Package ubic.gemma.web.controller.expression.experiment

Class DEDVController

java.lang.Object
ubic.gemma.web.controller.expression.experiment.DEDVController
@Controller @RequestMapping("/dedv") public class DEDVController extends Object
Exposes methods for accessing underlying Design Element Data Vectors. eg: ajax methods for visualization
Author:
kelsey

  • Constructor Details

    • DEDVController

      public DEDVController()

  • Method Details

    • getDEDV

      public Map<BioAssaySetValueObject,Map<Long,Collection<DoubleVectorValueObject>>> getDEDV(Collection<Long> eeIds, Collection<Long> geneIds)
      Given a collection of expression experiment Ids and a geneId returns a map of DEDV value objects to a collection of genes. The EE info is in the value object. FIXME handle subsets.

      AJAX

    • getDEDVForCoexpressionVisualization

      public VisualizationValueObject[] getDEDVForCoexpressionVisualization(Collection<Long> eeIds, Long queryGeneId, Long coexpressedGeneId)
      AJAX exposed method

    • getDEDVForDiffExVisualization

      public VisualizationValueObject[] getDEDVForDiffExVisualization(Collection<Long> eeIds, Collection<Long> geneIds, Double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap)
      AJAX exposed method - for ProbeLevelDiffExGrid, VisualizationDifferentialWindow, DifferentialExpressionAnalysesSummaryTree
      Parameters:
      eeIds - FIXME accommodate ExpressionExperimentSubSets. Currently we pass in the "source experiment" so we don't get the slice.
      geneIds - (could be just one)
      threshold - for 'significance'
      factorMap - Collection of DiffExpressionSelectedFactorCommand showing which factors to use.

    • getDEDVForDiffExVisualizationByExperiment

      public VisualizationValueObject[] getDEDVForDiffExVisualizationByExperiment(Long eeId, Long geneId, Double threshold, Boolean isSubset)
      AJAX exposed method Batch factor value analyses are filtered out; for ProbeLevelDiffExGrid:VisualizationDifferentialWindow.

    • getDEDVForDiffExVisualizationByThreshold

      public VisualizationValueObject[] getDEDVForDiffExVisualizationByThreshold(Long resultSetId, Double givenThreshold, @Nullable Long primaryFactorID)
      AJAX exposed method
      Parameters:
      resultSetId - The resultset we're specifically interested. Note that this is what is used to choose the vectors, since it could be a subset of an experiment.
      givenThreshold - If non-null, a P-value threshold for retrieving associated vectors
      primaryFactorID - If non-null, the factor to use for sorting the samples before other factors are considered
      Returns:
      collection of visualization value objects

    • getDEDVForPcaVisualization

      public VisualizationValueObject[] getDEDVForPcaVisualization(Long eeId, int component, int count)
      AJAX

    • getDEDVForVisualization

      public VisualizationValueObject[] getDEDVForVisualization(Collection<Long> eeIds, Collection<Long> geneIds)
      AJAX exposed method

    • getDEDVForVisualizationByProbe

      public VisualizationValueObject[] getDEDVForVisualizationByProbe(Collection<Long> eeIds, Collection<Long> probeIds)
      AJAX exposed method

    • downloadPCA

      @RequestMapping(value="/downloadDEDV.html", method={GET,HEAD}, params="pca") public org.springframework.web.servlet.ModelAndView downloadPCA(@RequestParam("ee") Long eeId, @RequestParam("pca") String pca, @RequestParam(value="component",required=false) Integer component, @RequestParam(value="thresh",defaultValue="100") int thresh)

    • downloadDEDV

      @RequestMapping(value="/downloadDEDV.html", method={GET,HEAD}, params="rs") public org.springframework.web.servlet.ModelAndView downloadDEDV(@RequestParam("ee") Long eeId, @RequestParam("rs") Long resultSetId, @RequestParam(value="g",required=false) String gS, @RequestParam(value="thresh",defaultValue="0.05") double thresh)

    • downloadDEDV

      @RequestMapping(value="/downloadDEDV.html", method={GET,HEAD}) public org.springframework.web.servlet.ModelAndView downloadDEDV(@RequestParam("ee") Long eeId, @RequestParam(value="g",required=false) String gS)
      Handle case of text export of the results.