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

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 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).

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)