Package ubic.gemma.core.visualization

Class ExperimentalDesignVisualizationServiceImpl

java.lang.Object

ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl

All Implemented Interfaces:

ExperimentalDesignVisualizationService

@Component
public class ExperimentalDesignVisualizationServiceImpl
extends Object
implements ExperimentalDesignVisualizationService

Tools for visualizing experimental designs. The idea is to generate a overview of the design that can be put over heat maps or line graphs.

Author:

paul

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignVisualizationServiceImpl(ExpressionExperimentService expressionExperimentService)

Method Summary

Modifier and Type	Method	Description
void	clearCaches(Long eeId)	removed the cached layouts and cached BioAssayDimensions for this experiment (could be a subset?).
protected void	plotExperimentalDesign(ExpressionExperiment e)	Test method for now, shows how this can be used.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs)	Put data vectors in the order you'd want to display the experimental design.
Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>>	sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs, ExperimentalFactor primaryFactor)	Put data vectors in the order you'd want to display the experimental design.

Methods inherited from class java.lang.Object

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

Constructor Detail

ExperimentalDesignVisualizationServiceImpl

@Autowired
public ExperimentalDesignVisualizationServiceImpl(ExpressionExperimentService expressionExperimentService)

Method Detail

sortVectorDataByDesign

public Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>> sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs)

Description copied from interface: ExperimentalDesignVisualizationService

Put data vectors in the order you'd want to display the experimental design. This causes the "isReorganized" flag of the dedVs to be set to true.

Specified by:

sortVectorDataByDesign in interface ExperimentalDesignVisualizationService

Parameters:

dedVs - dedVs, already sliced for the subset of samples needed for display (if necessary); will be modified

Returns:

Map of EE ids to "layouts", which are Maps of BioAssays to map of experimental factors to doubles.

sortVectorDataByDesign

public Map<Long,LinkedHashMap<BioAssayValueObject,LinkedHashMap<ExperimentalFactor,Double>>> sortVectorDataByDesign(Collection<DoubleVectorValueObject> dedVs,
                                                                                                                                      ExperimentalFactor primaryFactor)

Description copied from interface: ExperimentalDesignVisualizationService

Put data vectors in the order you'd want to display the experimental design. This causes the "isReorganized" flag of the dedVs to be set to true.

Specified by:

sortVectorDataByDesign in interface ExperimentalDesignVisualizationService

Parameters:

dedVs - dedVs, already sliced for the subset of samples needed for display (if necessary); will be modified

primaryFactor - if non-null this factor will be used to order the data, otherwise the first factor will be chosen using built-in heuristics. Set this to ensure that the data is ordered by the factor you want as in the case of showing DE genes

Returns:

Map of EE ids to "layouts", which are Maps of BioAssays to map of experimental factors to doubles.

clearCaches

public void clearCaches(Long eeId)

Description copied from interface: ExperimentalDesignVisualizationService

removed the cached layouts and cached BioAssayDimensions for this experiment (could be a subset?).

Specified by:

clearCaches in interface ExperimentalDesignVisualizationService

Parameters:

eeId - ee id

plotExperimentalDesign

protected void plotExperimentalDesign(ExpressionExperiment e)

Test method for now, shows how this can be used.

Parameters:

e - ee