# Interactive SummarizedExperiment Explorer

## Documentation for package ‘iSEE’ version 2.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E F G I J L M O P R S T U V misc

## -- A --

aes-utils | Generate ggplot aesthetic instructions
assay-method | ExperimentColorMap class
assayColorMap | ExperimentColorMap class
assayColorMap-method | ExperimentColorMap class
assayColorMap<- | ExperimentColorMap class
assayColorMap<--method | ExperimentColorMap class
assayNames-method | ExperimentColorMap class
assayNames<--method | ExperimentColorMap class
assays-method | ExperimentColorMap class
assays<--method | ExperimentColorMap class

## -- C --

cache-utils | Caching utilities
checkColormapCompatibility | Check compatibility between ExperimentColorMap and SummarizedExperiment objects
class-utils | Set default slot values
class:ExperimentColorMap | ExperimentColorMap class
cleanDataset | Clean the dataset
cleanDataset-method | Clean the dataset
colData-method | ExperimentColorMap class
colData<--method | ExperimentColorMap class
colDataColorMap | ExperimentColorMap class
colDataColorMap-method | ExperimentColorMap class
colDataColorMap<- | ExperimentColorMap class
colDataColorMap<--method | ExperimentColorMap class
collapseBox | A collapsible box
ColumnDataPlot | The ColumnDataPlot panel
ColumnDataPlot-class | The ColumnDataPlot panel
ColumnDataTable | The ColumnDataTable panel
ColumnDataTable-class | The ColumnDataTable panel
ColumnDotPlot-class | The ColumnDotPlot virtual class
columnSelectionColorMap | Define the selection colormap
ColumnTable-class | The ColumnTable class
ComplexHeatmapPlot | The ComplexHeatmapPlot panel
ComplexHeatmapPlot-class | The ComplexHeatmapPlot panel
createCustomPanels | Create custom panels
createCustomPlot | Create custom panels
createCustomTable | Create custom panels
createLandingPage | Create a landing page

## -- D --

defaultTour | Define the default tour
documentation-generics | Documentation generics
DotPlot-class | The DotPlot virtual class

## -- E --

ExperimentColorMap | ExperimentColorMap class
ExperimentColorMap-class | ExperimentColorMap class

## -- F --

FeatureAssayPlot | The FeatureAssayPlot panel
FeatureAssayPlot-class | The FeatureAssayPlot panel
filterDT | Filter 'DT' columns
filterDTColumn | Filter 'DT' columns

## -- G --

getAllAppOptions | Set and get app-level options
getAppOption | Set and get app-level options
getPanelDefault | Panel defaults

## -- I --

initialize-method | The ColumnDataPlot panel
initialize-method | The ColumnDataTable panel
initialize-method | The ColumnDotPlot virtual class
initialize-method | The ColumnTable class
initialize-method | The ComplexHeatmapPlot panel
initialize-method | The DotPlot virtual class
initialize-method | The FeatureAssayPlot panel
initialize-method | The Panel virtual class
initialize-method | The ReducedDimensionPlot panel
initialize-method | The RowDataPlot panel
initialize-method | The RowDataTable panel
initialize-method | The RowDotPlot virtual class
initialize-method | The RowTable class
initialize-method | The SampleAssayPlot panel
initialize-method | The Table class
interface-generics | Generics for the panel interface
interface-wrappers | 'iSEE' UI element wrappers
iSEE | iSEE: interactive SummarizedExperiment Explorer
iSEE-pkg | iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer
iSEEOptions | Global 'iSEE' options

## -- J --

jitterSquarePoints | Jitter points for categorical variables
jitterViolinPoints | Jitter points for categorical variables

## -- L --

lassoPoints | Find rows of data within a closed lasso

## -- M --

manage_commands | Manage commands to be evaluated
metadata-plot-generics | Generics for row/column metadata plots
multi-select-generics | Generics for controlling multiple selections
multiSelectionToFactor | Convert multiple selections into a factor

## -- O --

observer-generics | Generic for the panel observers
output-generics | Generics for Panel outputs

## -- P --

Panel-class | The Panel virtual class
panelDefaults | Panel defaults
plot-generics | Generics for DotPlot plotting
plot-utils | Process faceting choices

## -- R --

ReducedDimensionPlot | The ReducedDimensionPlot panel
ReducedDimensionPlot-class | The ReducedDimensionPlot panel
registerAppOptions | Set and get app-level options
rowData-method | ExperimentColorMap class
rowData<--method | ExperimentColorMap class
rowDataColorMap | ExperimentColorMap class
rowDataColorMap-method | ExperimentColorMap class
rowDataColorMap<- | ExperimentColorMap class
rowDataColorMap<--method | ExperimentColorMap class
RowDataPlot | The RowDataPlot panel
RowDataPlot-class | The RowDataPlot panel
RowDataTable | The RowDataTable panel
RowDataTable-class | The RowDataTable panel
RowDotPlot-class | The RowDotPlot virtual class
rowSelectionColorMap | Define the selection colormap
RowTable-class | The RowTable class

## -- S --

SampleAssayPlot | The SampleAssayPlot panel
SampleAssayPlot-class | The SampleAssayPlot panel
setup-generics | Generics for setting up parameters
show-method | ExperimentColorMap class
show-method | The Panel virtual class
single-select-generics | Generics for controlling single selections
specific-tours | UI-specific tour management utilities
subsetPointsByGrid | Subset points for faster plotting
synchronizeAssays | Synchronize assay colormaps to match those in a SummarizedExperiment

## -- T --

Table-class | The Table class
table-generics | Generics for table construction
track-utils | Track internal events

## -- U --

updateObject-method | The ColumnDotPlot virtual class
updateObject-method | The ComplexHeatmapPlot panel
updateObject-method | The DotPlot virtual class
updateObject-method | The Panel virtual class
updateObject-method | The RowDotPlot virtual class
updateObject-method | The Table class

## -- V --

validate-utils | Validation error utilites
visual-parameters-generics | Generics for visual DotPlot parameters

## -- misc --

.activateAppOptionRegistry | Set and get app-level options
.addCustomLabelsCommands | Add custom label plotting commands
.addFacets | Process faceting choices
.addLabelCentersCommands | Add centered label plotting commands
.addMultiSelectionPlotCommands | Add multiple selection plotting commands
.addSpecificTour | UI-specific tour management utilities
.addTourStep | Add a step to the tour
.allowableChoiceError | Validation error utilites
.allowableColorByDataChoices | Generics for visual DotPlot parameters
.allowableColorByDataChoices-method | The DotPlot virtual class
.allowableXAxisChoices | Generics for row/column metadata plots
.allowableXAxisChoices-method | The ColumnDataPlot panel
.allowableXAxisChoices-method | The RowDataPlot panel
.allowableYAxisChoices | Generics for row/column metadata plots
.allowableYAxisChoices-method | The ColumnDataPlot panel
.allowableYAxisChoices-method | The RowDataPlot panel
.buildAes | Generate ggplot aesthetic instructions
.buildLabs | Generate ggplot title and label instructions
.cacheCommonInfo | Generics for setting up parameters
.cacheCommonInfo-method | The ColumnDataTable panel
.cacheCommonInfo-method | The ColumnDotPlot virtual class
.cacheCommonInfo-method | The ComplexHeatmapPlot panel
.cacheCommonInfo-method | The DotPlot virtual class
.cacheCommonInfo-method | The Panel virtual class
.cacheCommonInfo-method | The ReducedDimensionPlot panel
.cacheCommonInfo-method | The RowDataTable panel
.cacheCommonInfo-method | The RowDotPlot virtual class
.checkboxGroupInput.iSEE | 'iSEE' UI element wrappers
.checkboxInput.iSEE | 'iSEE' UI element wrappers
.clearSpecificTours | UI-specific tour management utilities
.colorByNoneDotPlotField | Generics for DotPlot plotting
.colorByNoneDotPlotField-method | The DotPlot virtual class
.colorByNoneDotPlotScale | Generics for DotPlot plotting
.colorByNoneDotPlotScale-method | The DotPlot virtual class
.conditionalOnCheckGroup | Conditional elements on radio or checkbox selection
.conditionalOnCheckSolo | Conditional elements on radio or checkbox selection
.conditionalOnRadio | Conditional elements on radio or checkbox selection
.createCustomDimnamesModalObservers | Create observers for a modal for custom dimnames
.createObservers | Generic for the panel observers
.createObservers-method | The ColumnDataPlot panel
.createObservers-method | The ColumnDotPlot virtual class
.createObservers-method | The ColumnTable class
.createObservers-method | The ComplexHeatmapPlot panel
.createObservers-method | The DotPlot virtual class
.createObservers-method | The FeatureAssayPlot panel
.createObservers-method | The Panel virtual class
.createObservers-method | The ReducedDimensionPlot panel
.createObservers-method | The RowDataPlot panel
.createObservers-method | The RowDotPlot virtual class
.createObservers-method | The RowTable class
.createObservers-method | The SampleAssayPlot panel
.createObservers-method | The Table class
.createProtectedParameterObservers | Define parameter observers
.createUnprotectedParameterObservers | Define parameter observers
.deactivateAppOptionRegistry | Set and get app-level options
.defineDataInterface | Generics for the panel interface
.defineDataInterface-method | The ColumnDataPlot panel
.defineDataInterface-method | The ComplexHeatmapPlot panel
.defineDataInterface-method | The FeatureAssayPlot panel
.defineDataInterface-method | The Panel virtual class
.defineDataInterface-method | The ReducedDimensionPlot panel
.defineDataInterface-method | The RowDataPlot panel
.defineDataInterface-method | The SampleAssayPlot panel
.defineDataInterface-method | The Table class
.defineInterface | Generics for the panel interface
.defineInterface-method | The ColumnDotPlot virtual class
.defineInterface-method | The ColumnTable class
.defineInterface-method | The ComplexHeatmapPlot panel
.defineInterface-method | The DotPlot virtual class
.defineInterface-method | The Panel virtual class
.defineInterface-method | The RowDotPlot virtual class
.defineInterface-method | The RowTable class
.defineOutput | Generics for Panel outputs
.defineOutput-method | The ComplexHeatmapPlot panel
.defineOutput-method | The DotPlot virtual class
.defineOutput-method | The Table class
.definePanelTour | Documentation generics
.definePanelTour-method | The ColumnDataPlot panel
.definePanelTour-method | The ColumnDataTable panel
.definePanelTour-method | The ColumnDotPlot virtual class
.definePanelTour-method | The ComplexHeatmapPlot panel
.definePanelTour-method | The DotPlot virtual class
.definePanelTour-method | The FeatureAssayPlot panel
.definePanelTour-method | The Panel virtual class
.definePanelTour-method | The ReducedDimensionPlot panel
.definePanelTour-method | The RowDataPlot panel
.definePanelTour-method | The RowDataTable panel
.definePanelTour-method | The RowDotPlot virtual class
.definePanelTour-method | The SampleAssayPlot panel
.definePanelTour-method | The Table class
.defineVisualColorInterface | Generics for visual DotPlot parameters
.defineVisualColorInterface-method | The DotPlot virtual class
.defineVisualFacetInterface | Generics for visual DotPlot parameters
.defineVisualFacetInterface-method | The DotPlot virtual class
.defineVisualOtherInterface | Generics for visual DotPlot parameters
.defineVisualOtherInterface-method | The DotPlot virtual class
.defineVisualPointInterface | Generics for visual DotPlot parameters
.defineVisualPointInterface-method | The DotPlot virtual class
.defineVisualShapeInterface | Generics for visual DotPlot parameters
.defineVisualShapeInterface-method | The DotPlot virtual class
.defineVisualSizeInterface | Generics for visual DotPlot parameters
.defineVisualSizeInterface-method | The DotPlot virtual class
.defineVisualTextInterface | Generics for visual DotPlot parameters
.defineVisualTextInterface-method | The DotPlot virtual class
.emptyDefault | Set default slot values
.exportOutput | Generics for Panel outputs
.exportOutput-method | The ComplexHeatmapPlot panel
.exportOutput-method | The DotPlot virtual class
.exportOutput-method | The Panel virtual class
.exportOutput-method | The Table class
.extractAssaySubmatrix | Extract assay submatrix
.findAtomicFields | Caching utilities
.fullName | Get panel names
.fullName-method | The ColumnDataPlot panel
.fullName-method | The ColumnDataTable panel
.fullName-method | The ComplexHeatmapPlot panel
.fullName-method | The FeatureAssayPlot panel
.fullName-method | The ReducedDimensionPlot panel
.fullName-method | The RowDataPlot panel
.fullName-method | The RowDataTable panel
.fullName-method | The SampleAssayPlot panel
.generateDotPlot | Generics for DotPlot plotting
.generateDotPlot-method | The DotPlot virtual class
.generateDotPlotData | Generics for DotPlot plotting
.generateDotPlotData-method | The ColumnDataPlot panel
.generateDotPlotData-method | The FeatureAssayPlot panel
.generateDotPlotData-method | The ReducedDimensionPlot panel
.generateDotPlotData-method | The RowDataPlot panel
.generateDotPlotData-method | The SampleAssayPlot panel
.generateOutput | Generics for Panel outputs
.generateOutput-method | The ComplexHeatmapPlot panel
.generateOutput-method | The DotPlot virtual class
.generateOutput-method | The Table class
.generateTable | Generics for table construction
.generateTable-method | The ColumnDataTable panel
.generateTable-method | The RowDataTable panel
.getCachedCommonInfo | Set and get cached commons
.getDotPlotColorHelp | Documentation generics
.getDotPlotColorHelp-method | The ColumnDotPlot virtual class
.getDotPlotColorHelp-method | The RowDotPlot virtual class
.getEncodedName | Get panel names
.getFullName | Get panel names
.getPanelColor | Get panel colors
.getSpecificTours | UI-specific tour management utilities
.hideInterface | Generics for the panel interface
.hideInterface-method | The ColumnDotPlot virtual class
.hideInterface-method | The ColumnTable class
.hideInterface-method | The ComplexHeatmapPlot panel
.hideInterface-method | The DotPlot virtual class
.hideInterface-method | The Panel virtual class
.hideInterface-method | The RowDotPlot virtual class
.hideInterface-method | The RowTable class
.hideInterface-method | The Table class
.isAssayNumeric | Caching utilities
.multipleChoiceError | Validation error utilites
.multiSelectionActive | Generics for controlling multiple selections
.multiSelectionActive-method | The DotPlot virtual class
.multiSelectionActive-method | The Panel virtual class
.multiSelectionActive-method | The Table class
.multiSelectionAvailable | Generics for controlling multiple selections
.multiSelectionAvailable-method | The Panel virtual class
.multiSelectionClear | Generics for controlling multiple selections
.multiSelectionClear-method | The DotPlot virtual class
.multiSelectionClear-method | The Panel virtual class
.multiSelectionCommands | Generics for controlling multiple selections
.multiSelectionCommands-method | The DotPlot virtual class
.multiSelectionCommands-method | The Table class
.multiSelectionDimension | Generics for controlling multiple selections
.multiSelectionDimension-method | The ColumnDotPlot virtual class
.multiSelectionDimension-method | The ColumnTable class
.multiSelectionDimension-method | The DotPlot virtual class
.multiSelectionDimension-method | The Panel virtual class
.multiSelectionDimension-method | The RowDotPlot virtual class
.multiSelectionDimension-method | The RowTable class
.multiSelectionInvalidated | Generics for controlling multiple selections
.multiSelectionInvalidated-method | The ColumnDataPlot panel
.multiSelectionInvalidated-method | The ColumnDotPlot virtual class
.multiSelectionInvalidated-method | The FeatureAssayPlot panel
.multiSelectionInvalidated-method | The Panel virtual class
.multiSelectionInvalidated-method | The RowDataPlot panel
.multiSelectionInvalidated-method | The RowDotPlot virtual class
.multiSelectionInvalidated-method | The SampleAssayPlot panel
.multiSelectionRestricted | Generics for controlling multiple selections
.multiSelectionRestricted-method | The ColumnDotPlot virtual class
.multiSelectionRestricted-method | The Panel virtual class
.multiSelectionRestricted-method | The RowDotPlot virtual class
.multiSelectionRestricted-method | The Table class
.numericInput.iSEE | 'iSEE' UI element wrappers
.panelColor | Get panel colors
.panelColor-method | The ColumnDataPlot panel
.panelColor-method | The ColumnDataTable panel
.panelColor-method | The ComplexHeatmapPlot panel
.panelColor-method | The FeatureAssayPlot panel
.panelColor-method | The ReducedDimensionPlot panel
.panelColor-method | The RowDataPlot panel
.panelColor-method | The RowDataTable panel
.panelColor-method | The SampleAssayPlot panel
.prioritizeDotPlotData | Generics for DotPlot plotting
.prioritizeDotPlotData-method | The DotPlot virtual class
.processMultiSelections | Process multiple selections
.radioButtons.iSEE | 'iSEE' UI element wrappers
.refineParameters | Generics for setting up parameters
.refineParameters-method | The ColumnDataPlot panel
.refineParameters-method | The ColumnDataTable panel
.refineParameters-method | The ColumnDotPlot virtual class
.refineParameters-method | The ColumnTable class
.refineParameters-method | The ComplexHeatmapPlot panel
.refineParameters-method | The DotPlot virtual class
.refineParameters-method | The FeatureAssayPlot panel
.refineParameters-method | The Panel virtual class
.refineParameters-method | The ReducedDimensionPlot panel
.refineParameters-method | The RowDataPlot panel
.refineParameters-method | The RowDataTable panel
.refineParameters-method | The RowDotPlot virtual class
.refineParameters-method | The RowTable class
.refineParameters-method | The SampleAssayPlot panel
.refineParameters-method | The Table class
.renderOutput | Generics for Panel outputs
.renderOutput-method | The ComplexHeatmapPlot panel
.renderOutput-method | The DotPlot virtual class
.renderOutput-method | The Panel virtual class
.renderOutput-method | The Table class
.replaceMissingWithFirst | Replace with first choice
.requestActiveSelectionUpdate | Request Panel updates
.requestCleanUpdate | Request Panel updates
.requestUpdate | Request Panel updates
.retrieveOutput | Retrieve the panel output
.selectInput.iSEE | 'iSEE' UI element wrappers
.selectizeInput.iSEE | 'iSEE' UI element wrappers
.setCachedCommonInfo | Set and get cached commons
.showSelectionDetails | Generics for table construction
.showSelectionDetails-method | The ColumnTable class
.showSelectionDetails-method | The RowTable class
.singleSelectionDimension | Generics for controlling single selections
.singleSelectionDimension-method | The ColumnDotPlot virtual class
.singleSelectionDimension-method | The ColumnTable class
.singleSelectionDimension-method | The Panel virtual class
.singleSelectionDimension-method | The RowDotPlot virtual class
.singleSelectionDimension-method | The RowTable class
.singleSelectionSlots | Generics for controlling single selections
.singleSelectionSlots-method | The DotPlot virtual class
.singleSelectionSlots-method | The FeatureAssayPlot panel
.singleSelectionSlots-method | The Panel virtual class
.singleSelectionSlots-method | The SampleAssayPlot panel
.singleSelectionValue | Generics for controlling single selections
.singleSelectionValue-method | The DotPlot virtual class
.singleSelectionValue-method | The Panel virtual class
.singleSelectionValue-method | The Table class
.singleStringError | Validation error utilites
.sliderInput.iSEE | 'iSEE' UI element wrappers
.textEval | Manage commands to be evaluated
.trackMultiSelection | Track internal events
.trackRelinkedSelection | Track internal events
.trackSingleSelection | Track internal events
.trackUpdate | Track internal events
.validLogicalError | Validation error utilites
.validNumberError | Validation error utilites
.validStringError | Validation error utilites
.whichGroupable | Caching utilities
.whichNumeric | Caching utilities
[[-method | The ColumnDotPlot virtual class
[[-method | The ComplexHeatmapPlot panel
[[-method | The DotPlot virtual class
[[-method | The Panel virtual class
[[-method | The RowDotPlot virtual class
[[<--method | The ColumnDotPlot virtual class
[[<--method | The ComplexHeatmapPlot panel
[[<--method | The DotPlot virtual class
[[<--method | The Panel virtual class
[[<--method | The RowDotPlot virtual class