Package ubic.gemma.core.loader.expression.singleCell

Class AnnDataSingleCellDataLoader

java.lang.Object

ubic.gemma.core.loader.expression.singleCell.AnnDataSingleCellDataLoader

All Implemented Interfaces:

Closeable, AutoCloseable, DataLoader, SequencingDataLoader, SingleCellDataLoader

public class AnnDataSingleCellDataLoader
extends Object
implements SingleCellDataLoader

Reads single-cell vectors from the AnnData on-disk HDF5 format.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
AnnDataSingleCellDataLoader(Path file)

Method Summary

Modifier and Type	Method	Description
void	close()	Free any resources that the loaded has setup.
Set<CellTypeAssignment>	getCellTypeAssignments(SingleCellDimension dimension)	Load single-cell type assignments present in the data.
Set<ExperimentalFactor>	getFactors(Collection<BioAssay> samples, Map<BioMaterial,Set<FactorValue>> factorValueAssignments)	Load experimental factors present in the data.
Set<String>	getGenes()	Load gene identifiers present in the data.
Set<String>	getGenes(QuantitationType qt)	Obtain the genes for a specific QT.
Set<CellLevelCharacteristics>	getOtherCellLevelCharacteristics(SingleCellDimension dimension)	Load cell-level characteristics that are not cell type assignments present in the data.
Set<QuantitationType>	getQuantitationTypes()	Load quantitation types present in the data.
Set<String>	getSampleNames()	Obtain the sample names present in the data.
Map<BioMaterial,Set<Characteristic>>	getSamplesCharacteristics(Collection<BioAssay> samples)	Load samples characteristics present in the data.
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(Collection<BioAssay> samples)	Retrieve various sequencing metadata if counting data is present.
Map<BioAssay,SequencingMetadata>	getSequencingMetadata(SingleCellDimension dimension)
SingleCellDimension	getSingleCellDimension(Collection<BioAssay> bioAssays)	Load the single-cell dimension present in the data.
Stream<SingleCellExpressionDataVector>	loadVectors(Collection<CompositeSequence> designElements, SingleCellDimension dimension, QuantitationType quantitationType)	Produces a stream of single-cell expression data vectors for the given QuantitationType.
void	setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)	Set the strategy used for mapping BioAssay to sample names from the data.
void	setCellTypeFactorName(String cellTypeFactorName)	The name of the cell type factor under /var.
void	setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)	Set the strategy used for mapping CompositeSequence to gene identifiers from the data.
void	setIgnoreCellTypeFactor(boolean ignoreCellTypeFactor)	Ignore cell type assignment.
void	setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)	Ignore unmatched design elements from the data when creating vectors.
void	setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)	Ignore unmatched samples from the data.
void	setMaxCharacteristics(int maxCharacteristics)	Maximum number of characteristics to consider when loading a cell-level characteristic.
void	setSampleFactorName(String sampleFactorName)	The name of the sample factor under /var.
void	setTranspose(boolean transpose)	Transpose obs/var dataframes.
void	setUnknownCellTypeIndicator(String unknownCellTypeIndicator)	An indicator for unknown cell type if the dataset uses something else than the -1 code.
void	setUseRawX(Boolean useRawX)	Use or not the raw.X layer.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

AnnDataSingleCellDataLoader

public AnnDataSingleCellDataLoader(Path file)

Method Details

getSampleNames

public Set<String> getSampleNames()
                           throws IOException

Description copied from interface: DataLoader

Obtain the sample names present in the data.

Specified by:

getSampleNames in interface DataLoader

Throws:

IOException

getSingleCellDimension

public SingleCellDimension getSingleCellDimension(Collection<BioAssay> bioAssays)
                                           throws IOException

Description copied from interface: SingleCellDataLoader

Load the single-cell dimension present in the data.

Not all samples might be present and thus the returned SingleCellDimension will have a expression data for a subset of the data.

Specified by:

getSingleCellDimension in interface SingleCellDataLoader

Parameters:

bioAssays - a set of bioassays to use when populating the dimension, not all bioassays may be used

Throws:

IOException

getQuantitationTypes

public Set<QuantitationType> getQuantitationTypes()
                                           throws IOException

Description copied from interface: DataLoader

Load quantitation types present in the data.

Specified by:

getQuantitationTypes in interface DataLoader

Throws:

IOException

getCellTypeAssignments

public Set<CellTypeAssignment> getCellTypeAssignments(SingleCellDimension dimension)
                                               throws IOException

Description copied from interface: SingleCellDataLoader

Load single-cell type assignments present in the data.

Specified by:

getCellTypeAssignments in interface SingleCellDataLoader

Throws:

IOException

getOtherCellLevelCharacteristics

public Set<CellLevelCharacteristics> getOtherCellLevelCharacteristics(SingleCellDimension dimension)
                                                               throws IOException

Description copied from interface: SingleCellDataLoader

Load cell-level characteristics that are not cell type assignments present in the data.

Specified by:

getOtherCellLevelCharacteristics in interface SingleCellDataLoader

Throws:

IOException

getFactors

public Set<ExperimentalFactor> getFactors(Collection<BioAssay> samples,
 @Nullable
 Map<BioMaterial,Set<FactorValue>> factorValueAssignments)
                                   throws IOException

Description copied from interface: DataLoader

Load experimental factors present in the data.

Specified by:

getFactors in interface DataLoader

Parameters:

samples - samples to use when determining which factors to load

factorValueAssignments - if non-null, the proposed assignment of factor values to samples are populated in the mapping.

Returns:

a set of factors present in the data

Throws:

IOException

getSamplesCharacteristics

public Map<BioMaterial,Set<Characteristic>> getSamplesCharacteristics(Collection<BioAssay> samples)
                                                               throws IOException

Description copied from interface: DataLoader

Load samples characteristics present in the data.

Specified by:

getSamplesCharacteristics in interface DataLoader

Parameters:

samples - to use when determining which characteristics to load

Returns:

proposed characteristics grouped by sample

Throws:

IOException

getGenes

public Set<String> getGenes()
                     throws IOException

Description copied from interface: DataLoader

Load gene identifiers present in the data.

Specified by:

getGenes in interface DataLoader

Throws:

IOException

getSequencingMetadata

public Map<BioAssay,SequencingMetadata> getSequencingMetadata(Collection<BioAssay> samples)
                                                       throws IOException

Description copied from interface: SequencingDataLoader

Retrieve various sequencing metadata if counting data is present.

Specified by:

getSequencingMetadata in interface SequencingDataLoader

Throws:

IOException

getSequencingMetadata

public Map<BioAssay,SequencingMetadata> getSequencingMetadata(SingleCellDimension dimension)
                                                       throws IOException

Specified by:

getSequencingMetadata in interface SingleCellDataLoader

Throws:

IOException

getGenes

public Set<String> getGenes(QuantitationType qt)
                     throws IOException

Obtain the genes for a specific QT.

Throws:

IOException

loadVectors

public Stream<SingleCellExpressionDataVector> loadVectors(Collection<CompositeSequence> designElements,
 SingleCellDimension dimension,
 QuantitationType quantitationType)
                                                   throws IOException,
IllegalArgumentException

Description copied from interface: SingleCellDataLoader

Produces a stream of single-cell expression data vectors for the given QuantitationType.

Specified by:

loadVectors in interface SingleCellDataLoader

Parameters:

designElements - a collection of design elements for mapping of element names used in the dataset to CompositeSequence

dimension - a dimension to use for creating vectors, may be loaded from the single-cell data with SingleCellDataLoader.getSingleCellDimension(Collection)

quantitationType - a quantitation type to extract from the data for, may be loaded from the single-cell data with DataLoader.getQuantitationTypes()

Returns:

a stream of single-cell expression data vectors that must be closed when done, preferably using a try-with-resource block.

Throws:

IllegalArgumentException - if a design element present in the data cannot be matched to one of the supplied elements, requires setting DataLoader.setIgnoreUnmatchedDesignElements(boolean) to false

IOException

close

public void close()
           throws IOException

Description copied from interface: DataLoader

Free any resources that the loaded has setup.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface Closeable

Specified by:

close in interface DataLoader

Throws:

IOException

setBioAssayToSampleNameMapper

public void setBioAssayToSampleNameMapper(BioAssayMapper bioAssayToSampleNameMapper)

Description copied from interface: DataLoader

Set the strategy used for mapping BioAssay to sample names from the data.

Specified by:

setBioAssayToSampleNameMapper in interface DataLoader

setIgnoreUnmatchedSamples

public void setIgnoreUnmatchedSamples(boolean ignoreUnmatchedSamples)

Description copied from interface: DataLoader

Ignore unmatched samples from the data.

This defaults to true.

Specified by:

setIgnoreUnmatchedSamples in interface DataLoader

setDesignElementToGeneMapper

public void setDesignElementToGeneMapper(DesignElementMapper designElementToGeneMapper)

Description copied from interface: DataLoader

Set the strategy used for mapping CompositeSequence to gene identifiers from the data.

Specified by:

setDesignElementToGeneMapper in interface DataLoader

setIgnoreUnmatchedDesignElements

public void setIgnoreUnmatchedDesignElements(boolean ignoreUnmatchedDesignElements)

Description copied from interface: DataLoader

Ignore unmatched design elements from the data when creating vectors.

This defaults to true.

There's a discussions to make this default in false in general for sequencing data.

Specified by:

setIgnoreUnmatchedDesignElements in interface DataLoader

setSampleFactorName

public void setSampleFactorName(String sampleFactorName)

The name of the sample factor under /var.

setCellTypeFactorName

public void setCellTypeFactorName(@Nullable
 String cellTypeFactorName)

The name of the cell type factor under /var.

setIgnoreCellTypeFactor

public void setIgnoreCellTypeFactor(boolean ignoreCellTypeFactor)

Ignore cell type assignment.

setUnknownCellTypeIndicator

public void setUnknownCellTypeIndicator(@Nullable
 String unknownCellTypeIndicator)

An indicator for unknown cell type if the dataset uses something else than the -1 code.

setUseRawX

public void setUseRawX(@Nullable
 Boolean useRawX)

Use or not the raw.X layer.

The default is to use X if raw.X is not present. If raw.X is present and no value is specified, an exception will be raised.

setTranspose

public void setTranspose(boolean transpose)

Transpose obs/var dataframes.

setMaxCharacteristics

public void setMaxCharacteristics(int maxCharacteristics)

Maximum number of characteristics to consider when loading a cell-level characteristic.