Package: iSEE 2.19.0
Kevin Rue-Albrecht
iSEE: Interactive SummarizedExperiment Explorer
Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.
Authors:
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iSEE.pdf |iSEE.html✨
iSEE/json (API)
NEWS
| # Install 'iSEE' in R: |
| install.packages('iSEE', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/isee/isee/issues
On BioConductor:iSEE-2.17.4(bioc 3.20)iSEE-2.16.0(bioc 3.19)
cellbasedassaysclusteringdimensionreductionfeatureextractiongeneexpressionguiimmunooncologyshinyappssinglecelltranscriptiontranscriptomicsvisualizationdimension-reductionfeature-extractiongene-expressionhacktoberfesthuman-cell-atlasshinysingle-cell
Last updated 23 days agofrom:98a4067774. Checks:OK: 1 NOTE: 4 ERROR: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 30 2024 |
| R-4.5-win | NOTE | Oct 31 2024 |
| R-4.5-linux | NOTE | Oct 30 2024 |
| R-4.4-win | NOTE | Oct 31 2024 |
| R-4.4-mac | NOTE | Oct 31 2024 |
| R-4.3-win | ERROR | Oct 31 2024 |
| R-4.3-mac | ERROR | Oct 31 2024 |
Exports:.activateAppOptionRegistry.addCustomLabelsCommands.addFacets.addLabelCentersCommands.addMultiSelectionPlotCommands.addSpecificTour.addTourStep.allowableChoiceError.allowableColorByDataChoices.allowableXAxisChoices.allowableYAxisChoices.buildAes.buildLabs.cacheCommonInfo.checkboxGroupInput.iSEE.checkboxInput.iSEE.clearSpecificTours.colorByNoneDotPlotField.colorByNoneDotPlotScale.conditionalOnCheckGroup.conditionalOnCheckSolo.conditionalOnRadio.createCustomDimnamesModalObservers.createObservers.createProtectedParameterObservers.createUnprotectedParameterObservers.dataParamBoxOpen.deactivateAppOptionRegistry.defineDataInterface.defineInterface.defineOutput.definePanelTour.defineVisualColorInterface.defineVisualFacetInterface.defineVisualOtherInterface.defineVisualPointInterface.defineVisualShapeInterface.defineVisualSizeInterface.defineVisualTextInterface.emptyDefault.exportOutput.extractAssaySubmatrix.findAtomicFields.fullName.generateDotPlot.generateDotPlotData.generateOutput.generateTable.getCachedCommonInfo.getDotPlotColorHelp.getEncodedName.getFullName.getPanelColor.getSpecificTours.getTooltipUI.hideInterface.isAssayNumeric.isBrushable.multipleChoiceError.multiSelectHistory.multiSelectionActive.multiSelectionAvailable.multiSelectionClear.multiSelectionCommands.multiSelectionDimension.multiSelectionInvalidated.multiSelectionResponsive.multiSelectionRestricted.noSelection.numericInput.iSEE.organizationHeight.organizationWidth.panelColor.prioritizeDotPlotData.processMultiSelections.radioButtons.iSEE.refineParameters.removeInvalidChoices.renderOutput.replaceMissingWithFirst.requestActiveSelectionUpdate.requestCleanUpdate.requestUpdate.retrieveOutput.selectInput.iSEE.selectInputHidden.selectizeInput.iSEE.setCachedCommonInfo.showSelectionDetails.singleSelectionDimension.singleSelectionSlots.singleSelectionValue.singleStringError.sliderInput.iSEE.textEval.trackMultiSelection.trackRelinkedSelection.trackSingleSelection.trackUpdate.validLogicalError.validNumberError.validStringError.whichGroupable.whichNumericassayColorMapassayColorMap<-checkColormapCompatibilitycleanDatasetcolDataColorMapcolDataColorMap<-collapseBoxColumnDataPlotColumnDataTablecolumnSelectionColorMapComplexHeatmapPlotcreateCustomPlotcreateCustomTablecreateLandingPagedefaultTourExperimentColorMapFeatureAssayPlotfilterDTfilterDTColumngetAllAppOptionsgetAppOptiongetPanelDefaultinitializeiSEEiSEEOptionsjitterSquarePointsjitterViolinPointslassoPointsmultiSelectionToFactorpanelDefaultsReducedDimensionPlotregisterAppOptionsrowDataColorMaprowDataColorMap<-RowDataPlotRowDataTablerowSelectionColorMapSampleAssayPlotshowsubsetPointsByGridsynchronizeAssaysupdateObject
Dependencies:abindaskpassbase64encBiobaseBiocGenericsbslibcachemcirclizecliclueclustercodetoolscolorspacecolourpickercommonmarkComplexHeatmapcpp11crayoncrosstalkcurlDelayedArraydigestdoParallelDTevaluatefansifarverfastmapfontawesomeforeachfsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggplot2ggrepelGlobalOptionsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphIRangesisobanditeratorsjquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelistviewermagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgconfigpngpromisesR6rappdirsRColorBrewerRcpprintrojsrjsonrlangrmarkdownS4ArraysS4VectorssassscalesshapeshinyshinyAceshinydashboardshinyjsshinyWidgetsSingleCellExperimentsourcetoolsSparseArraySummarizedExperimentsystibbletinytexUCSC.utilsutf8vctrsviporviridisLitewithrxfunxtableXVectoryamlzlibbioc
An introduction to the iSEE interface
Rendered frombasic.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-10-07
Started: 2018-07-05
Sharing information across iSEE panels
Rendered fromlinks.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-10-07
Started: 2020-05-04
Configuring iSEE apps
Rendered fromconfigure.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-10-07
Started: 2018-08-13
Describing the ExperimentColorMap class
Rendered fromecm.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-10-07
Started: 2018-07-05
Deploying custom panels in the iSEE interface
Rendered fromcustom.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-10-07
Started: 2018-08-13
How to use iSEE with big data
Rendered frombigdata.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-10-07
Started: 2020-05-03
Controlling the iSEE interface using speech recognition
Rendered fromvoice.Rmdusingknitr::rmarkdownon Oct 30 2024.Last update: 2024-04-04
Started: 2018-11-30
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add custom label plotting commands | .addCustomLabelsCommands |
| Add centered label plotting commands | .addLabelCentersCommands |
| Add multiple selection plotting commands | .addMultiSelectionPlotCommands |
| Add a step to the tour | .addTourStep |
| Generate ggplot title and label instructions | .buildLabs |
| Conditional elements on radio or checkbox selection | .conditionalOnCheckGroup .conditionalOnCheckSolo .conditionalOnRadio |
| Create observers for a modal for custom dimnames | .createCustomDimnamesModalObservers |
| Define parameter observers | .createProtectedParameterObservers .createUnprotectedParameterObservers |
| Extract assay submatrix | .extractAssaySubmatrix |
| Get panel names | .fullName .getEncodedName .getFullName |
| Get panel colors | .getPanelColor .panelColor |
| Process multiple selections | .processMultiSelections |
| Remove invalid values in multiple choices | .removeInvalidChoices |
| Replace with first choice | .replaceMissingWithFirst |
| Request Panel updates | .requestActiveSelectionUpdate .requestCleanUpdate .requestUpdate |
| Retrieve the panel output | .retrieveOutput |
| Set and get cached commons | .getCachedCommonInfo .setCachedCommonInfo |
| Generate ggplot aesthetic instructions | .buildAes aes-utils |
| Caching utilities | .findAtomicFields .isAssayNumeric .whichGroupable .whichNumeric cache-utils |
| Check compatibility between ExperimentColorMap and SummarizedExperiment objects | checkColormapCompatibility |
| Set default slot values | .emptyDefault class-utils |
| Clean the dataset | cleanDataset cleanDataset,SingleCellExperiment-method cleanDataset,SummarizedExperiment-method |
| A collapsible box | collapseBox |
| The ColumnDataPlot panel | .allowableXAxisChoices,ColumnDataPlot-method .allowableYAxisChoices,ColumnDataPlot-method .createObservers,ColumnDataPlot-method .defineDataInterface,ColumnDataPlot-method .definePanelTour,ColumnDataPlot-method .fullName,ColumnDataPlot-method .generateDotPlotData,ColumnDataPlot-method .multiSelectionInvalidated,ColumnDataPlot-method .panelColor,ColumnDataPlot-method .refineParameters,ColumnDataPlot-method ColumnDataPlot ColumnDataPlot-class initialize,ColumnDataPlot-method |
| The ColumnDataTable panel | .cacheCommonInfo,ColumnDataTable-method .definePanelTour,ColumnDataTable-method .fullName,ColumnDataTable-method .generateTable,ColumnDataTable-method .panelColor,ColumnDataTable-method .refineParameters,ColumnDataTable-method ColumnDataTable ColumnDataTable-class initialize,ColumnDataTable-method |
| The ColumnDotPlot virtual class | .cacheCommonInfo,ColumnDotPlot-method .createObservers,ColumnDotPlot-method .defineInterface,ColumnDotPlot-method .definePanelTour,ColumnDotPlot-method .getDotPlotColorHelp,ColumnDotPlot-method .getTooltipUI,ColumnDotPlot-method .hideInterface,ColumnDotPlot-method .multiSelectionDimension,ColumnDotPlot-method .multiSelectionInvalidated,ColumnDotPlot-method .multiSelectionResponsive,ColumnDotPlot-method .multiSelectionRestricted,ColumnDotPlot-method .refineParameters,ColumnDotPlot-method .singleSelectionDimension,ColumnDotPlot-method ColumnDotPlot-class initialize,ColumnDotPlot-method updateObject,ColumnDotPlot-method [[,ColumnDotPlot,ANY,ANY-method [[,ColumnDotPlot-method [[<-,ColumnDotPlot,ANY,ANY-method [[<-,ColumnDotPlot-method |
| Define the selection colormap | columnSelectionColorMap rowSelectionColorMap |
| The ColumnTable class | .createObservers,ColumnTable-method .defineInterface,ColumnTable-method .hideInterface,ColumnTable-method .multiSelectionDimension,ColumnTable-method .multiSelectionResponsive,ColumnTable-method .refineParameters,ColumnTable-method .showSelectionDetails,ColumnTable-method .singleSelectionDimension,ColumnTable-method ColumnTable-class initialize,ColumnTable-method |
| The ComplexHeatmapPlot panel | .cacheCommonInfo,ComplexHeatmapPlot-method .createObservers,ComplexHeatmapPlot-method .defineDataInterface,ComplexHeatmapPlot-method .defineInterface,ComplexHeatmapPlot-method .defineOutput,ComplexHeatmapPlot-method .definePanelTour,ComplexHeatmapPlot-method .exportOutput,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 ComplexHeatmapPlot ComplexHeatmapPlot-class initialize,ComplexHeatmapPlot-method updateObject,ComplexHeatmapPlot-method [[,ComplexHeatmapPlot,ANY,ANY-method [[,ComplexHeatmapPlot-method [[<-,ComplexHeatmapPlot,ANY,ANY-method [[<-,ComplexHeatmapPlot-method |
| Constants | .dataParamBoxOpen .multiSelectHistory .noSelection .organizationHeight .organizationWidth constants |
| Create custom panels | createCustomPanels createCustomPlot createCustomTable |
| Create a landing page | createLandingPage |
| Define the default tour | defaultTour |
| Documentation generics | .definePanelTour .getDotPlotColorHelp documentation-generics |
| The DotPlot virtual class | .allowableColorByDataChoices,DotPlot-method .cacheCommonInfo,DotPlot-method .colorByNoneDotPlotField,DotPlot-method .colorByNoneDotPlotScale,DotPlot-method .createObservers,DotPlot-method .defineInterface,DotPlot-method .defineOutput,DotPlot-method .definePanelTour,DotPlot-method .defineVisualColorInterface,DotPlot-method .defineVisualFacetInterface,DotPlot-method .defineVisualOtherInterface,DotPlot-method .defineVisualPointInterface,DotPlot-method .defineVisualShapeInterface,DotPlot-method .defineVisualSizeInterface,DotPlot-method .defineVisualTextInterface,DotPlot-method .exportOutput,DotPlot-method .generateDotPlot,DotPlot-method .generateOutput,DotPlot-method .hideInterface,DotPlot-method .isBrushable,DotPlot-method .multiSelectionActive,DotPlot-method .multiSelectionClear,DotPlot-method .multiSelectionCommands,DotPlot-method .multiSelectionDimension,DotPlot-method .prioritizeDotPlotData,DotPlot-method .refineParameters,DotPlot-method .renderOutput,DotPlot-method .singleSelectionSlots,DotPlot-method .singleSelectionValue,DotPlot-method DotPlot-class initialize,DotPlot-method updateObject,DotPlot-method [[,DotPlot,ANY,ANY-method [[,DotPlot-method [[<-,DotPlot,ANY,ANY-method [[<-,DotPlot-method |
| ExperimentColorMap class | assay,ExperimentColorMap,character-method assay,ExperimentColorMap,numeric-method assayColorMap assayColorMap,ExperimentColorMap,character-method assayColorMap,ExperimentColorMap,missing-method assayColorMap,ExperimentColorMap,numeric-method assayColorMap<- assayColorMap<-,ExperimentColorMap,character-method assayColorMap<-,ExperimentColorMap,numeric-method assayNames,ExperimentColorMap-method assayNames<-,ExperimentColorMap,ANY-method assays,ExperimentColorMap-method assays<-,ExperimentColorMap,list-method class:ExperimentColorMap colData,ExperimentColorMap-method colData<-,ExperimentColorMap,ANY-method colDataColorMap colDataColorMap,ExperimentColorMap,character-method colDataColorMap,ExperimentColorMap,missing-method colDataColorMap<- colDataColorMap<-,ExperimentColorMap,character-method ExperimentColorMap ExperimentColorMap-class rowData,ExperimentColorMap-method rowData<-,ExperimentColorMap,ANY-method rowDataColorMap rowDataColorMap,ExperimentColorMap,character-method rowDataColorMap,ExperimentColorMap,missing-method rowDataColorMap<- rowDataColorMap<-,ExperimentColorMap,character-method show,ExperimentColorMap-method |
| The FeatureAssayPlot panel | .createObservers,FeatureAssayPlot-method .defineDataInterface,FeatureAssayPlot-method .definePanelTour,FeatureAssayPlot-method .fullName,FeatureAssayPlot-method .generateDotPlotData,FeatureAssayPlot-method .multiSelectionInvalidated,FeatureAssayPlot-method .panelColor,FeatureAssayPlot-method .refineParameters,FeatureAssayPlot-method .singleSelectionSlots,FeatureAssayPlot-method FeatureAssayPlot FeatureAssayPlot-class initialize,FeatureAssayPlot-method |
| Filter 'DT' columns | filterDT filterDTColumn |
| Hidden interface elements | .selectInputHidden hidden-inputs |
| Generics for the panel interface | .defineDataInterface .defineInterface .hideInterface interface-generics |
| 'iSEE' UI element wrappers | .checkboxGroupInput.iSEE .checkboxInput.iSEE .numericInput.iSEE .radioButtons.iSEE .selectInput.iSEE .selectizeInput.iSEE .sliderInput.iSEE interface-wrappers |
| iSEE: interactive SummarizedExperiment Explorer | iSEE |
| iSEE: interactive SummarizedExperiment/SingleCellExperiment Explorer | iSEE-package iSEE-pkg |
| Global 'iSEE' options | iSEEOptions |
| Jitter points for categorical variables | jitterSquarePoints jitterViolinPoints |
| Find rows of data within a closed lasso | lassoPoints |
| Manage commands to be evaluated | .textEval manage_commands |
| Generics for row/column metadata plots | .allowableXAxisChoices .allowableYAxisChoices metadata-plot-generics |
| Generics for controlling multiple selections | .isBrushable .multiSelectionActive .multiSelectionAvailable .multiSelectionClear .multiSelectionCommands .multiSelectionDimension .multiSelectionInvalidated .multiSelectionResponsive .multiSelectionRestricted multi-select-generics |
| Convert multiple selections into a factor | multiSelectionToFactor |
| Generic for the panel observers | .createObservers observer-generics |
| Generics for Panel outputs | .defineOutput .exportOutput .generateOutput .renderOutput output-generics |
| The Panel virtual class | .cacheCommonInfo,Panel-method .createObservers,Panel-method .defineDataInterface,Panel-method .defineInterface,Panel-method .definePanelTour,Panel-method .exportOutput,Panel-method .hideInterface,Panel-method .isBrushable,Panel-method .multiSelectionActive,Panel-method .multiSelectionAvailable,Panel-method .multiSelectionClear,Panel-method .multiSelectionDimension,Panel-method .multiSelectionInvalidated,Panel-method .multiSelectionRestricted,Panel-method .refineParameters,Panel-method .renderOutput,Panel-method .singleSelectionDimension,Panel-method .singleSelectionSlots,Panel-method .singleSelectionValue,Panel-method initialize,Panel-method Panel-class show,Panel-method updateObject,Panel-method [[,Panel,ANY,ANY-method [[,Panel-method [[<-,Panel,ANY,ANY-method [[<-,Panel-method |
| Panel defaults | getPanelDefault panelDefaults |
| Generics for DotPlot plotting | .colorByNoneDotPlotField .colorByNoneDotPlotScale .generateDotPlot .generateDotPlotData .prioritizeDotPlotData plot-generics |
| Process faceting choices | .addFacets plot-utils |
| The ReducedDimensionPlot panel | .cacheCommonInfo,ReducedDimensionPlot-method .createObservers,ReducedDimensionPlot-method .defineDataInterface,ReducedDimensionPlot-method .definePanelTour,ReducedDimensionPlot-method .fullName,ReducedDimensionPlot-method .generateDotPlotData,ReducedDimensionPlot-method .panelColor,ReducedDimensionPlot-method .refineParameters,ReducedDimensionPlot-method initialize,ReducedDimensionPlot-method ReducedDimensionPlot ReducedDimensionPlot-class |
| Set and get app-level options | .activateAppOptionRegistry .deactivateAppOptionRegistry getAllAppOptions getAppOption registerAppOptions |
| The RowDataPlot panel | .allowableXAxisChoices,RowDataPlot-method .allowableYAxisChoices,RowDataPlot-method .createObservers,RowDataPlot-method .defineDataInterface,RowDataPlot-method .definePanelTour,RowDataPlot-method .fullName,RowDataPlot-method .generateDotPlotData,RowDataPlot-method .multiSelectionInvalidated,RowDataPlot-method .panelColor,RowDataPlot-method .refineParameters,RowDataPlot-method initialize,RowDataPlot-method RowDataPlot RowDataPlot-class |
| The RowDataTable panel | .cacheCommonInfo,RowDataTable-method .definePanelTour,RowDataTable-method .fullName,RowDataTable-method .generateTable,RowDataTable-method .panelColor,RowDataTable-method .refineParameters,RowDataTable-method initialize,RowDataTable-method RowDataTable RowDataTable-class |
| The RowDotPlot virtual class | .cacheCommonInfo,RowDotPlot-method .createObservers,RowDotPlot-method .defineInterface,RowDotPlot-method .definePanelTour,RowDotPlot-method .getDotPlotColorHelp,RowDotPlot-method .getTooltipUI,RowDotPlot-method .hideInterface,RowDotPlot-method .multiSelectionDimension,RowDotPlot-method .multiSelectionInvalidated,RowDotPlot-method .multiSelectionResponsive,RowDotPlot-method .multiSelectionRestricted,RowDotPlot-method .refineParameters,RowDotPlot-method .singleSelectionDimension,RowDotPlot-method initialize,RowDotPlot-method RowDotPlot-class updateObject,RowDotPlot-method [[,RowDotPlot,ANY,ANY-method [[,RowDotPlot-method [[<-,RowDotPlot,ANY,ANY-method [[<-,RowDotPlot-method |
| The RowTable class | .createObservers,RowTable-method .defineInterface,RowTable-method .hideInterface,RowTable-method .multiSelectionDimension,RowTable-method .multiSelectionResponsive,RowTable-method .refineParameters,RowTable-method .showSelectionDetails,RowTable-method .singleSelectionDimension,RowTable-method initialize,RowTable-method RowTable-class |
| The SampleAssayPlot panel | .createObservers,SampleAssayPlot-method .defineDataInterface,SampleAssayPlot-method .definePanelTour,SampleAssayPlot-method .fullName,SampleAssayPlot-method .generateDotPlotData,SampleAssayPlot-method .multiSelectionInvalidated,SampleAssayPlot-method .panelColor,SampleAssayPlot-method .refineParameters,SampleAssayPlot-method .singleSelectionSlots,SampleAssayPlot-method initialize,SampleAssayPlot-method SampleAssayPlot SampleAssayPlot-class |
| Generics for setting up parameters | .cacheCommonInfo .refineParameters setup-generics |
| Generics for controlling single selections | .singleSelectionDimension .singleSelectionSlots .singleSelectionValue single-select-generics |
| UI-specific tour management utilities | .addSpecificTour .clearSpecificTours .getSpecificTours specific-tours |
| Subset points for faster plotting | subsetPointsByGrid |
| Synchronize assay colormaps to match those in a SummarizedExperiment | synchronizeAssays |
| The Table class | .createObservers,Table-method .defineDataInterface,Table-method .defineOutput,Table-method .definePanelTour,Table-method .exportOutput,Table-method .generateOutput,Table-method .hideInterface,Table-method .multiSelectionActive,Table-method .multiSelectionCommands,Table-method .multiSelectionRestricted,Table-method .refineParameters,Table-method .renderOutput,Table-method .singleSelectionValue,Table-method initialize,Table-method Table-class updateObject,Table-method |
| Generics for table construction | .generateTable .showSelectionDetails table-generics |
| Track internal events | .trackMultiSelection .trackRelinkedSelection .trackSingleSelection .trackUpdate track-utils |
| Validation error utilities | .allowableChoiceError .multipleChoiceError .singleStringError .validLogicalError .validNumberError .validStringError validate-utils |
| Generics for visual DotPlot parameters | .allowableColorByDataChoices .defineVisualColorInterface .defineVisualFacetInterface .defineVisualOtherInterface .defineVisualPointInterface .defineVisualShapeInterface .defineVisualSizeInterface .defineVisualTextInterface .getTooltipUI visual-parameters-generics |
