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

Class ExpressionExperimentQCController

java.lang.Object

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

@Controller
public class ExpressionExperimentQCController
extends Object

Author:

paul

Field Summary

Fields

Modifier and Type	Field	Description
static final int	DEFAULT_QC_IMAGE_SIZE_PX	Default size for an image, in pixel.
static final int	MAX_QC_IMAGE_SIZE_PX	Maximum size for an image, in pixels.
protected org.springframework.context.MessageSource	messageSource
protected MessageUtil	messageUtil

Constructor Summary

Constructors

Constructor	Description
ExpressionExperimentQCController()

Method Summary

Modifier and Type	Method	Description
void	detailedFactorAnalysis(Long id, double sizeFactor, String font, 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, double sizeFactor, String font, javax.servlet.http.HttpServletResponse response)
void	pcaScree(Long id, double sizeFactor, String font, 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, int offset, int limit, Integer cellSize, boolean transpose, javax.servlet.http.HttpServletResponse response)
void	visualizeMeanVariance(Long id, double sizeFactor, boolean text, String font, javax.servlet.http.HttpServletResponse response)
void	visualizeProbeCorrDist(Long id, double sizeFactor, String font, javax.servlet.http.HttpServletResponse response)
void	visualizePvalueDist(Long id, Long analysisId, Long rsid, Integer size, double sizeFactor, String font, javax.servlet.http.HttpServletResponse response)
void	visualizeSingleCellDataBoxplot(Long id, Long quantitationTypeId, Long designElementId, Long[] assayIds, String ctaIdentifier, String clcIdentifier, Long focusedCharacteristicId, double sizeFactor, String font, boolean showTitle, javax.servlet.http.HttpServletResponse response)
void	visualizeSingleCellSparsityHeatmap(Long id, String type, Integer cellSize, boolean transpose, javax.servlet.http.HttpServletResponse response)
void	visualizeSubSetHeatmap(Long id, int offset, int 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 Details

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

MAX_QC_IMAGE_SIZE_PX

public static final int MAX_QC_IMAGE_SIZE_PX

Maximum size for an image, in pixels.

See Also:

• Constant Field Values

messageSource

@Autowired
protected org.springframework.context.MessageSource messageSource

messageUtil

@Autowired
protected MessageUtil messageUtil

Constructor Details

ExpressionExperimentQCController

public ExpressionExperimentQCController()

Method Details

detailedFactorAnalysis

@RequestMapping(value="/expressionExperiment/detailedFactorAnalysis.html",
                method={GET,HEAD})
public void detailedFactorAnalysis(@RequestParam("id")
 Long id,
 @RequestParam(value="size",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 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,
 @RequestParam(value="size",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 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,
 @RequestParam(value="size",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 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",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="text",defaultValue="false")
 boolean text,
 @RequestParam(value="showLabels",defaultValue="false")
 boolean showLabels,
 @RequestParam(value="forceShowLabels",defaultValue="false")
 boolean forceShowLabels,
 @RequestParam(value="reg",defaultValue="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 void visualizeMeanVariance(@RequestParam("id")
 Long id,
 @RequestParam(value="size",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="text",defaultValue="false")
 boolean text,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 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

Throws:

Exception

visualizeProbeCorrDist

@RequestMapping(value="/expressionExperiment/visualizeProbeCorrDist.html",
                method={GET,HEAD})
public void visualizeProbeCorrDist(@RequestParam("id")
 Long id,
 @RequestParam(value="size",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 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) @Nullable
 Integer size,
 @RequestParam(value="sizeFactor",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 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) @Nullable
 Integer cellSize,
 @RequestParam(value="transpose",defaultValue="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",defaultValue="0")
 int offset,
 @RequestParam(value="limit",defaultValue="10")
 int limit,
 @RequestParam(value="cellSize",required=false) @Nullable
 Integer cellSize,
 @RequestParam(value="transpose",defaultValue="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",defaultValue="0")
 int offset,
 @RequestParam(value="limit",defaultValue="10")
 int limit,
 @RequestParam(value="cellSize",required=false) @Nullable
 Integer cellSize,
 @RequestParam(value="transpose",defaultValue="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) @Nullable
 Long[] assayIds,
 @RequestParam(value="cellTypeAssignment",required=false) @Nullable
 String ctaIdentifier,
 @RequestParam(value="cellLevelCharacteristics",required=false) @Nullable
 String clcIdentifier,
 @RequestParam(value="focusedCharacteristic",required=false) @Nullable
 Long focusedCharacteristicId,
 @RequestParam(value="size",defaultValue="1.0")
 double sizeFactor,
 @RequestParam(value="font",defaultValue="Arial")
 String font,
 @RequestParam(value="showTitle",defaultValue="false")
 boolean showTitle,
 javax.servlet.http.HttpServletResponse response)
                                    throws IOException

Throws:

IOException