Package ubic.gemma.persistence.service.expression.experiment

Interface SingleCellExpressionExperimentService

All Known Implementing Classes:

SingleCellExpressionExperimentServiceImpl

public interface SingleCellExpressionExperimentService

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig
static class	SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig

Method Summary

Modifier and Type	Method	Description
CellLevelCharacteristics	addCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Add new cell-level characteristics.
CellTypeAssignment	addCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, SingleCellDimension dimension, CellTypeAssignment cellTypeAssignment)
int	addSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)	Add single-cell data vectors.
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain CLC for given category.
List<CellLevelCharacteristics>	getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
CellLevelCharacteristics	getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, String name)	Obtain a CLC by name.
Category	getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Collection<CellLevelCharacteristics>	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellLevelCharacteristics	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellLevelCharacteristics	getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String clcName)
Optional<CellLevelCharacteristics>	getCellLevelMask(ExpressionExperiment expressionExperiment, QuantitationType qt)	Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.
CellTypeAssignment	getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, Long ctaId)	Obtain a cell type assignment by ID.
CellTypeAssignment	getCellTypeAssignment(ExpressionExperiment expressionExperiment, QuantitationType qt, String ctaName)	Obtain a cell type assignment by name.
Collection<CellTypeAssignment>	getCellTypeAssignmentByProtocol(ExpressionExperiment ee, QuantitationType qt, String protocolName)	Obtain a cell type assignment by a protocol identifier.
Collection<Protocol>	getCellTypeAssignmentProtocols()	Obtain a collection of protocols used to assign cell types to single-cell vectors.
List<CellTypeAssignment>	getCellTypeAssignments(ExpressionExperiment ee)	Obtain all the cell type labellings from all single-cell vectors.
List<CellTypeAssignment>	getCellTypeAssignments(ExpressionExperiment expressionExperiment, QuantitationType qt)
Collection<CellTypeAssignment>	getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
CellTypeAssignment	getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, Long ctaId)
CellTypeAssignment	getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt, String ctaName)
Characteristic	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int cellIndex)
Characteristic[]	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, Long ctaId, int startIndex, int endIndexExclusive)
Characteristic	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int cellIndex)
Characteristic[]	getCellTypeAt(ExpressionExperiment ee, QuantitationType qt, String ctaName, int startIndex, int endIndexExclusive)
Optional<ExperimentalFactor>	getCellTypeFactor(ExpressionExperiment ee)	Obtain the cell type factor.
List<Characteristic>	getCellTypes(ExpressionExperiment ee)	Obtain the cell types of a given single-cell dataset.
long	getNumberOfNonZeroes(ExpressionExperiment ee, QuantitationType qt)
Map<BioAssay,Long>	getNumberOfNonZeroesBySample(ExpressionExperiment ee, QuantitationType qt, int fetchSize, boolean useCursorFetchIfSupported)
long	getNumberOfSingleCellDataVectors(ExpressionExperiment ee, QuantitationType qt)	Obtain the number of single-cell vectors for a given quantitation type.
Optional<CellTypeAssignment>	getPreferredCellTypeAssignment(ExpressionExperiment ee)	Obtain the preferred cell type labelling from the preferred single-cell vectors.
Optional<CellTypeAssignment>	getPreferredCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt)
Optional<CellTypeAssignment>	getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee, QuantitationType qt)
Optional<Collection<SingleCellExpressionDataVector>>	getPreferredSingleCellDataVectors(ExpressionExperiment ee)	Obtain preferred single-cell vectors.
Optional<SingleCellDimension>	getPreferredSingleCellDimension(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)	Obtain the preferred single-cell dimension.
Optional<SingleCellDimension>	getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)	Obtain the preferred single-cell dimension without its cell IDs.
Optional<SingleCellDimension>	getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
Optional<QuantitationType>	getPreferredSingleCellQuantitationType(ExpressionExperiment ee)	Obtain the preferred single-cell quantitation type.
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType)	Obtain single-cell vectors for a particular sample.
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Obtain single-cell vectors for a given quantitation type.
Collection<SingleCellExpressionDataVector>	getSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
SingleCellExpressionDataVector	getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee, QuantitationType quantitationType, CompositeSequence designElement)	Obtain a single single-cell vector without initializing cell IDs.
SingleCellDimension	getSingleCellDimension(ExpressionExperiment ee, QuantitationType qt)	Obtain a single-cell dimension used for a given dataset and QT.
List<SingleCellDimension>	getSingleCellDimensions(ExpressionExperiment ee)	Obtain all the single-cell dimensions used by a given dataset.
List<SingleCellDimension>	getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)
List<SingleCellDimension>	getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
SingleCellDimension	getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)	Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.
SingleCellDimension	getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt)
SingleCellDimension	getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee, QuantitationType qt, SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)
SingleCellExpressionDataMatrix<?>	getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, List<BioAssay> samples, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
SingleCellExpressionDataMatrix<?>	getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment, QuantitationType quantitationType)	Obtain a single-cell expression data matrix for the given quantitation type.
Collection<QuantitationType>	getSingleCellQuantitationTypes(ExpressionExperiment ee)
ExpressionExperiment	loadWithSingleCellVectors(Long id)	Load an experiment with its single-cell data vectors initialized.
ExperimentalFactor	recreateCellTypeFactor(ExpressionExperiment ee)	Recreate the cell type factor based on the preferred labelling of the preferred single-cell vectors.
CellTypeAssignment	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.
long	removeAllCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt)
long	removeAllCellTypeAssignments(ExpressionExperiment ee, QuantitationType qt)
void	removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)	Remove existing cell-level characteristics by QT.
void	removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Remove existing cell-level characteristics.
void	removeCellLevelCharacteristicsByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
void	removeCellTypeAssignment(ExpressionExperiment ee, QuantitationType qt, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment by QT.
void	removeCellTypeAssignment(ExpressionExperiment ee, SingleCellDimension scd, CellTypeAssignment cellTypeAssignment)	Remove the given cell type assignment.
void	removeCellTypeAssignmentByName(ExpressionExperiment ee, SingleCellDimension dimension, String name)
int	removeSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType)	Remove single-cell data vectors for the given quantitation type.
int	replaceSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, Collection<SingleCellExpressionDataVector> vectors, String details)	Replace existing single-cell data vectors for the given quantitation type.
Optional<Stream<String>>	streamCellIds(ExpressionExperiment ee, boolean createNewSession)
Stream<String>	streamCellIds(ExpressionExperiment ee, QuantitationType qt, boolean createNewSession)
Stream<Characteristic>	streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	streamCellTypes(ExpressionExperiment ee, CellTypeAssignment cta, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, List<BioAssay> samples, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession)	Obtain a stream over single-cell vectors for a given quantitation type.
Stream<SingleCellExpressionDataVector>	streamSingleCellDataVectors(ExpressionExperiment ee, QuantitationType quantitationType, int fetchSize, boolean useCursorFetchIfSupported, boolean createNewSession, SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)
void	updateSparsityMetrics(ExpressionExperiment ee)	Update the sparsity metrics.

Method Details

loadWithSingleCellVectors

@Nullable
@Secured({"GROUP_USER","AFTER_ACL_READ"})
ExpressionExperiment loadWithSingleCellVectors(Long id)

Load an experiment with its single-cell data vectors initialized.

The rest of the experiment is also initialized as per ExpressionExperimentDao.thawLite(ExpressionExperiment).

getSingleCellQuantitationTypes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<QuantitationType> getSingleCellQuantitationTypes(ExpressionExperiment ee)

getPreferredSingleCellQuantitationType

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<QuantitationType> getPreferredSingleCellQuantitationType(ExpressionExperiment ee)

Obtain the preferred single-cell quantitation type.

getPreferredSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<Collection<SingleCellExpressionDataVector>> getPreferredSingleCellDataVectors(ExpressionExperiment ee)

Obtain preferred single-cell vectors.

getSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType)

Obtain single-cell vectors for a given quantitation type.

getSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

getSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType)

Obtain single-cell vectors for a particular sample.

getSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<SingleCellExpressionDataVector> getSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

streamSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession)

Obtain a stream over single-cell vectors for a given quantitation type.

streamSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

streamSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession,
 SingleCellExpressionExperimentService.SingleCellVectorInitializationConfig config)

streamSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<SingleCellExpressionDataVector> streamSingleCellDataVectors(ExpressionExperiment ee,
 List<BioAssay> samples,
 QuantitationType quantitationType,
 int fetchSize,
 boolean useCursorFetchIfSupported,
 boolean createNewSession)

getSingleCellDataVectorWithoutCellIds

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellExpressionDataVector getSingleCellDataVectorWithoutCellIds(ExpressionExperiment ee,
 QuantitationType quantitationType,
 CompositeSequence designElement)

Obtain a single single-cell vector without initializing cell IDs.

See Also:

• getSingleCellDimensionWithoutCellIds(ExpressionExperiment, QuantitationType)

getNumberOfSingleCellDataVectors

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long getNumberOfSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType qt)

Obtain the number of single-cell vectors for a given quantitation type.

getNumberOfNonZeroes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
long getNumberOfNonZeroes(ExpressionExperiment ee,
 QuantitationType qt)

getNumberOfNonZeroesBySample

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Map<BioAssay,Long> getNumberOfNonZeroesBySample(ExpressionExperiment ee,
 QuantitationType qt,
 int fetchSize,
 boolean useCursorFetchIfSupported)

getSingleCellExpressionDataMatrix

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellExpressionDataMatrix<?> getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 List<BioAssay> samples,
 QuantitationType quantitationType)

Obtain a single-cell expression data matrix for the given quantitation type.

getSingleCellExpressionDataMatrix

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellExpressionDataMatrix<?> getSingleCellExpressionDataMatrix(ExpressionExperiment expressionExperiment,
 QuantitationType quantitationType)

Obtain a single-cell expression data matrix for the given quantitation type.

addSingleCellDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int addSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<SingleCellExpressionDataVector> vectors,
 @Nullable
 String details)

Add single-cell data vectors.

Returns:

the number of vectors that were added

replaceSingleCellDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int replaceSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType,
 Collection<SingleCellExpressionDataVector> vectors,
 @Nullable
 String details)

Replace existing single-cell data vectors for the given quantitation type.

Parameters:

details - additional details to include in the audit event

Returns:

the number of vectors that were replaced

updateSparsityMetrics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void updateSparsityMetrics(ExpressionExperiment ee)

Update the sparsity metrics.

If no preferred single-cell vectors are present, the sparsity metrics will be cleared.

removeSingleCellDataVectors

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
int removeSingleCellDataVectors(ExpressionExperiment ee,
 QuantitationType quantitationType)

Remove single-cell data vectors for the given quantitation type.

Returns:

the number of vectors that were removed

getSingleCellDimensions

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<SingleCellDimension> getSingleCellDimensions(ExpressionExperiment ee)

Obtain all the single-cell dimensions used by a given dataset.

getSingleCellDimensionsWithoutCellIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee)

getSingleCellDimensionsWithoutCellIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<SingleCellDimension> getSingleCellDimensionsWithoutCellIds(ExpressionExperiment ee,
 SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)

getSingleCellDimension

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellDimension getSingleCellDimension(ExpressionExperiment ee,
 QuantitationType qt)

Obtain a single-cell dimension used for a given dataset and QT.

getSingleCellDimensionWithCellLevelCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellDimension getSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt)

getSingleCellDimensionWithAssaysAndCellLevelCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellDimension getSingleCellDimensionWithAssaysAndCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt)

Retrieve a single-cell dimension with its bioassays and cell-level characteristics initialized.

getSingleCellDimensionWithoutCellIds

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 QuantitationType qt)

getSingleCellDimensionWithoutCellIds

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
SingleCellDimension getSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 QuantitationType qt,
 SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)

getPreferredSingleCellDimension

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<SingleCellDimension> getPreferredSingleCellDimension(ExpressionExperiment ee)

Obtain the preferred single-cell dimension.

Cell type assignments and other cell-level characteristics are eagerly initialized.

getPreferredSingleCellDimensionWithoutCellIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<SingleCellDimension> getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee)

Obtain the preferred single-cell dimension without its cell IDs.

The returned object is not persistent since it's a projection.

getPreferredSingleCellDimensionWithoutCellIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<SingleCellDimension> getPreferredSingleCellDimensionWithoutCellIds(ExpressionExperiment ee,
 SingleCellExpressionExperimentService.SingleCellDimensionInitializationConfig singleCellDimensionInitializationConfig)

getPreferredSingleCellDimensionWithCellLevelCharacteristics

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<SingleCellDimension> getPreferredSingleCellDimensionWithCellLevelCharacteristics(ExpressionExperiment ee)

Obtain the preferred single-cell dimension.

Cell type assignments and other cell-level characteristics are eagerly initialized.

streamCellIds

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<Stream<String>> streamCellIds(ExpressionExperiment ee,
 boolean createNewSession)

streamCellIds

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<String> streamCellIds(ExpressionExperiment ee,
 QuantitationType qt,
 boolean createNewSession)

streamCellTypes

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<Characteristic> streamCellTypes(ExpressionExperiment ee,
 CellTypeAssignment cta,
 boolean createNewSession)

getCellTypeAt

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Characteristic getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId,
 int cellIndex)

getCellTypeAt

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Characteristic[] getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId,
 int startIndex,
 int endIndexExclusive)

getCellTypeAt

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Characteristic getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 String ctaName,
 int cellIndex)

getCellTypeAt

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Characteristic[] getCellTypeAt(ExpressionExperiment ee,
 QuantitationType qt,
 String ctaName,
 int startIndex,
 int endIndexExclusive)

getCellLevelCharacteristicsCategory

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Category getCellLevelCharacteristicsCategory(ExpressionExperiment ee,
 CellLevelCharacteristics clc)

streamCellLevelCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Stream<Characteristic> streamCellLevelCharacteristics(ExpressionExperiment ee,
 CellLevelCharacteristics clc,
 boolean createNewSession)

relabelCellTypes

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
CellTypeAssignment relabelCellTypes(ExpressionExperiment ee,
 QuantitationType qt,
 SingleCellDimension dimension,
 List<String> newCellTypeLabels,
 @Nullable
 Protocol labellingProtocol,
 @Nullable
 String description)

Relabel the cell types of an existing set of single-cell vectors.

Parameters:

newCellTypeLabels - the new cell types labels, must match the number of cells

labellingProtocol - the protocol used to generate the new labelling, or null if unknown

Returns:

a new, preferred cell type labelling

addCellTypeAssignment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
CellTypeAssignment addCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt,
 SingleCellDimension dimension,
 CellTypeAssignment cellTypeAssignment)

removeCellTypeAssignment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCellTypeAssignment(ExpressionExperiment ee,
 SingleCellDimension scd,
 CellTypeAssignment cellTypeAssignment)

Remove the given cell type assignment.

If the cell type labelling is preferred and applies to the preferred vectors as per getPreferredCellTypeAssignment(ExpressionExperiment), the cell type factor will be removed.

removeCellTypeAssignment

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt,
 CellTypeAssignment cellTypeAssignment)

Remove the given cell type assignment by QT.

See Also:

• removeCellTypeAssignment(ExpressionExperiment, SingleCellDimension, CellTypeAssignment)

removeCellTypeAssignmentByName

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCellTypeAssignmentByName(ExpressionExperiment ee,
 SingleCellDimension dimension,
 String name)

removeAllCellTypeAssignments

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
long removeAllCellTypeAssignments(ExpressionExperiment ee,
 QuantitationType qt)

getCellTypeAssignments

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment ee)

Obtain all the cell type labellings from all single-cell vectors.

getCellTypeAssignments

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<CellTypeAssignment> getCellTypeAssignments(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

getCellTypeAssignment

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Long ctaId)

Obtain a cell type assignment by ID.

Returns:

that cell type assignmente, or null if none is found

getCellTypeAssignment

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellTypeAssignment getCellTypeAssignment(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 String ctaName)

Obtain a cell type assignment by name.

Returns:

that cell type assignmente, or null if none is found

getCellTypeAssignmentWithoutIndices

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId)

getCellTypeAssignmentWithoutIndices

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellTypeAssignment getCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 String ctaName)

getCellTypeAssignmentsWithoutIndices

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<CellTypeAssignment> getCellTypeAssignmentsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

getCellTypeAssignmentProtocols

Collection<Protocol> getCellTypeAssignmentProtocols()

Obtain a collection of protocols used to assign cell types to single-cell vectors.

getCellTypeAssignmentByProtocol

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<CellTypeAssignment> getCellTypeAssignmentByProtocol(ExpressionExperiment ee,
 QuantitationType qt,
 String protocolName)

Obtain a cell type assignment by a protocol identifier.

getPreferredCellTypeAssignment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<CellTypeAssignment> getPreferredCellTypeAssignment(ExpressionExperiment ee)

Obtain the preferred cell type labelling from the preferred single-cell vectors.

getPreferredCellTypeAssignment

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<CellTypeAssignment> getPreferredCellTypeAssignment(ExpressionExperiment ee,
 QuantitationType qt)

getPreferredCellTypeAssignmentWithoutIndices

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<CellTypeAssignment> getPreferredCellTypeAssignmentWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

addCellLevelCharacteristics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
CellLevelCharacteristics addCellLevelCharacteristics(ExpressionExperiment ee,
 SingleCellDimension scd,
 CellLevelCharacteristics clc)

Add new cell-level characteristics.

removeCellLevelCharacteristics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCellLevelCharacteristics(ExpressionExperiment ee,
 SingleCellDimension scd,
 CellLevelCharacteristics clc)

Remove existing cell-level characteristics.

removeCellLevelCharacteristics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt,
 CellLevelCharacteristics clc)

Remove existing cell-level characteristics by QT.

removeCellLevelCharacteristicsByName

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
void removeCellLevelCharacteristicsByName(ExpressionExperiment ee,
 SingleCellDimension dimension,
 String name)

removeAllCellLevelCharacteristics

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
long removeAllCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt)

getCellLevelCharacteristics

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee)

See Also:

• ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment)

getCellLevelCharacteristics

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment ee,
 Category category)

Obtain CLC for given category.

getCellLevelCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt,
 Long id)

getCellLevelCharacteristics

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellLevelCharacteristics getCellLevelCharacteristics(ExpressionExperiment ee,
 QuantitationType qt,
 String name)

Obtain a CLC by name.

getCellLevelCharacteristics

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<CellLevelCharacteristics> getCellLevelCharacteristics(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

getCellLevelCharacteristicsWithoutIndices

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 Long ctaId)

getCellLevelCharacteristicsWithoutIndices

@Nullable
@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
CellLevelCharacteristics getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt,
 String clcName)

getCellLevelCharacteristicsWithoutIndices

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Collection<CellLevelCharacteristics> getCellLevelCharacteristicsWithoutIndices(ExpressionExperiment ee,
 QuantitationType qt)

getCellLevelMask

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<CellLevelCharacteristics> getCellLevelMask(ExpressionExperiment expressionExperiment,
 QuantitationType qt)

Obtain a mask if one is unambiguously defined for the given experiment and quantitation type.

getCellTypes

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
List<Characteristic> getCellTypes(ExpressionExperiment ee)

Obtain the cell types of a given single-cell dataset.

Only the cell types applicable to the preferred single-cell vectors and labelling are returned.

getCellTypeFactor

@Secured({"IS_AUTHENTICATED_ANONYMOUSLY","ACL_SECURABLE_READ"})
Optional<ExperimentalFactor> getCellTypeFactor(ExpressionExperiment ee)

Obtain the cell type factor.

Returns:

a cell type factor, or null of none exist

Throws:

IllegalStateException - if there is more than one such factor

recreateCellTypeFactor

@Secured({"GROUP_USER","ACL_SECURABLE_EDIT"})
ExperimentalFactor recreateCellTypeFactor(ExpressionExperiment ee)

Recreate the cell type factor based on the preferred labelling of the preferred single-cell vectors.

Analyses involving the factor are removed and samples mentioning the factor values are updated as per ExperimentalFactorService.remove(ExperimentalFactor).

Returns:

the created cell type factor

Throws:

IllegalStateException - if the dataset does not have a preferred cell type labelling for its preferred set of single-cell vectors or if there is more than one cell type factor present in the dataset