Package ubic.gemma.core.visualization

Interface ExperimentalDesignVisualizationService

All Known Implementing Classes:

ExperimentalDesignVisualizationServiceImpl

public interface ExperimentalDesignVisualizationService

Author:

Paul

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?).
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.

Method Detail

sortVectorDataByDesign

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

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.

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.

sortVectorDataByDesign

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. This causes the "isReorganized" flag of the dedVs to be set to true.

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.

clearCaches

void clearCaches(Long eeId)

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

Parameters:

eeId - ee id