iSEE Universe

---

Documentation for package ‘iSEEu’ version 1.14.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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 --

defunct	Defunct functions
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
getAveAbFields	Register DE-related fields
getAveAbPattern	Global DE prefixes
getAveAbPatterns	Register DE-related fields
getFeatureSetCollections	Register feature set collections
getFeatureSetCommands	Register feature set collections
getLogFCFields	Register DE-related fields
getLogFCPattern	Global DE prefixes
getLogFCPatterns	Register DE-related fields
getPValueFields	Register DE-related fields
getPValuePattern	Global DE prefixes
getPValuePatterns	Register DE-related fields
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 MarkdownBoard 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
MarkdownBoard	The MarkdownBoard class
MarkdownBoard-class	The MarkdownBoard 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 --

registerAveAbFields	Register DE-related fields
registerAveAbPatterns	Register DE-related fields
registerDEFields	Register DE-related fields
registerFeatureSetCollections	Register feature set collections
registerFeatureSetCommands	Register feature set collections
registerLogFCFields	Register DE-related fields
registerLogFCPatterns	Register DE-related fields
registerPValueFields	Register DE-related fields
registerPValuePatterns	Register DE-related fields

-- 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-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 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 MarkdownBoard 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 MarkdownBoard 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
.defineOutput-method	The MarkdownBoard class
.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 MarkdownBoard class
.definePanelTour-method	The VolcanoPlot class
.exportOutput-method	The AggregatedDotPlot class
.exportOutput-method	The MarkdownBoard 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 MarkdownBoard class
.fullName-method	The VolcanoPlot class
.generateDotPlot-method	The LogFCLogFCPlot class
.generateDotPlot-method	The MAPlot 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
.generateOutput-method	The MarkdownBoard class
.generateTable-method	Dynamic marker table
.getAcceptableAveAbFields	Defunct functions
.getAcceptableLogFCFields	Defunct functions
.getAcceptablePValueFields	Defunct functions
.getDotPlotColorHelp-method	The LogFCLogFCPlot class
.getDotPlotColorHelp-method	The MAPlot class
.getDotPlotColorHelp-method	The VolcanoPlot class
.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 MarkdownBoard 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 MarkdownBoard 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
.renderOutput-method	The MarkdownBoard class
.setAcceptableAveAbFields	Defunct functions
.setAcceptableLogFCFields	Defunct functions
.setAcceptablePValueFields	Defunct functions
.setGeneSetCommands	Gene set utilities
.setIdentifierType	Gene set utilities
.setOrganism	Gene set utilities