Package ubic.gemma.core.visualization

Class ExperimentalDesignVisualizationServiceImpl

java.lang.Object

ubic.gemma.core.visualization.ExperimentalDesignVisualizationServiceImpl

All Implemented Interfaces:

ExperimentalDesignVisualizationService

@Service
public class ExperimentalDesignVisualizationServiceImpl
extends Object
implements ExperimentalDesignVisualizationService

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

Author:

paul

Constructor Summary

Constructors

Constructor	Description
ExperimentalDesignVisualizationServiceImpl()

Method Summary

Modifier and Type	Method	Description
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

public ExperimentalDesignVisualizationServiceImpl()

Method Detail

sortVectorDataByDesign

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