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

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentQCController()

Method Summary

Modifier and Type	Method	Description
void	detailedFactorAnalysis(Long id, javax.servlet.http.HttpServletResponse response)
ModelAndView	identifyOutliersRemoved(Long id)
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)
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)
ModelAndView	writeEigenGenes(Long eeid)

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

addMessage, getMessageUtil, getText, getText, saveMessage, saveMessage, sendConfirmationEmail, setMessageUtil

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 ModelAndView identifyOutliersRemoved(@RequestParam("id")
                                            Long id)
                                     throws IOException

Throws:

IOException

identifyPossibleOutliers

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

Throws:

IOException