Uses of Interface
ubic.gemma.model.expression.bioAssayData.CellLevelCharacteristics

Packages that use CellLevelCharacteristics

Package	Description
ubic.gemma.cli.util
ubic.gemma.core.analysis.singleCell	This package contains classes for analysing single-cell expression data.
ubic.gemma.core.analysis.singleCell.aggregate	This packge contains classes for splitting and aggregating single-cell data.
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.model.expression.bioAssayData
ubic.gemma.persistence.service.expression.experiment
ubic.gemma.persistence.util

Uses of CellLevelCharacteristics in ubic.gemma.cli.util

Methods in ubic.gemma.cli.util that return CellLevelCharacteristics

Modifier and Type	Method	Description
CellLevelCharacteristics	EntityLocator.locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)
CellLevelCharacteristics	EntityLocatorImpl.locateCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, String clcIdentifier)

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

Methods in ubic.gemma.core.analysis.singleCell that return types with arguments of type CellLevelCharacteristics

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

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

Modifier and Type	Method	Description
void	SingleCellSparsityMetrics.addExpressedCells(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex, boolean[] isExpressed)	Populate a boolean vector that indicates if a cell has at least one expressed gene.
static int	SingleCellDescriptive.countFast(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
int	SingleCellSparsityMetrics.getNumberOfCells(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of cells with at least one gene expressed.
int	SingleCellSparsityMetrics.getNumberOfCellsByDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)	Calculate the number of expressed cell by gene pairs.
int	SingleCellSparsityMetrics.getNumberOfCellsByDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int characteristicIndex)
int	SingleCellSparsityMetrics.getNumberOfDesignElements(Collection<SingleCellExpressionDataVector> vectors, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)	Calculate the number of genes expressed in at least one cell.
int	SingleCellSparsityMetrics.getNumberOfDesignElements(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics characteristic, int characteristicIndex)
static double	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[][]	SingleCellDescriptive.max(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double	SingleCellDescriptive.mean(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double	SingleCellDescriptive.median(SingleCellExpressionDataVector vector, int column, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static double[][]	SingleCellDescriptive.min(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)
static double	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[]	SingleCellDescriptive.quantile(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics, int row, double q)
static double[][]	SingleCellDescriptive.sum(SingleCellExpressionDataVector vector, CellLevelCharacteristics cellLevelCharacteristics)

Uses of CellLevelCharacteristics in ubic.gemma.core.analysis.singleCell.aggregate

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

Modifier and Type	Method	Description
static Collection<RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.aggregate(Collection<SingleCellExpressionDataVector> vectors, SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics)	Aggregate a collection of vectors.
QuantitationType	SingleCellExpressionExperimentAggregatorService.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, AggregateConfig config)	Aggregate preferred single-cell data vectors by the given cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentAggregatorServiceImpl.aggregateVectors(ExpressionExperiment ee, QuantitationType qt, List<BioAssay> cellBAs, CellLevelCharacteristics cellLevelCharacteristics, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellType2Factor, AggregateConfig config)
static Function<SingleCellExpressionDataVector,RawExpressionDataVector>	SingleCellDataVectorAggregatorUtils.createAggregator(SingleCellDataVectorAggregatorUtils.SingleCellAggregationMethod method, CellLevelCharacteristics cellLevelCharacteristics)	Create an aggregator that can be used on a Stream of vectors.
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingByFactorValueCharacteristics(CellLevelCharacteristics cta, ExperimentalFactor factor)	Map the cell types from a cell type assignment to factor values in a cell type factor.
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue,ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.
static Map<Characteristic,FactorValue>	CellLevelCharacteristicsMappingUtils.readMappingFromFile(CellLevelCharacteristics clc, ExperimentalFactor factor, Path cellTypeMappingFile)	Create a mapping of cell type assignments to factor values from a file.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateService.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)	Re-aggregate a dataset by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateServiceImpl.redoAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> c2f, BioAssayDimension dimension, QuantitationType previousQt, AggregateConfig config)
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitService.split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> cellTypeMapping, SplitConfig config)	Split biomaterials and bioassays by the given CellLevelCharacteristics.
List<ExpressionExperimentSubSet>	SingleCellExpressionExperimentSplitServiceImpl.split(ExpressionExperiment ee, CellLevelCharacteristics clc, ExperimentalFactor factor, Map<Characteristic,FactorValue> mappedCellTypeFactors, SplitConfig config)
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateService.splitAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics cta, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SplitConfig splitConfig, AggregateConfig config)	Split and aggregate by any cell-level characteristics.
QuantitationType	SingleCellExpressionExperimentSplitAndAggregateServiceImpl.splitAndAggregate(ExpressionExperiment expressionExperiment, QuantitationType scQt, CellLevelCharacteristics clc, ExperimentalFactor cellTypeFactor, Map<Characteristic,FactorValue> c2f, SplitConfig splitConfig, AggregateConfig config)
static void	CellLevelCharacteristicsMappingUtils.writeMapping(CellLevelCharacteristics cta, ExperimentalFactor factor, Map<Characteristic,FactorValue> cta2f, Writer dest)	Create a mapping of cell type assignments to factor values from a file.

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

Methods in ubic.gemma.core.loader.expression.singleCell that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
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.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e. anything that is not a cell type assignment), the data type is automatically detected.
Collection<CellLevelCharacteristics>	SingleCellDataLoaderService.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)	Load other cell-level characteristics (i.e. anything that is not a cell type assignment).
Collection<CellLevelCharacteristics>	SingleCellDataLoaderServiceImpl.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataLoaderConfig config)
Collection<CellLevelCharacteristics>	SingleCellDataLoaderServiceImpl.loadOtherCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDataType dataType, SingleCellDataLoaderConfig config)

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

Methods in ubic.gemma.core.loader.expression.singleCell.metadata that return types with arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
Set<CellLevelCharacteristics>	GenericMetadataSingleCellDataLoader.getOtherCellLevelCharacteristics(SingleCellDimension dimension)

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

Modifier and Type	Method	Description
void	CellLevelCharacteristicsWriter.write(CellLevelCharacteristics cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write a single set of cell-level characteristics to a writer.

Method parameters in ubic.gemma.core.loader.expression.singleCell.metadata with type arguments of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	CellLevelCharacteristicsWriter.write(Collection<CellLevelCharacteristics> cellLevelCharacteristics, SingleCellDimension dimension, Writer writer)	Write multiple sets of cell-level characteristics to a writer.

Uses of CellLevelCharacteristics in ubic.gemma.core.visualization

Methods in ubic.gemma.core.visualization with parameters of type CellLevelCharacteristics

Modifier and Type	Method	Description
void	SingleCellDataBoxplot.setCellLevelCharacteristics(CellLevelCharacteristics cellLevelCharacteristics)

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

Classes in ubic.gemma.model.expression.bioAssayData that implement CellLevelCharacteristics

Modifier and Type	Class	Description
class	CellTypeAssignment	Represents a cell type assignment where cells from a given dataset are assigned cell types.
class	GenericCellLevelCharacteristics	Generic cell-level characteristics.

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

Modifier and Type	Method	Description
static CellLevelCharacteristics	CellLevelCharacteristics.Factory.newInstance(List<Characteristic> characteristics, int[] indices)

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

Modifier and Type	Method	Description
static double[]	SingleCellExpressionDataVectorUtils.getSampleDataAsDoubles(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static float[]	SingleCellExpressionDataVectorUtils.getSampleDataAsFloats(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)	Obtain the data of a sample.
static int[]	SingleCellExpressionDataVectorUtils.getSampleDataAsInts(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)
static long[]	SingleCellExpressionDataVectorUtils.getSampleDataAsLongs(SingleCellExpressionDataVector vector, int sampleIndex, CellLevelCharacteristics cellLevelCharacteristics, int row)

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

Constructor	Description
CellLevelCharacteristicsValueObject(CellLevelCharacteristics cellLevelCharacteristics, boolean excludeCharacteristicIds)

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

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

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)
CellLevelCharacteristics	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)	Obtain a specific cell-level characteristic by ID.
CellLevelCharacteristics	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, Long clcId)
CellLevelCharacteristics	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)
CellLevelCharacteristics	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt, Long id)

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

Modifier and Type	Method	Description
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee)	Obtain all cell-level characteristics from all single cell dimensions.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain all cell-level characteristics from all single cell dimensions matching the given category.
List<CellLevelCharacteristics>	ExpressionExperimentDao.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	ExpressionExperimentDaoImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)	Obtain CLC for given category.
List<CellLevelCharacteristics>	SingleCellExpressionExperimentService.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment ee, Category category)
List<CellLevelCharacteristics>	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristics(ExpressionExperiment expressionExperiment, QuantitationType qt)

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

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)
Characteristic	ExpressionExperimentDao.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)	Obtain the characteristic at a given cell index.
Characteristic[]	ExpressionExperimentDao.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)
Characteristic	ExpressionExperimentDaoImpl.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int cellIndex)
Characteristic[]	ExpressionExperimentDaoImpl.getCellLevelCharacteristicAt(CellLevelCharacteristics clc, int startIndex, int endIndexExclusive)
Category	ExpressionExperimentDao.getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)	Obtain the category of a cell-level characteristic.
Category	ExpressionExperimentDaoImpl.getCellLevelCharacteristicsCategory(CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentService.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
Category	SingleCellExpressionExperimentServiceImpl.getCellLevelCharacteristicsCategory(ExpressionExperiment ee, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)	Remove existing cell-level characteristics by QT.
void	SingleCellExpressionExperimentService.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)	Remove existing cell-level characteristics.
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, QuantitationType qt, CellLevelCharacteristics clc)
void	SingleCellExpressionExperimentServiceImpl.removeCellLevelCharacteristics(ExpressionExperiment ee, SingleCellDimension scd, CellLevelCharacteristics clc)
Stream<Characteristic>	ExpressionExperimentDao.streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	ExpressionExperimentDaoImpl.streamCellLevelCharacteristics(CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentService.streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)
Stream<Characteristic>	SingleCellExpressionExperimentServiceImpl.streamCellLevelCharacteristics(ExpressionExperiment ee, CellLevelCharacteristics clc, boolean createNewSession)

Uses of CellLevelCharacteristics in ubic.gemma.persistence.util

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

Modifier and Type	Method	Description
EntityUrlBuilder.ExpressionExperimentWebUrl	EntityUrlBuilder.ExpressionExperimentWebUrl.visualizeSingleCellBoxPlot(QuantitationType quantitationType, CompositeSequence designElement, CellLevelCharacteristics cellLevelCharacteristics, Characteristic focusedCharacteristic)