ColumnDataPlot-class ColumnDataPlot initialize,ColumnDataPlot-method .refineParameters,ColumnDataPlot-method .defineDataInterface,ColumnDataPlot-method .createObservers,ColumnDataPlot-method .fullName,ColumnDataPlot-method .panelColor,ColumnDataPlot-method .generateDotPlotData,ColumnDataPlot-method .multiSelectionInvalidated,ColumnDataPlot-method .allowableXAxisChoices,ColumnDataPlot-method .allowableYAxisChoices,ColumnDataPlot-method .definePanelTour,ColumnDataPlot-method
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The ColumnDataPlot panel |
ColumnDataTable-class ColumnDataTable initialize,ColumnDataTable-method .cacheCommonInfo,ColumnDataTable-method .refineParameters,ColumnDataTable-method .generateTable,ColumnDataTable-method .panelColor,ColumnDataTable-method .fullName,ColumnDataTable-method .definePanelTour,ColumnDataTable-method
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The ColumnDataTable panel |
ColumnDotPlot-class initialize,ColumnDotPlot-method .cacheCommonInfo,ColumnDotPlot-method .refineParameters,ColumnDotPlot-method .defineInterface,ColumnDotPlot-method .createObservers,ColumnDotPlot-method .getTooltipUI,ColumnDotPlot-method .hideInterface,ColumnDotPlot-method .multiSelectionDimension,ColumnDotPlot-method .multiSelectionResponsive,ColumnDotPlot-method .multiSelectionRestricted,ColumnDotPlot-method .multiSelectionInvalidated,ColumnDotPlot-method .singleSelectionDimension,ColumnDotPlot-method .definePanelTour,ColumnDotPlot-method .getDotPlotColorHelp,ColumnDotPlot-method [[,ColumnDotPlot-method [[,ColumnDotPlot,ANY,ANY-method [[ [[ updateObject,ColumnDotPlot-method
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The ColumnDotPlot virtual class |
ColumnTable-class initialize,ColumnTable-method .refineParameters,ColumnTable-method .defineInterface,ColumnTable-method .createObservers,ColumnTable-method .hideInterface,ColumnTable-method .multiSelectionDimension,ColumnTable-method .multiSelectionResponsive,ColumnTable-method .singleSelectionDimension,ColumnTable-method .showSelectionDetails,ColumnTable-method
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The ColumnTable class |
ComplexHeatmapPlot-class ComplexHeatmapPlot .cacheCommonInfo,ComplexHeatmapPlot-method .createObservers,ComplexHeatmapPlot-method .defineDataInterface,ComplexHeatmapPlot-method .defineInterface,ComplexHeatmapPlot-method .defineOutput,ComplexHeatmapPlot-method .fullName,ComplexHeatmapPlot-method .generateOutput,ComplexHeatmapPlot-method .hideInterface,ComplexHeatmapPlot-method .multiSelectionResponsive,ComplexHeatmapPlot-method .multiSelectionRestricted,ComplexHeatmapPlot-method .panelColor,ComplexHeatmapPlot-method .refineParameters,ComplexHeatmapPlot-method .renderOutput,ComplexHeatmapPlot-method .exportOutput,ComplexHeatmapPlot-method initialize,ComplexHeatmapPlot-method .definePanelTour,ComplexHeatmapPlot-method [[,ComplexHeatmapPlot-method [[,ComplexHeatmapPlot,ANY,ANY-method [[ [[ updateObject,ComplexHeatmapPlot-method
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The ComplexHeatmapPlot panel |
DotPlot-class initialize,DotPlot-method updateObject,DotPlot-method .defineOutput,DotPlot-method .generateOutput,DotPlot-method .generateDotPlot,DotPlot-method .renderOutput,DotPlot-method .exportOutput,DotPlot-method .refineParameters,DotPlot-method .cacheCommonInfo,DotPlot-method .createObservers,DotPlot-method .hideInterface,DotPlot-method .multiSelectionActive,DotPlot-method .multiSelectionCommands,DotPlot-method .multiSelectionClear,DotPlot-method .multiSelectionDimension,DotPlot-method .isBrushable,DotPlot-method .singleSelectionValue,DotPlot-method .singleSelectionSlots,DotPlot-method .prioritizeDotPlotData,DotPlot-method .colorByNoneDotPlotField,DotPlot-method .colorByNoneDotPlotScale,DotPlot-method .defineInterface,DotPlot-method .defineVisualColorInterface,DotPlot-method .defineVisualSizeInterface,DotPlot-method .defineVisualShapeInterface,DotPlot-method .defineVisualTextInterface,DotPlot-method .defineVisualPointInterface,DotPlot-method .defineVisualOtherInterface,DotPlot-method .defineVisualFacetInterface,DotPlot-method .allowableColorByDataChoices,DotPlot-method .definePanelTour,DotPlot-method [[,DotPlot-method [[,DotPlot,ANY,ANY-method [[ [[
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The DotPlot virtual class |
ExperimentColorMap()
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ExperimentColorMap class |
FeatureAssayPlot-class FeatureAssayPlot initialize,FeatureAssayPlot-method .refineParameters,FeatureAssayPlot-method .defineDataInterface,FeatureAssayPlot-method .createObservers,FeatureAssayPlot-method .singleSelectionSlots,FeatureAssayPlot-method .multiSelectionInvalidated,FeatureAssayPlot-method .fullName,FeatureAssayPlot-method .panelColor,FeatureAssayPlot-method .generateDotPlotData,FeatureAssayPlot-method .definePanelTour,FeatureAssayPlot-method
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The FeatureAssayPlot panel |
Panel-class initialize,Panel-method [[,Panel-method [[ [[,Panel,ANY,ANY-method [[ show,Panel-method .defineInterface,Panel-method .refineParameters,Panel-method .cacheCommonInfo,Panel-method .createObservers,Panel-method .hideInterface,Panel-method .defineDataInterface,Panel-method .renderOutput,Panel-method .exportOutput,Panel-method .multiSelectionRestricted,Panel-method .multiSelectionDimension,Panel-method .multiSelectionClear,Panel-method .multiSelectionActive,Panel-method .multiSelectionInvalidated,Panel-method .multiSelectionAvailable,Panel-method .isBrushable,Panel-method .singleSelectionDimension,Panel-method .singleSelectionValue,Panel-method .singleSelectionSlots,Panel-method .definePanelTour,Panel-method updateObject,Panel-method
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The Panel virtual class |
ReducedDimensionPlot-class ReducedDimensionPlot initialize,ReducedDimensionPlot-method .refineParameters,ReducedDimensionPlot-method .cacheCommonInfo,ReducedDimensionPlot-method .defineDataInterface,ReducedDimensionPlot-method .createObservers,ReducedDimensionPlot-method .fullName,ReducedDimensionPlot-method .panelColor,ReducedDimensionPlot-method .generateDotPlotData,ReducedDimensionPlot-method .definePanelTour,ReducedDimensionPlot-method
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The ReducedDimensionPlot panel |
RowDataPlot-class RowDataPlot initialize,RowDataPlot-method .refineParameters,RowDataPlot-method .defineDataInterface,RowDataPlot-method .createObservers,RowDataPlot-method .fullName,RowDataPlot-method .panelColor,RowDataPlot-method .multiSelectionInvalidated,RowDataPlot-method .generateDotPlotData,RowDataPlot-method .allowableXAxisChoices,RowDataPlot-method .allowableYAxisChoices,RowDataPlot-method .definePanelTour,RowDataPlot-method
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The RowDataPlot panel |
RowDataTable-class RowDataTable initialize,RowDataTable-method .cacheCommonInfo,RowDataTable-method .refineParameters,RowDataTable-method .generateTable,RowDataTable-method .panelColor,RowDataTable-method .fullName,RowDataTable-method .definePanelTour,RowDataTable-method
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The RowDataTable panel |
RowDotPlot-class initialize,RowDotPlot-method .cacheCommonInfo,RowDotPlot-method .refineParameters,RowDotPlot-method .defineInterface,RowDotPlot-method .createObservers,RowDotPlot-method .getTooltipUI,RowDotPlot-method .hideInterface,RowDotPlot-method .multiSelectionDimension,RowDotPlot-method .multiSelectionResponsive,RowDotPlot-method .multiSelectionRestricted,RowDotPlot-method .multiSelectionInvalidated,RowDotPlot-method .singleSelectionDimension,RowDotPlot-method .definePanelTour,RowDotPlot-method .getDotPlotColorHelp,RowDotPlot-method [[,RowDotPlot-method [[,RowDotPlot,ANY,ANY-method [[ [[ updateObject,RowDotPlot-method
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The RowDotPlot virtual class |
RowTable-class initialize,RowTable-method .refineParameters,RowTable-method .defineInterface,RowTable-method .createObservers,RowTable-method .hideInterface,RowTable-method .multiSelectionDimension,RowTable-method .multiSelectionResponsive,RowTable-method .singleSelectionDimension,RowTable-method .showSelectionDetails,RowTable-method
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The RowTable class |
SampleAssayPlot-class SampleAssayPlot initialize,SampleAssayPlot-method .refineParameters,SampleAssayPlot-method .defineDataInterface,SampleAssayPlot-method .createObservers,SampleAssayPlot-method .singleSelectionSlots,SampleAssayPlot-method .multiSelectionInvalidated,SampleAssayPlot-method .fullName,SampleAssayPlot-method .panelColor,SampleAssayPlot-method .generateDotPlotData,SampleAssayPlot-method .definePanelTour,SampleAssayPlot-method
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The SampleAssayPlot panel |
Table-class initialize,Table-method .refineParameters,Table-method .createObservers,Table-method .generateOutput,Table-method .renderOutput,Table-method .defineOutput,Table-method .exportOutput,Table-method .hideInterface,Table-method .multiSelectionCommands,Table-method .multiSelectionActive,Table-method .multiSelectionRestricted,Table-method .singleSelectionValue,Table-method .definePanelTour,Table-method .defineDataInterface,Table-method updateObject,Table-method
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The Table class |
.addCustomLabelsCommands()
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Add custom label plotting commands |
.addLabelCentersCommands()
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Add centered label plotting commands |
.addMultiSelectionPlotCommands()
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Add multiple selection plotting commands |
.addTourStep()
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Add a step to the tour |
.buildAes()
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Generate ggplot aesthetic instructions |
.findAtomicFields() .whichGroupable() .whichNumeric() .isAssayNumeric()
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Caching utilities |
checkColormapCompatibility()
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Check compatibility between ExperimentColorMap and SummarizedExperiment
objects |
.emptyDefault()
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Set default slot values |
cleanDataset()
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Clean the dataset |
collapseBox()
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A collapsible box |
.conditionalOnRadio() .conditionalOnCheckSolo() .conditionalOnCheckGroup()
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Conditional elements on radio or checkbox selection |
constants .dataParamBoxOpen .multiSelectHistory .noSelection .organizationHeight .organizationWidth
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Constants |
.createCustomDimnamesModalObservers()
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Create observers for a modal for custom dimnames |
createCustomTable() createCustomPlot()
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Create custom panels |
createLandingPage()
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Create a landing page |
.createUnprotectedParameterObservers() .createProtectedParameterObservers()
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Define parameter observers |
defaultTour()
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Define the default tour |
documentation-generics .definePanelTour .getDotPlotColorHelp
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Documentation generics |
.extractAssaySubmatrix()
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Extract assay submatrix |
filterDTColumn() filterDT()
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Filter DT columns |
.fullName() .getEncodedName() .getFullName()
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Get panel names |
.panelColor() .getPanelColor()
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Get panel colors |
iSEE-pkg
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iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer |
iSEE()
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iSEE: interactive SummarizedExperiment Explorer |
iSEEOptions
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Global iSEE options |
interface-generics .defineInterface .defineDataInterface .hideInterface
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Generics for the panel interface |
.selectInput.iSEE() .selectizeInput.iSEE() .checkboxInput.iSEE() .checkboxGroupInput.iSEE() .sliderInput.iSEE() .numericInput.iSEE() .radioButtons.iSEE()
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iSEE UI element wrappers |
jitterSquarePoints() jitterViolinPoints()
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Jitter points for categorical variables |
.buildLabs()
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Generate ggplot title and label instructions |
lassoPoints()
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Find rows of data within a closed lasso |
.textEval()
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Manage commands to be evaluated |
metadata-plot-generics .allowableYAxisChoices .allowableXAxisChoices
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Generics for row/column metadata plots |
multi-select-generics .multiSelectionDimension .isBrushable .multiSelectionRestricted .multiSelectionActive .multiSelectionCommands .multiSelectionClear .multiSelectionInvalidated .multiSelectionAvailable .multiSelectionResponsive
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Generics for controlling multiple selections |
multiSelectionToFactor()
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Convert multiple selections into a factor |
observer-generics .createObservers
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Generic for the panel observers |
output-generics .renderOutput .defineOutput .generateOutput .exportOutput
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Generics for Panel outputs |
panelDefaults() getPanelDefault()
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Panel defaults |
plot-generics .generateDotPlotData .generateDotPlot .prioritizeDotPlotData .colorByNoneDotPlotField .colorByNoneDotPlotScale
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Generics for DotPlot plotting |
.addFacets()
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Process faceting choices |
.processMultiSelections()
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Process multiple selections |
registerAppOptions() getAppOption() getAllAppOptions()
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Set and get app-level options |
.removeInvalidChoices()
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Remove invalid values in multiple choices |
.replaceMissingWithFirst()
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Replace with first choice |
.requestUpdate() .requestCleanUpdate() .requestActiveSelectionUpdate()
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Request Panel updates |
.retrieveOutput()
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Retrieve the panel output |
columnSelectionColorMap() rowSelectionColorMap()
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Define the selection colormap |
.setCachedCommonInfo() .getCachedCommonInfo()
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Set and get cached commons |
setup-generics .refineParameters .cacheCommonInfo
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Generics for setting up parameters |
single-select-generics .singleSelectionDimension .singleSelectionValue .singleSelectionSlots
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Generics for controlling single selections |
.addSpecificTour() .getSpecificTours() .clearSpecificTours()
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UI-specific tour management utilities |
subsetPointsByGrid()
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Subset points for faster plotting |
synchronizeAssays()
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Synchronize assay colormaps to match those in a SummarizedExperiment |
table-generics .generateTable .showSelectionDetails
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Generics for table construction |
.trackUpdate() .trackSingleSelection() .trackMultiSelection() .trackRelinkedSelection()
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Track internal events |
.singleStringError() .validLogicalError() .validStringError() .allowableChoiceError() .multipleChoiceError() .validNumberError()
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Validation error utilites |
visual-parameters-generics .defineVisualColorInterface .defineVisualShapeInterface .defineVisualSizeInterface .defineVisualPointInterface .defineVisualFacetInterface .defineVisualTextInterface .defineVisualOtherInterface .allowableColorByDataChoices .getTooltipUI
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Generics for visual DotPlot parameters |