Package index

All functions

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 [[<-,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 [[<-,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 [[<-,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-method [[,Panel,ANY,ANY-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 .multiSelectionResponsive,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 [[<-,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