iSEE Universe

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Documentation for package ‘iSEEu’ version 1.2.0

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A C D F G I L M R S U V misc

-- A --

AggregatedDotPlot The AggregatedDotPlot class
AggregatedDotPlot-class The AggregatedDotPlot class

-- C --

createGeneSetCommands Create gene set commands

-- D --

DifferentialStatisticsTable Dynamic marker table
DynamicMarkerTable Dynamic marker table
DynamicMarkerTable-class Dynamic marker table
DynamicReducedDimensionPlot Dynamic reduced dimension plot
DynamicReducedDimensionPlot-class Dynamic reduced dimension plot

-- F --

FeatureSetTable Feature set table
FeatureSetTable-class Feature set table

-- G --

GeneSetTable Gene set table
GeneSetTable-class Gene set table
getAveAbPattern Global DE prefixes
getFeatureSetCommands Global feature set commands
getLogFCPattern Global DE prefixes
getPValuePattern Global DE prefixes
getTableExtraFields Global extra table fields

-- I --

initialize-method The AggregatedDotPlot class
initialize-method Dynamic marker table
initialize-method Dynamic reduced dimension plot
initialize-method Feature set table
initialize-method Gene set table
initialize-method The LogFCLogFCPlot class
initialize-method The MAPlot class
initialize-method The ReducedDimensionHexPlot class
initialize-method The VolcanoPlot class

-- L --

LogFCLogFCPlot The LogFCLogFCPlot class
LogFCLogFCPlot-class The LogFCLogFCPlot class

-- M --

MAPlot The MAPlot class
MAPlot-class The MAPlot class
modeEmpty App pre-configured to launch with no visible panel
modeGating App pre-configured to link multiple feature assay plots
modeReducedDim App pre-configured to compare multiple reduced dimension plots

-- R --

ReducedDimensionHexPlot The ReducedDimensionHexPlot class
ReducedDimensionHexPlot-class The ReducedDimensionHexPlot class

-- S --

setAveAbPattern Global DE prefixes
setFeatureSetCommands Global feature set commands
setLogFCPattern Global DE prefixes
setPValuePattern Global DE prefixes
setTableExtraFields Global extra table fields

-- U --

utils-de Acceptable fields for DE panels
utils-geneset Gene set utilities

-- V --

VolcanoPlot The VolcanoPlot class
VolcanoPlot-class The VolcanoPlot class

-- misc --

.allowableXAxisChoices-method The LogFCLogFCPlot class
.allowableXAxisChoices-method The MAPlot class
.allowableXAxisChoices-method The VolcanoPlot class
.allowableYAxisChoices-method The LogFCLogFCPlot class
.allowableYAxisChoices-method The MAPlot class
.allowableYAxisChoices-method The VolcanoPlot class
.cacheCommonInfo-method The AggregatedDotPlot class
.cacheCommonInfo-method Dynamic marker table
.cacheCommonInfo-method Dynamic reduced dimension plot
.cacheCommonInfo-method Feature set table
.cacheCommonInfo-method The LogFCLogFCPlot class
.cacheCommonInfo-method The MAPlot class
.cacheCommonInfo-method The ReducedDimensionHexPlot class
.cacheCommonInfo-method The VolcanoPlot class
.colorByNoneDotPlotField-method The LogFCLogFCPlot class
.colorByNoneDotPlotField-method The MAPlot class
.colorByNoneDotPlotField-method The VolcanoPlot class
.colorByNoneDotPlotScale-method The LogFCLogFCPlot class
.colorByNoneDotPlotScale-method The MAPlot class
.colorByNoneDotPlotScale-method The VolcanoPlot class
.createObservers-method The AggregatedDotPlot class
.createObservers-method Dynamic marker table
.createObservers-method Dynamic reduced dimension plot
.createObservers-method Feature set table
.createObservers-method Gene set table
.createObservers-method The LogFCLogFCPlot class
.createObservers-method The MAPlot class
.createObservers-method The ReducedDimensionHexPlot class
.createObservers-method The VolcanoPlot class
.defineDataInterface-method The AggregatedDotPlot class
.defineDataInterface-method Dynamic marker table
.defineDataInterface-method Dynamic reduced dimension plot
.defineDataInterface-method Feature set table
.defineDataInterface-method Gene set table
.defineDataInterface-method The LogFCLogFCPlot class
.defineDataInterface-method The MAPlot class
.defineDataInterface-method The VolcanoPlot class
.defineInterface-method The AggregatedDotPlot class
.defineOutput-method The AggregatedDotPlot class
.defineOutput-method Feature set table
.defineOutput-method Gene set table
.definePanelTour-method The AggregatedDotPlot class
.definePanelTour-method Dynamic marker table
.definePanelTour-method Dynamic reduced dimension plot
.definePanelTour-method Feature set table
.definePanelTour-method The LogFCLogFCPlot class
.definePanelTour-method The MAPlot class
.definePanelTour-method The ReducedDimensionHexPlot class
.definePanelTour-method The VolcanoPlot class
.defineVisualOtherInterface-method The ReducedDimensionHexPlot class
.defineVisualShapeInterface-method The ReducedDimensionHexPlot class
.defineVisualSizeInterface-method The ReducedDimensionHexPlot class
.exportOutput-method The AggregatedDotPlot class
.fullName-method The AggregatedDotPlot class
.fullName-method Dynamic marker table
.fullName-method Dynamic reduced dimension plot
.fullName-method Feature set table
.fullName-method Gene set table
.fullName-method The LogFCLogFCPlot class
.fullName-method The MAPlot class
.fullName-method The ReducedDimensionHexPlot class
.fullName-method The VolcanoPlot class
.generateDotPlot-method The LogFCLogFCPlot class
.generateDotPlot-method The MAPlot class
.generateDotPlot-method The ReducedDimensionHexPlot class
.generateDotPlot-method The VolcanoPlot class
.generateDotPlotData-method Dynamic reduced dimension plot
.generateDotPlotData-method The LogFCLogFCPlot class
.generateDotPlotData-method The MAPlot class
.generateDotPlotData-method The VolcanoPlot class
.generateOutput-method The AggregatedDotPlot class
.generateOutput-method Feature set table
.generateOutput-method Gene set table
.generateTable-method Dynamic marker table
.getAcceptableAveAbFields Acceptable fields for DE panels
.getAcceptableLogFCFields Acceptable fields for DE panels
.getAcceptablePValueFields Acceptable fields for DE panels
.getGeneSetCommands Gene set utilities
.getIdentifierType Gene set utilities
.getOrganism Gene set utilities
.hideInterface-method The AggregatedDotPlot class
.hideInterface-method Dynamic marker table
.hideInterface-method Feature set table
.hideInterface-method Gene set table
.hideInterface-method The LogFCLogFCPlot class
.hideInterface-method The MAPlot class
.hideInterface-method The ReducedDimensionHexPlot class
.hideInterface-method The VolcanoPlot class
.multiSelectionActive-method Feature set table
.multiSelectionActive-method Gene set table
.multiSelectionAvailable-method Feature set table
.multiSelectionAvailable-method Gene set table
.multiSelectionClear-method Feature set table
.multiSelectionClear-method Gene set table
.multiSelectionCommands-method Feature set table
.multiSelectionCommands-method Gene set table
.multiSelectionDimension-method Feature set table
.multiSelectionDimension-method Gene set table
.multiSelectionInvalidated-method Dynamic marker table
.multiSelectionInvalidated-method Dynamic reduced dimension plot
.panelColor-method The AggregatedDotPlot class
.panelColor-method Dynamic marker table
.panelColor-method Dynamic reduced dimension plot
.panelColor-method Feature set table
.panelColor-method Gene set table
.panelColor-method The LogFCLogFCPlot class
.panelColor-method The MAPlot class
.panelColor-method The ReducedDimensionHexPlot class
.panelColor-method The VolcanoPlot class
.prioritizeDotPlotData-method The LogFCLogFCPlot class
.prioritizeDotPlotData-method The MAPlot class
.prioritizeDotPlotData-method The VolcanoPlot class
.refineParameters-method The AggregatedDotPlot class
.refineParameters-method Dynamic marker table
.refineParameters-method Dynamic reduced dimension plot
.refineParameters-method Feature set table
.refineParameters-method The LogFCLogFCPlot class
.refineParameters-method The MAPlot class
.refineParameters-method The VolcanoPlot class
.renderOutput-method The AggregatedDotPlot class
.renderOutput-method Feature set table
.renderOutput-method Gene set table
.setAcceptableAveAbFields Acceptable fields for DE panels
.setAcceptableLogFCFields Acceptable fields for DE panels
.setAcceptablePValueFields Acceptable fields for DE panels
.setGeneSetCommands Gene set utilities
.setIdentifierType Gene set utilities
.setOrganism Gene set utilities