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

Class ExpressionExperimentQCController

java.lang.Object

ubic.gemma.web.controller.BaseController

ubic.gemma.web.controller.expression.experiment.ExpressionExperimentQCController

@Controller
public class ExpressionExperimentQCController
extends BaseController

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static int	DEFAULT_QC_IMAGE_SIZE_PX	Default size for an image, in pixel.

Fields inherited from class ubic.gemma.web.controller.BaseController

log, messageSource, messageUtil

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentQCController()

Method Summary

Modifier and Type	Method	Description
void	detailedFactorAnalysis(Long id, javax.servlet.http.HttpServletResponse response)
org.springframework.web.servlet.ModelAndView	identifyOutliersRemoved(Long id)
org.springframework.web.servlet.ModelAndView	identifyPossibleOutliers(Long id)
void	pcaFactors(Long id, javax.servlet.http.HttpServletResponse response)
void	pcaScree(Long id, javax.servlet.http.HttpServletResponse response)
void	visualizeCorrMat(Long id, Double sizeFactor, Boolean text, Boolean showLabels, Boolean forceShowLabels, Boolean reg, javax.servlet.http.HttpServletResponse response)
void	visualizeHeatmap(Long id, Long dimensionId, Integer offset, Integer limit, Integer cellSize, Boolean transpose, javax.servlet.http.HttpServletResponse response)
org.springframework.web.servlet.ModelAndView	visualizeMeanVariance(Long id, Double sizeFactor, Boolean text, javax.servlet.http.HttpServletResponse response)
void	visualizeProbeCorrDist(Long id, javax.servlet.http.HttpServletResponse response)
void	visualizePvalueDist(Long id, Long analysisId, Long rsid, Integer size, javax.servlet.http.HttpServletResponse response)
void	visualizeSingleCellDataBoxplot(Long id, Long quantitationTypeId, Long designElementId, Long[] assayIds, String ctaName, Long clcId, Long focusedCharacteristicId, javax.servlet.http.HttpServletResponse response)
void	visualizeSingleCellSparsityHeatmap(Long id, String type, Integer cellSize, Boolean transpose, javax.servlet.http.HttpServletResponse response)
void	visualizeSubSetHeatmap(Long id, Integer offset, Integer limit, Integer cellSize, Boolean transpose, javax.servlet.http.HttpServletResponse response)
org.springframework.web.servlet.ModelAndView	writeEigenGenes(Long eeid)

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_QC_IMAGE_SIZE_PX

public static final int DEFAULT_QC_IMAGE_SIZE_PX

Default size for an image, in pixel.

See Also:

Constant Field Values

Constructor Detail

ExpressionExperimentQCController

public ExpressionExperimentQCController()

Method Detail

detailedFactorAnalysis

@RequestMapping(value="/expressionExperiment/detailedFactorAnalysis.html",
                method={GET,HEAD})
public void detailedFactorAnalysis(@RequestParam("id")
                                   Long id,
                                   javax.servlet.http.HttpServletResponse response)
                            throws Exception

Throws:

Exception

identifyOutliersRemoved

@RequestMapping(value="/expressionExperiment/outliersRemoved.html",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView identifyOutliersRemoved(@RequestParam("id")
                                                                            Long id)
                                                                     throws IOException

Throws:

IOException

identifyPossibleOutliers

@RequestMapping(value="/expressionExperiment/possibleOutliers.html",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView identifyPossibleOutliers(@RequestParam("id")
                                                                             Long id)
                                                                      throws IOException

Throws:

IOException

pcaFactors

@RequestMapping(value="/expressionExperiment/pcaFactors.html",
                method={GET,HEAD})
public void pcaFactors(@RequestParam("id")
                       Long id,
                       javax.servlet.http.HttpServletResponse response)
                throws Exception

Throws:

Exception

pcaScree

@RequestMapping(value="/expressionExperiment/pcaScree.html",
                method={GET,HEAD})
public void pcaScree(@RequestParam("id")
                     Long id,
                     javax.servlet.http.HttpServletResponse response)
              throws Exception

Throws:

Exception

visualizeCorrMat

@RequestMapping(value="/expressionExperiment/visualizeCorrMat.html",
                method={GET,HEAD})
public void visualizeCorrMat(@RequestParam("id")
                             Long id,
                             @RequestParam(value="size",required=false)
                             Double sizeFactor,
                             @RequestParam(value="text",required=false)
                             Boolean text,
                             @RequestParam(value="showLabels",required=false)
                             Boolean showLabels,
                             @RequestParam(value="forceShowLabels",required=false)
                             Boolean forceShowLabels,
                             @RequestParam(value="reg",required=false)
                             Boolean reg,
                             javax.servlet.http.HttpServletResponse response)
                      throws Exception

Parameters:

id - of experiment

sizeFactor - Multiplier on the cell size. 1 or null for standard small size.

text - if true, output a tabbed file instead of a png

showLabels - if the row and column labels of the matrix should be shown.

forceShowLabels - forces the display of labels in the picture

reg - uses the regressed matrix (if available).

Throws:

Exception

visualizeMeanVariance

@RequestMapping(value="/expressionExperiment/visualizeMeanVariance.html",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView visualizeMeanVariance(@RequestParam("id")
                                                                          Long id,
                                                                          @RequestParam(value="size",required=false)
                                                                          Double sizeFactor,
                                                                          @RequestParam(value="text",required=false)
                                                                          Boolean text,
                                                                          javax.servlet.http.HttpServletResponse response)
                                                                   throws Exception

Parameters:

id - of experiment

sizeFactor - Multiplier on the cell size. 1 or null for standard small size.

text - if true, output a tabbed file instead of a png

Returns:

ModelAndView object if text is true, otherwise null

Throws:

Exception

visualizeProbeCorrDist

@RequestMapping(value="/expressionExperiment/visualizeProbeCorrDist.html",
                method={GET,HEAD})
public void visualizeProbeCorrDist(@RequestParam("id")
                                   Long id,
                                   javax.servlet.http.HttpServletResponse response)
                            throws Exception

Throws:

Exception

visualizePvalueDist

@RequestMapping(value="/expressionExperiment/visualizePvalueDist.html",
                method={GET,HEAD})
public void visualizePvalueDist(@RequestParam("id")
                                Long id,
                                @RequestParam("analysisId")
                                Long analysisId,
                                @RequestParam("rsid")
                                Long rsid,
                                @RequestParam(value="size",required=false)
                                Integer size,
                                javax.servlet.http.HttpServletResponse response)
                         throws Exception

Parameters:

id - of the experiment

analysisId - of the analysis

rsid - resultSet Id

size - of the image.

response - stream to write the image to.

Throws:

Exception

writeEigenGenes

@RequestMapping(value="/expressionExperiment/eigenGenes.html",
                method={GET,HEAD})
public org.springframework.web.servlet.ModelAndView writeEigenGenes(@RequestParam("eeid")
                                                                    Long eeid)
                                                             throws IOException

Throws:

IOException

visualizeSingleCellSparsityHeatmap

@RequestMapping(value="/expressionExperiment/visualizeSingleCellSparsityHeatmap.html",
                method={GET,HEAD})
public void visualizeSingleCellSparsityHeatmap(@RequestParam("id")
                                               Long id,
                                               @RequestParam("type")
                                               String type,
                                               @RequestParam(value="cellSize",required=false)
                                               Integer cellSize,
                                               @RequestParam(value="transpose",required=false)
                                               Boolean transpose,
                                               javax.servlet.http.HttpServletResponse response)
                                        throws IOException

Throws:

IOException

visualizeHeatmap

@RequestMapping(value="/expressionExperiment/visualizeHeatmap.html",
                method={GET,HEAD})
public void visualizeHeatmap(@RequestParam("id")
                             Long id,
                             @RequestParam(value="dimension",required=false)
                             Long dimensionId,
                             @RequestParam(value="offset",required=false)
                             Integer offset,
                             @RequestParam(value="limit",required=false)
                             Integer limit,
                             @RequestParam(value="cellSize",required=false)
                             Integer cellSize,
                             @RequestParam(value="transpose",required=false)
                             Boolean transpose,
                             javax.servlet.http.HttpServletResponse response)
                      throws IOException

Throws:

IOException

visualizeSubSetHeatmap

@RequestMapping(value="/expressionExperiment/visualizeSubSetHeatmap.html",
                method={GET,HEAD})
public void visualizeSubSetHeatmap(@RequestParam("id")
                                   Long id,
                                   @RequestParam(value="offset",required=false)
                                   Integer offset,
                                   @RequestParam(value="limit",required=false)
                                   Integer limit,
                                   @RequestParam(value="cellSize",required=false)
                                   Integer cellSize,
                                   @RequestParam(value="transpose",required=false)
                                   Boolean transpose,
                                   javax.servlet.http.HttpServletResponse response)
                            throws IOException

Throws:

IOException

visualizeSingleCellDataBoxplot

@RequestMapping(value="/expressionExperiment/visualizeSingleCellDataBoxplot.html",
                method={GET,HEAD})
public void visualizeSingleCellDataBoxplot(@RequestParam("id")
                                           Long id,
                                           @RequestParam(value="quantitationType",required=false) @Nullable
                                           Long quantitationTypeId,
                                           @RequestParam("designElement")
                                           Long designElementId,
                                           @RequestParam(value="assays",required=false)
                                           Long[] assayIds,
                                           @RequestParam(value="cellTypeAssignment",required=false)
                                           String ctaName,
                                           @RequestParam(value="cellLevelCharacteristics",required=false)
                                           Long clcId,
                                           @RequestParam(value="focusedCharacteristic",required=false)
                                           Long focusedCharacteristicId,
                                           javax.servlet.http.HttpServletResponse response)
                                    throws IOException

Throws:

IOException