Interactive SummarizedExperiment Explorer
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Documentation for package ‘iSEE’ version 2.16.0
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A C D E F G I J L M O P R S T U V misc
| iSEE-package | iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer |
-- 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 |
| constants | Constants |
| 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 utilities |
| 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 utilities |
| .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 |
| .dataParamBoxOpen | Constants |
| .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 |
| .getTooltipUI | Generics for visual DotPlot parameters |
| .getTooltipUI-method | The ColumnDotPlot virtual class |
| .getTooltipUI-method | The RowDotPlot virtual class |
| .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 |
| .isBrushable | Generics for controlling multiple selections |
| .isBrushable-method | The DotPlot virtual class |
| .isBrushable-method | The Panel virtual class |
| .multipleChoiceError | Validation error utilities |
| .multiSelectHistory | Constants |
| .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 |
| .multiSelectionResponsive | Generics for controlling multiple selections |
| .multiSelectionResponsive-method | The ColumnDotPlot virtual class |
| .multiSelectionResponsive-method | The ColumnTable class |
| .multiSelectionResponsive-method | The ComplexHeatmapPlot panel |
| .multiSelectionResponsive-method | The RowDotPlot virtual class |
| .multiSelectionResponsive-method | The RowTable class |
| .multiSelectionRestricted | Generics for controlling multiple selections |
| .multiSelectionRestricted-method | The ColumnDotPlot virtual class |
| .multiSelectionRestricted-method | The ComplexHeatmapPlot panel |
| .multiSelectionRestricted-method | The Panel virtual class |
| .multiSelectionRestricted-method | The RowDotPlot virtual class |
| .multiSelectionRestricted-method | The Table class |
| .noSelection | Constants |
| .numericInput.iSEE | 'iSEE' UI element wrappers |
| .organizationHeight | Constants |
| .organizationWidth | Constants |
| .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 |
| .removeInvalidChoices | Remove invalid values in multiple choices |
| .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 utilities |
| .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 utilities |
| .validNumberError | Validation error utilities |
| .validStringError | Validation error utilities |
| .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 |