateImage(SingleCellSparsityHeatmap.SingleCellHeatmapType type)
BufferedImage	createImage(int cellSize)	Render a heatmap image.
int	getCellSize()	Get the size of a cell in pixels.
Map<BioAssay,Long>	getDesignElementsPerSample()
BioAssayDimension	getDimension()
ExpressionExperiment	getExpressionExperiment()
List<BioAssay>	getSamples()
SingleCellDimension	getSingleCellDimension()
List<ExpressionExperimentSubSet>	getSubSets()
SingleCellSparsityHeatmap.SingleCellHeatmapType	getType()
List<String>	getXLabels()
List<String>	getYLabels()
boolean	isTranspose()	Indicate if this heatmap is transposed.
void	setCellSize(int cellSize)
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

Constructor Details

SingleCellSparsityHeatmap

public SingleCellSparsityHeatmap(ExpressionExperiment expressionExperiment,
 SingleCellDimension singleCellDimension,
 BioAssayDimension dimension,
 Collection<ExpressionExperimentSubSet> subSets,
 @Nullable
 Map<BioAssay,Long> designElementsPerSample,
 @Nullable
 SingleCellSparsityHeatmap.SingleCellHeatmapType type)

Parameters:

expressionExperiment - an experiment containing single-cell data

singleCellDimension - a single-cell dimension

dimension - a regular dimension for aggregated data

subSets - a set of subsets containing aggregated data

designElementsPerSample - the number of design elements for the platform of each sample

type - the type of heatmap to generate

Method Details

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

createAggregateImage

public BufferedImage createAggregateImage(SingleCellSparsityHeatmap.SingleCellHeatmapType type)

getXLabels

public List<String> getXLabels()

Specified by:

getXLabels in interface Heatmap

getYLabels

public List<String> getYLabels()

Specified by:

getYLabels in interface Heatmap

getExpressionExperiment

public ExpressionExperiment getExpressionExperiment()

getSamples

public List<BioAssay> getSamples()

getSingleCellDimension

public SingleCellDimension getSingleCellDimension()

getDimension

public BioAssayDimension getDimension()

getSubSets

public List<ExpressionExperimentSubSet> getSubSets()

getDesignElementsPerSample

@Nullable
public Map<BioAssay,Long> getDesignElementsPerSample()

getType

@Nullable
public SingleCellSparsityHeatmap.SingleCellHeatmapType getType()

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

setCellSize

public void setCellSize(int cellSize)

setTranspose

public void setTranspose(boolean transpose)