Package index

All functions

AggregatedDotPlot AggregatedDotPlot-class .cacheCommonInfo,AggregatedDotPlot-method .refineParameters,AggregatedDotplot-method .defineOutput,AggregatedDotPlot-method .generateOutput,AggregatedDotPlot-method .renderOutput,AggregatedDotPlot-method .exportOutput,AggregatedDotPlot-method .defineDataInterface,AggregatedDotPlot-method .defineInterface,AggregatedDotPlot-method .hideInterface,AggregatedDotPlot-method .panelColor,AggregatedDotPlot-method .fullName,AggregatedDotPlot-method .definePanelTour,AggregatedDotPlot-method .createObservers,AggregatedDotPlot-method .refineParameters,AggregatedDotPlot-method initialize,AggregatedDotPlot-method

The AggregatedDotPlot class

DynamicMarkerTable-class DynamicMarkerTable DifferentialStatisticsTable initialize,DynamicMarkerTable-method .fullName,DynamicMarkerTable-method .panelColor,DynamicMarkerTable-method .defineDataInterface,DynamicMarkerTable-method .hideInterface,DynamicMarkerTable-method .generateTable,DynamicMarkerTable-method .createObservers,DynamicMarkerTable-method .cacheCommonInfo,DynamicMarkerTable-method .refineParameters,DynamicMarkerTable-method .multiSelectionInvalidated,DynamicMarkerTable-method .definePanelTour,DynamicMarkerTable-method

Dynamic marker table

DynamicReducedDimensionPlot-class DynamicReducedDimensionPlot initialize,DynamicReducedDimensionPlot-method .fullName,DynamicReducedDimensionPlot-method .panelColor,DynamicReducedDimensionPlot-method .defineDataInterface,DynamicReducedDimensionPlot-method .generateDotPlotData,DynamicReducedDimensionPlot-method .createObservers,DynamicReducedDimensionPlot-method .cacheCommonInfo,DynamicReducedDimensionPlot-method .refineParameters,DynamicReducedDimensionPlot-method .multiSelectionInvalidated,DynamicReducedDimensionPlot-method .definePanelTour,DynamicReducedDimensionPlot-method

Dynamic reduced dimension plot

FeatureSetTable-class FeatureSetTable initialize,FeatureSetTable-method .fullName,FeatureSetTable-method .panelColor,FeatureSetTable-method .cacheCommonInfo,FeatureSetTable-method .refineParameters,FeatureSetTable-method .defineDataInterface,FeatureSetTable-method .hideInterface,FeatureSetTable-method .defineOutput,FeatureSetTable-method .generateOutput,FeatureSetTable-method .createObservers,FeatureSetTable-method .renderOutput,FeatureSetTable-method .multiSelectionDimension,FeatureSetTable-method .multiSelectionActive,FeatureSetTable-method .multiSelectionCommands,FeatureSetTable-method .multiSelectionAvailable,FeatureSetTable-method .multiSelectionClear,FeatureSetTable-method .definePanelTour,FeatureSetTable-method

Feature set table

GeneSetTable-class GeneSetTable initialize,GeneSetTable-method .fullName,GeneSetTable-method .panelColor,GeneSetTable-method .defineDataInterface,GeneSetTable-method .hideInterface,GeneSetTable-method .defineOutput,GeneSetTable-method .generateOutput,GeneSetTable-method .createObservers,GeneSetTable-method .renderOutput,GeneSetTable-method .multiSelectionDimension,GeneSetTable-method .multiSelectionActive,GeneSetTable-method .multiSelectionCommands,GeneSetTable-method .multiSelectionAvailable,GeneSetTable-method .multiSelectionClear,GeneSetTable-method

Gene set table

LogFCLogFCPlot-class LogFCLogFCPlot initialize,LogFCLogFCPlot-method .cacheCommonInfo,LogFCLogFCPlot-method .refineParameters,LogFCLogFCPlot-method .defineDataInterface,LogFCLogFCPlot-method .createObservers,LogFCLogFCPlot-method .hideInterface,LogFCLogFCPlot-method .fullName,LogFCLogFCPlot-method .panelColor,LogFCLogFCPlot-method .generateDotPlotData,LogFCLogFCPlot-method .allowableXAxisChoices,LogFCLogFCPlot-method .allowableYAxisChoices,LogFCLogFCPlot-method .prioritizeDotPlotData,LogFCLogFCPlot-method .colorByNoneDotPlotField,LogFCLogFCPlot-method .colorByNoneDotPlotScale,LogFCLogFCPlot-method .generateDotPlot,LogFCLogFCPlot-method .definePanelTour,LogFCLogFCPlot-method .getDotPlotColorHelp,LogFCLogFCPlot-method

The LogFCLogFCPlot class

MAPlot-class MAPlot initialize,MAPlot-method .cacheCommonInfo,MAPlot-method .refineParameters,MAPlot-method .defineDataInterface,MAPlot-method .createObservers,MAPlot-method .hideInterface,MAPlot-method .fullName,MAPlot-method .panelColor,MAPlot-method .generateDotPlotData,MAPlot-method .allowableXAxisChoices,MAPlot-method .allowableYAxisChoices,MAPlot-method .prioritizeDotPlotData,MAPlot-method .colorByNoneDotPlotField,MAPlot-method .colorByNoneDotPlotScale,MAPlot-method .generateDotPlot,MAPlot-method .definePanelTour,MAPlot-method .getDotPlotColorHelp,MAPlot-method

The MAPlot class

MarkdownBoard-class MarkdownBoard initialize,MarkdownBoard-method .defineDataInterface,MarkdownBoard-method .createObservers,MarkdownBoard-method .hideInterface,MarkdownBoard-method .fullName,MarkdownBoard-method .panelColor,MarkdownBoard-method .generateOutput,MarkdownBoard-method .renderOutput,MarkdownBoard-method .defineOutput,MarkdownBoard-method .exportOutput,MarkdownBoard-method .definePanelTour,MarkdownBoard-method

The MarkdownBoard class

VolcanoPlot-class VolcanoPlot initialize,VolcanoPlot-method .cacheCommonInfo,VolcanoPlot-method .refineParameters,VolcanoPlot-method .defineDataInterface,VolcanoPlot-method .createObservers,VolcanoPlot-method .hideInterface,VolcanoPlot-method .fullName,VolcanoPlot-method .panelColor,VolcanoPlot-method .generateDotPlotData,VolcanoPlot-method .allowableXAxisChoices,VolcanoPlot-method .allowableYAxisChoices,VolcanoPlot-method .prioritizeDotPlotData,VolcanoPlot-method .colorByNoneDotPlotField,VolcanoPlot-method .colorByNoneDotPlotScale,VolcanoPlot-method .generateDotPlot,VolcanoPlot-method .definePanelTour,VolcanoPlot-method .getDotPlotColorHelp,VolcanoPlot-method

The VolcanoPlot class

createGeneSetCommands()

Create gene set commands

.getAcceptablePValueFields() .getAcceptableAveAbFields() .getAcceptableLogFCFields() .setAcceptablePValueFields() .setAcceptableAveAbFields() .setAcceptableLogFCFields()

Defunct functions

setFeatureSetCommands()

Global feature set commands

getTableExtraFields() setTableExtraFields()

Global extra table fields

getPValuePattern() getLogFCPattern() getAveAbPattern() setPValuePattern() setLogFCPattern() setAveAbPattern()

Global DE prefixes

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

registerPValueFields() registerAveAbFields() registerLogFCFields() registerPValuePatterns() registerAveAbPatterns() registerLogFCPatterns() getPValueFields() getAveAbFields() getLogFCFields() getPValuePatterns() getAveAbPatterns() getLogFCPatterns()

Register DE-related fields

registerFeatureSetCollections() registerFeatureSetCommands() getFeatureSetCollections() getFeatureSetCommands()

Register feature set collections

.getIdentifierType() .setIdentifierType() .getOrganism() .setOrganism() .getGeneSetCommands() .setGeneSetCommands()

Gene set utilities