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