Package ubic.gemma.core.analysis.singleCell

Class CellLevelCharacteristicsMappingUtils

java.lang.Object

ubic.gemma.core.analysis.singleCell.CellLevelCharacteristicsMappingUtils

public class CellLevelCharacteristicsMappingUtils
extends Object

Utilities for creating, reading and writing mappings of CellLevelCharacteristics to ExperimentalFactor.

The most common use case for this is to map the cell type assigmnents from a CellTypeAssignment to a cell type factor.

Author:

poirigui

Constructor Summary

Constructors

Constructor	Description
CellLevelCharacteristicsMappingUtils()

Method Summary

Modifier and Type	Method	Description
static Map<Characteristic,FactorValue>	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>	createMappingBySubSetCharacteristics(CellLevelCharacteristics clc, ExperimentalFactor factor, Map<FactorValue,ExpressionExperimentSubSet> subsets)	Infer the mapping of cell type assignments to factor values using a subset structure.
static String	printMapping(Map<Characteristic,FactorValue> mappedCellTypeFactors)
static void	printMapping(Map<Characteristic,FactorValue> mappedCellTypeFactors, Appendable details)
static Map<Characteristic,FactorValue>	readMappingFromFile(CellLevelCharacteristics clc, ExperimentalFactor factor, Path cellTypeMappingFile)	Create a mapping of cell type assignments to factor values from a file.
static void	writeMapping(CellLevelCharacteristics cta, ExperimentalFactor factor, Map<Characteristic,FactorValue> cta2f, Writer dest)	Create a mapping of cell type assignments to factor values from a file.

Methods inherited from class java.lang.Object

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

Constructor Details

CellLevelCharacteristicsMappingUtils

public CellLevelCharacteristicsMappingUtils()

Method Details

createMappingByFactorValueCharacteristics

public static Map<Characteristic,FactorValue> createMappingByFactorValueCharacteristics(CellLevelCharacteristics cta,
 ExperimentalFactor factor)

Map the cell types from a cell type assignment to factor values in a cell type factor.

There is a possibility that no factor value is found for a given cell type, in which case it is ignored.

TODO: this should be private, but we reuse the same logic for aggregating in SingleCellExpressionExperimentAggregateServiceImpl.

Throws:

IllegalStateException - if there is more than one factor value mapping a given cell type

createMappingBySubSetCharacteristics

public static Map<Characteristic,FactorValue> createMappingBySubSetCharacteristics(CellLevelCharacteristics clc,
 ExperimentalFactor factor,
 Map<FactorValue,ExpressionExperimentSubSet> subsets)

Infer the mapping of cell type assignments to factor values using a subset structure.

This method is resilient to changes in the FactorValue as it will look up the characteristics of the subset via Investigation.getCharacteristics().

readMappingFromFile

public static Map<Characteristic,FactorValue> readMappingFromFile(CellLevelCharacteristics clc,
 ExperimentalFactor factor,
 Path cellTypeMappingFile)
                                                           throws IOException

Create a mapping of cell type assignments to factor values from a file.

Throws:

IOException

writeMapping

public static void writeMapping(CellLevelCharacteristics cta,
 ExperimentalFactor factor,
 Map<Characteristic,FactorValue> cta2f,
 Writer dest)
                         throws IOException

Create a mapping of cell type assignments to factor values from a file.

Throws:

IOException

printMapping

public static String printMapping(Map<Characteristic,FactorValue> mappedCellTypeFactors)

printMapping

public static void printMapping(Map<Characteristic,FactorValue> mappedCellTypeFactors,
 Appendable details)
                         throws IOException

Throws:

IOException