# Visualization for flow cytometry

## Documentation for package ‘flowViz’ version 1.6.2

## User Guides and Package Vignettes

Read overview or browse directory.

## Help Pages

A C D E F G H L P Q S T X

## -- --

flowViz-package | Visualization for flow cytometry

## -- A --

addName | Add gate names to a flowViz plot.
addName,curv1Filter,character-method | Add gate names to a flowViz plot.
addName,curv1Filter,logical-method | Add gate names to a flowViz plot.
addName,curv2Filter,character-method | Add gate names to a flowViz plot.
addName,curv2Filter,logical-method | Add gate names to a flowViz plot.
addName,ellipsoidGate,character-method | Add gate names to a flowViz plot.
addName,ellipsoidGate,logical-method | Add gate names to a flowViz plot.
addName,kmeansFilter,character-method | Add gate names to a flowViz plot.
addName,kmeansFilter,logical-method | Add gate names to a flowViz plot.
addName,polygonGate,character-method | Add gate names to a flowViz plot.
addName,polygonGate,logical-method | Add gate names to a flowViz plot.
addName,quadGate,character-method | Add gate names to a flowViz plot.
addName,quadGate,logical-method | Add gate names to a flowViz plot.
addName,quadGate,matrix-method | Add gate names to a flowViz plot.
addName,rectangleGate,character-method | Add gate names to a flowViz plot.
addName,rectangleGate,logical-method | Add gate names to a flowViz plot.
addName-methods | Add gate names to a flowViz plot.

## -- C --

contour | Contour plots for flow data
contour,ANY-method | Contour plots for flow data
contour,flowFrame-method | Contour plots for flow data
contour,flowSet-method | Contour plots for flow data
contour-methods | Contour plots for flow data

## -- D --

densityplot | One-dimensional density plots for flow data
densityplot,formula,flowSet-method | One-dimensional density plots for flow data
densityplot,formula,view-method | One-dimensional density plots for flow data
densityplot,view,missing-method | One-dimensional density plots for flow data

## -- E --

ecdfplot | Method implementing Lattice ECDF plots for flow data
ecdfplot,formula,flowSet-method | Method implementing Lattice ECDF plots for flow data

## -- F --

flowPlot | Standard Plots for Flow Cytometry Data
flowPlot,flowFrame-method | Standard Plots for Flow Cytometry Data
flowViz | Visualization for flow cytometry
flowViz.par.get | Query and set session-wide graphical parameter defaults.
flowViz.par.set | Query and set session-wide graphical parameter defaults.

## -- G --

glines | Drawing filter boundaries
glines,curv1Filter,ANY-method | Drawing filter boundaries
glines,curv1Filter,flowFrame-method | Drawing filter boundaries
glines,curv1Filter,missing-method | Drawing filter boundaries
glines,curv1Filter,multipleFilterResult-method | Drawing filter boundaries
glines,curv2Filter,ANY-method | Drawing filter boundaries
glines,curv2Filter,flowFrame-method | Drawing filter boundaries
glines,curv2Filter,multipleFilterResult-method | Drawing filter boundaries
glines,ellipsoidGate,character-method | Drawing filter boundaries
glines,ellipsoidGate,filterResult-method | Drawing filter boundaries
glines,ellipsoidGate,flowFrame-method | Drawing filter boundaries
glines,filter,missing-method | Drawing filter boundaries
glines,filterResult,ANY-method | Drawing filter boundaries
glines,filterResult,flowFrame-method | Drawing filter boundaries
glines,kmeansFilter,ANY-method | Drawing filter boundaries
glines,norm2Filter,ANY-method | Drawing filter boundaries
glines,norm2Filter,flowFrame-method | Drawing filter boundaries
glines,norm2Filter,logicalFilterResult-method | Drawing filter boundaries
glines,polygonGate,character-method | Drawing filter boundaries
glines,polygonGate,filterResult-method | Drawing filter boundaries
glines,polygonGate,flowFrame-method | Drawing filter boundaries
glines,quadGate,character-method | Drawing filter boundaries
glines,quadGate,filterResult-method | Drawing filter boundaries
glines,quadGate,flowFrame-method | Drawing filter boundaries
glines,rectangleGate,character-method | Drawing filter boundaries
glines,rectangleGate,filterResult-method | Drawing filter boundaries
glines,rectangleGate,flowFrame-method | Drawing filter boundaries
glines-methods | Drawing filter boundaries
glpoints | Adding points within a gate to a plot
glpoints,curv1Filter,flowFrame,character-method | Adding points within a gate to a plot
glpoints,curv2Filter,flowFrame,character-method | Adding points within a gate to a plot
glpoints,ellipsoidGate,flowFrame,character-method | Adding points within a gate to a plot
glpoints,filter,flowFrame,missing-method | Adding points within a gate to a plot
glpoints,filter,missing,ANY-method | Adding points within a gate to a plot
glpoints,filterResult,flowFrame,ANY-method | Adding points within a gate to a plot
glpoints,filterResult,flowFrame,character-method | Adding points within a gate to a plot
glpoints,kmeansFilter,flowFrame,character-method | Adding points within a gate to a plot
glpoints,norm2Filter,flowFrame,character-method | Adding points within a gate to a plot
glpoints,polygonGate,flowFrame,character-method | Adding points within a gate to a plot
glpoints,quadGate,flowFrame,character-method | Adding points within a gate to a plot
glpoints,rectangleGate,flowFrame,character-method | Adding points within a gate to a plot
glpoints,subsetFilter,flowFrame,ANY-method | Adding points within a gate to a plot
glpoints-methods | Adding points within a gate to a plot
glpolygon | Drawing filter regions
glpolygon,complementFilter,ANY-method | Drawing filter regions
glpolygon,curv1Filter,ANY-method | Drawing filter regions
glpolygon,curv1Filter,flowFrame-method | Drawing filter regions
glpolygon,curv1Filter,missing-method | Drawing filter regions
glpolygon,curv1Filter,multipleFilterResult-method | Drawing filter regions
glpolygon,curv2Filter,ANY-method | Drawing filter regions
glpolygon,curv2Filter,flowFrame-method | Drawing filter regions
glpolygon,curv2Filter,multipleFilterResult-method | Drawing filter regions
glpolygon,ellipsoidGate,character-method | Drawing filter regions
glpolygon,ellipsoidGate,filterResult-method | Drawing filter regions
glpolygon,ellipsoidGate,flowFrame-method | Drawing filter regions
glpolygon,filter,missing-method | Drawing filter regions
glpolygon,filterResult,ANY-method | Drawing filter regions
glpolygon,filterResult,flowFrame-method | Drawing filter regions
glpolygon,filterResult,missing-method | Drawing filter regions
glpolygon,kmeansFilter,ANY-method | Drawing filter regions
glpolygon,norm2Filter,ANY-method | Drawing filter regions
glpolygon,norm2Filter,flowFrame-method | Drawing filter regions
glpolygon,norm2Filter,logicalFilterResult-method | Drawing filter regions
glpolygon,polygonGate,character-method | Drawing filter regions
glpolygon,polygonGate,filterResult-method | Drawing filter regions
glpolygon,polygonGate,flowFrame-method | Drawing filter regions
glpolygon,quadGate,character-method | Drawing filter regions
glpolygon,quadGate,filterResult-method | Drawing filter regions
glpolygon,quadGate,flowFrame-method | Drawing filter regions
glpolygon,rectangleGate,character-method | Drawing filter regions
glpolygon,rectangleGate,filterResult-method | Drawing filter regions
glpolygon,rectangleGate,flowFrame-method | Drawing filter regions
glpolygon,subsetFilter,ANY-method | Drawing filter regions
glpolygon-methods | Drawing filter regions
gpoints | Adding points within a gate to a plot
gpoints,curv1Filter,flowFrame,character-method | Adding points within a gate to a plot
gpoints,curv2Filter,flowFrame,character-method | Adding points within a gate to a plot
gpoints,filter,flowFrame,missing-method | Adding points within a gate to a plot
gpoints,filter,missing,ANY-method | Adding points within a gate to a plot
gpoints,filterResult,flowFrame,character-method | Adding points within a gate to a plot
gpoints,kmeansFilter,flowFrame,character-method | Adding points within a gate to a plot
gpoints,norm2Filter,flowFrame,character-method | Adding points within a gate to a plot
gpoints,polygonGate,flowFrame,character-method | Adding points within a gate to a plot
gpoints,quadGate,flowFrame,character-method | Adding points within a gate to a plot
gpoints,rectangleGate,flowFrame,character-method | Adding points within a gate to a plot
gpoints-methods | Adding points within a gate to a plot
gpolygon | Drawing filter regions
gpolygon,curv1Filter,ANY-method | Drawing filter regions
gpolygon,curv1Filter,flowFrame-method | Drawing filter regions
gpolygon,curv1Filter,missing-method | Drawing filter regions
gpolygon,curv1Filter,multipleFilterResult-method | Drawing filter regions
gpolygon,curv2Filter,ANY-method | Drawing filter regions
gpolygon,curv2Filter,flowFrame-method | Drawing filter regions
gpolygon,curv2Filter,multipleFilterResult-method | Drawing filter regions
gpolygon,ellipsoidGate,character-method | Drawing filter regions
gpolygon,ellipsoidGate,filterResult-method | Drawing filter regions
gpolygon,ellipsoidGate,flowFrame-method | Drawing filter regions
gpolygon,filter,missing-method | Drawing filter regions
gpolygon,filterResult,ANY-method | Drawing filter regions
gpolygon,filterResult,flowFrame-method | Drawing filter regions
gpolygon,kmeansFilter,ANY-method | Drawing filter regions
gpolygon,norm2Filter,ANY-method | Drawing filter regions
gpolygon,norm2Filter,flowFrame-method | Drawing filter regions
gpolygon,norm2Filter,logicalFilterResult-method | Drawing filter regions
gpolygon,polygonGate,character-method | Drawing filter regions
gpolygon,polygonGate,filterResult-method | Drawing filter regions
gpolygon,polygonGate,flowFrame-method | Drawing filter regions
gpolygon,quadGate,character-method | Drawing filter regions
gpolygon,quadGate,filterResult-method | Drawing filter regions
gpolygon,quadGate,flowFrame-method | Drawing filter regions
gpolygon,rectangleGate,character-method | Drawing filter regions
gpolygon,rectangleGate,filterResult-method | Drawing filter regions
gpolygon,rectangleGate,flowFrame-method | Drawing filter regions
gpolygon-methods | Drawing filter regions

## -- H --

hexbin | Fast hexagon binning.

## -- L --

levelplot | Methods implementing Lattice displays for flow data
levelplot,formula,flowSet-method | Methods implementing Lattice displays for flow data

## -- P --

panel.densityplot.flowset | One-dimensional density plots for flow data
panel.ecdfplot.flowset | Method implementing Lattice ECDF plots for flow data
panel.splom.flowframe | Method implementing Lattice scatter plot matrices for flow data.
panel.xyplot.flowframe | Methods implementing Lattice xyplots for flow data.
panel.xyplot.flowset | Methods implementing Lattice xyplots for flow data.
parallel | Methods implementing Lattice displays for flow data
parallel,flowFrame,missing-method | Methods implementing Lattice displays for flow data
parallel,formula,flowSet-method | Methods implementing Lattice displays for flow data
plot | Very basic plotting of flowFrames
plot,flowFrame,ANY-method | Very basic plotting of flowFrames
plot,flowFrame,character-method | Very basic plotting of flowFrames
plot,flowFrame,missing-method | Very basic plotting of flowFrames
plot-methods | Very basic plotting of flowFrames
prepanel.densityplot.flowset | One-dimensional density plots for flow data
prepanel.ecdfplot.flowset | Method implementing Lattice ECDF plots for flow data
prepanel.xyplot.flowframe | Methods implementing Lattice xyplots for flow data.
prepanel.xyplot.flowset | Methods implementing Lattice xyplots for flow data.

## -- Q --

qqmath | Methods implementing Lattice displays for flow data
qqmath,formula,flowSet-method | Methods implementing Lattice displays for flow data

## -- S --

splom | Method implementing Lattice scatter plot matrices for flow data.
splom,flowFrame,missing-method | Method implementing Lattice scatter plot matrices for flow data.

## -- T --

timeLinePlot | Plot channel values against time
timeLinePlot,ANY,missing-method | Plot channel values against time
timeLinePlot,flowFrame,character-method | Plot channel values against time
timeLinePlot,flowSet,character-method | Plot channel values against time
timeLinePlot-methods | Plot channel values against time

## -- X --

xyplot | Methods implementing Lattice xyplots for flow data.
xyplot,flowFrame,missing-method | Methods implementing Lattice xyplots for flow data.
xyplot,formula,flowFrame-method | Methods implementing Lattice xyplots for flow data.
xyplot,formula,flowSet-method | Methods implementing Lattice xyplots for flow data.
xyplot,formula,gateView-method | Methods implementing Lattice xyplots for flow data.
xyplot,formula,view-method | Methods implementing Lattice xyplots for flow data.
xyplot,view,missing-method | Methods implementing Lattice xyplots for flow data.