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