Uses of Class
ubic.gemma.model.expression.bioAssayData.SingleCellDimension

Packages that use SingleCellDimension

Package	Description
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.datastructure.matrix	This package contains data structures for representing matrices of gene expression.
ubic.gemma.core.loader.expression.singleCell	This package contains classes for loading single-cell expression data.
ubic.gemma.core.loader.expression.singleCell.metadata	This package contains classes for loading single-cell metadata such as cell type assignment and cell-level characteristics.
ubic.gemma.core.visualization
ubic.gemma.core.visualization.cellbrowser	This package contains classes related to the Cell Browser visualization tool.
ubic.gemma.model.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util
ubic.gemma.web.controller.expression.experiment

Uses of SingleCellDimension in ubic.gemma.core.analysis.singleCell

Methods in ubic.gemma.core.analysis.singleCell with parameters of type SingleCellDimension

Modifier and Type	Method	Description
static List<String>	SingleCellSlicerUtils.sliceCellIds(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)
static Set<CellLevelCharacteristics>	SingleCellSlicerUtils.sliceClcs(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)
static Set<CellTypeAssignment>	SingleCellSlicerUtils.sliceCtas(SingleCellDimension singleCellDimension, List<BioAssay> assays, int[] starts, int[] ends, int numCells)

Uses of SingleCellDimension in ubic.gemma.core.datastructure.matrix

Methods in ubic.gemma.core.datastructure.matrix that return SingleCellDimension

Modifier and Type	Method	Description
SingleCellDimension	EmptySingleCellExpressionDataMatrix.getSingleCellDimension()
SingleCellDimension	SingleCellExpressionDataDoubleMatrix.getSingleCellDimension()
SingleCellDimension	SingleCellExpressionDataIntMatrix.getSingleCellDimension()
SingleCellDimension	SingleCellExpressionDataMatrix.getSingleCellDimension()	Return the single-cell dimension for this matrix.

Constructors in ubic.gemma.core.datastructure.matrix with parameters of type SingleCellDimension

Modifier	Constructor	Description
	EmptySingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, SingleCellDimension dimension, QuantitationType quantitationType)

Uses of SingleCellDimension in ubic.gemma.core.loader.expression.singleCell

Methods in ubic.gemma.core.loader.expression.singleCell that return SingleCellDimension

Modifier and Type	Method	Description
SingleCellDimension	AbstractDelegatingSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	AnnDataSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	MexSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	NullSingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)
SingleCellDimension	SingleCellDataLoader.getSingleCellDimension(Collection<BioAssay> bioAssays)	Load the single-cell dimension present in the data.

Methods in ubic.gemma.core.loader.expression.singleCell with parameters of type SingleCellDimension

Modifier and Type	Method	Description
Set<CellTypeAssignment>	AbstractDelegatingSingleCellDataLoader.getCellTypeAssignments(SingleCellDimension dimension)
Set<CellTypeAssignment>	AnnDataSingleCellDataLoader.getCellTypeAssignments(SingleCellDimension dimension)
Set<CellTypeAssignment>	MexSingleCellDataLoader.getCellTypeAssignments(SingleCellDimension dimension)	MEX does not provide cell type labels.
Set<CellTypeAssignment>	NullSingleCellDataLoader.getCellTypeAssignments(SingleCellDimension dimension)
Set<CellTypeAssignment>	SingleCellDataLoader.getCellTypeAssignments(SingleCellDimension dimension)	Load single-cell type assignments present in the data.
Set<CellLevelCharacteristics>	AbstractDelegatingSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	AnnDataSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	MexSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	NullSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
Set<CellLevelCharacteristics>	SingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)	Load cell-level characteristics that are not cell type assignments present in the data.
Map<BioAssay,SequencingMetadata>	AbstractDelegatingSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	AnnDataSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	MexSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	NullSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	SequencingMetadataFileSingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Map<BioAssay,SequencingMetadata>	SingleCellDataLoader.getSequencingMetadata(SingleCellDimension dimension)
Stream<SingleCellExpressionDataVector>	AbstractDelegatingSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	AnnDataSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	MexSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension scd, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	NullSingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)
Stream<SingleCellExpressionDataVector>	SingleCellDataLoader.loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.

Uses of SingleCellDimension in ubic.gemma.core.loader.expression.singleCell.metadata

Methods in ubic.gemma.core.loader.expression.singleCell.metadata with parameters of type SingleCellDimension

Modifier and Type	Method	Description
Set<CellTypeAssignment>	GenericMetadataSingleCellDataLoader.getCellTypeAssignments(SingleCellDimension singleCellDimension)
Set<CellLevelCharacteristics>	GenericMetadataSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)
void	CellLevelCharacteristicsWriter.write(Collection<CellLevelCharacteristics> cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write multiple sets of cell-level characteristics to a writer.
void	CellLevelCharacteristicsWriter.write(CellLevelCharacteristics cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write a single set of cell-level characteristics to a writer.
void	CellLevelCharacteristicsWriter.write(CellTypeAssignment cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write a single cell type assignment to a writer.
void	CellLevelCharacteristicsWriter.write(SingleCellDimension dimension, Writer writer)

Uses of SingleCellDimension in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization that return SingleCellDimension

Modifier and Type	Method	Description
SingleCellDimension	SingleCellSparsityHeatmap.getSingleCellDimension()

Constructors in ubic.gemma.core.visualization with parameters of type SingleCellDimension

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

Uses of SingleCellDimension in ubic.gemma.core.visualization.cellbrowser

Methods in ubic.gemma.core.visualization.cellbrowser with parameters of type SingleCellDimension

Modifier and Type	Method	Description
void	CellBrowserMetadataWriter.write(ExpressionExperiment ee, SingleCellDimension singleCellDimension, Writer writer)

Uses of SingleCellDimension in ubic.gemma.model.expression.bioAssayData

Methods in ubic.gemma.model.expression.bioAssayData that return SingleCellDimension

Modifier and Type	Method	Description
SingleCellDimension	SingleCellExpressionDataVector.getSingleCellDimension()	The dimension of the single-cell data which is shared among all the vectors.

Methods in ubic.gemma.model.expression.bioAssayData with parameters of type SingleCellDimension

Modifier and Type	Method	Description
static Map<BioAssay,Map<String,Integer>>	SingleCellDimensionUtils.createIndex(SingleCellDimension singleCellDimension)	Create an index of bioassays to their cell IDs and their position in the bioassays.
static Map<String,Map<BioAssay,Integer>>	SingleCellDimensionUtils.createReverseIndex(SingleCellDimension singleCellDimension)	Create a reverse index of cell IDs to their corresponding position in bioassays.
static int	SingleCellExpressionDataVectorUtils.getSampleEnd(SingleCellDimension dimension, int[] dataIndices, int sampleIndex, int after)	Only exposed for internal use, prefer SingleCellExpressionDataVectorUtils.getSampleEnd(SingleCellExpressionDataVector, int, int).
void	SingleCellExpressionDataVector.setSingleCellDimension(SingleCellDimension singleCellDimension)	The dimension of the single-cell data which is shared among all the vectors.

Constructors in ubic.gemma.model.expression.bioAssayData with parameters of type SingleCellDimension

Modifier	Constructor	Description
	SingleCellDimensionValueObject(SingleCellDimension singleCellDimension, boolean excludeBioAssayIds, boolean excludeCellTypeIds, boolean excludeCharacteristicIds)

Uses of SingleCellDimension in ubic.gemma.persistence.service.expression.experiment

Methods in ubic.gemma.persistence.service.expression.experiment that return SingleCellDimension

Modifier and Type	Method	Description
SingleCellDimension	ExpressionExperimentDao.getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single-cell dimension, that is the dimension associated to the preferred set of single-cell vectors.
SingleCellDimension	ExpressionExperimentDaoImpl.getPreferredSingleCellDimension(ExpressionExperiment ee)
SingleCellDimension	ExpressionExperimentDao.getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDaoImpl.getPreferredSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDao.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)	Load a single-cell dimension without its cell IDs.
SingleCellDimension	ExpressionExperimentDaoImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimension(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain the single-cell dimension used by a specific QT.
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)	Obtain a single-cell dimension used for a given dataset and QT.
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)	Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)	Load a single-cell dimension used by a specific QT without its cell IDs.
SingleCellDimension	ExpressionExperimentDao.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	ExpressionExperimentDaoImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentService.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)

Methods in ubic.gemma.persistence.service.expression.experiment that return types with arguments of type SingleCellDimension

Modifier and Type	Method	Description
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimension(ExpressionExperiment ee)
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)	Obtain the preferred single-cell dimension without its cell IDs.
Optional<SingleCellDimension>	SingleCellExpressionExperimentService.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)
Optional<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)
List<SingleCellDimension>	ExpressionExperimentDao.getSingleCellDimensions(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensions(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensions(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by a given dataset.
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensions(ExpressionExperiment ee)
List<SingleCellDimension>	ExpressionExperimentDao.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by the single-cell vectors of a given experiment.
List<SingleCellDimension>	ExpressionExperimentDao.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	ExpressionExperimentDaoImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, boolean includeBioAssays, boolean includeCtas, boolean includeClcs, boolean includeProtocol, boolean includeCharacteristics, boolean includeIndices)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentService.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	SingleCellExpressionExperimentServiceImpl.getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig config)

Methods in ubic.gemma.persistence.service.expression.experiment with parameters of type SingleCellDimension

Modifier and Type	Method	Description
CellLevelCharacteristics	SingleCellExpressionExperimentService.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Add new cell-level characteristics.
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
CellTypeAssignment	SingleCellExpressionExperimentService.addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cellTypeAssignment)
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cta)
void	ExpressionExperimentDao.createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Create a single-cell dimension for a given experiment.
void	ExpressionExperimentDaoImpl.createSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
void	ExpressionExperimentDao.deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Delete the given single-cell dimension.
void	ExpressionExperimentDaoImpl.deleteSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)
CellTypeAssignment	SingleCellExpressionExperimentService.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol labellingProtocol, String description)	Relabel the cell types of an existing set of single-cell vectors.
CellTypeAssignment	SingleCellExpressionExperimentServiceImpl.relabelCellTypes(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, List<String> newCellTypeLabels, Protocol protocol, String description)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Remove existing cell-level characteristics.
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristicsByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristicsByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	SingleCellExpressionExperimentService.removeCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension scd, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment.
void	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension dimension, CellTypeAssignment cellTypeAssignment)
void	SingleCellExpressionExperimentService.removeCellTypeAssignmentByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	SingleCellExpressionExperimentServiceImpl.removeCellTypeAssignmentByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
Stream<String>	ExpressionExperimentDao.streamCellIds(SingleCellDimension dimension, boolean createNewSession)	Stream the cell IDs of a dimension.
Stream<String>	ExpressionExperimentDaoImpl.streamCellIds(SingleCellDimension dimension, boolean createNewSession)
void	ExpressionExperimentDao.updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)	Update a single-cell dimensino for a given experiment.
void	ExpressionExperimentDaoImpl.updateSingleCellDimension(ExpressionExperiment ee, SingleCellDimension singleCellDimension)

Uses of SingleCellDimension in ubic.gemma.persistence.util

Methods in ubic.gemma.persistence.util with parameters of type SingleCellDimension

Modifier and Type	Method	Description
static void	Thaws.thawSingleCellDimension(SingleCellDimension singleCellDimension)	Thaw a single-cell dimension.

Uses of SingleCellDimension in ubic.gemma.web.controller.expression.experiment

Constructors in ubic.gemma.web.controller.expression.experiment with parameters of type SingleCellDimension

Modifier	Constructor	Description
	SingleCellDimensionEditForm(SingleCellDimension scd)