# Visualize Cytometry data with ggplot

## Documentation for package ‘ggcyto’ version 1.41.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A C F G I L M P R S T misc

## -- A --

as.ggplot | It fortifies the data, fills some default settings and returns a regular ggplot object.
autoplot | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.cytoframe | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.cytoset | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.flowFrame | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.flowSet | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.GatingHierarchy | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.GatingSet | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.GatingSetList | Plot cytometry data in one or two dimension with the ggcyto package.
autoplot.ncdfFlowList | Plot cytometry data in one or two dimension with the ggcyto package.
axis_x_inverse_trans | Display ggcyto axis labels using their raw values (as stored in the data structure)
axis_y_inverse_trans | Display ggcyto axis labels using their raw values (as stored in the data structure)

## -- C --

compute_stats | compute the statistics of the cell population defined by gates

## -- F --

faust_gating_plot | plot faust gating schemes
flowCore_asinht_trans | Inverse hyperbolic sine transformation(flowCore version).
fortify | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.cytoframe | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.cytoset | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.ellipsoidGate | Convert a ellipsoidGate to a data.table useful for ggplot
fortify.filterList | Convert a filterList to a data.table useful for ggplot
fortify.flowFrame | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.flowSet | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.GatingSet | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.GatingSetList | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.multiRangeGate | Convert a multiRangeGate to a data.table useful for ggplot
fortify.ncdfFlowList | Convert a flowFrame/flowSet/GatingSet to a ggplot-compatible data.table
fortify.polygonGate | Convert a polygonGate to a data.table useful for ggplot
fortify.rectangleGate | Convert a rectangleGate to a data.table useful for ggplot
fortify_fs | Fortify a model into flowSet object
fortify_fs.cytoframe | Fortify a model into flowSet object
fortify_fs.default | Fortify a model into flowSet object
fortify_fs.flowFrame | Fortify a model into flowSet object
fortify_fs.flowSet | Fortify a model into flowSet object
fortify_fs.GatingSet | Fortify a model into flowSet object
fortify_fs.GatingSetList | Fortify a model into flowSet object

## -- G --

gate_null | clear all the geom_gate() layer previously added
geom_gate | Add a gate layer to a ggcyto plot.
geom_gate.character | Add a gate layer to a ggcyto plot.
geom_gate.default | Add a gate layer to a ggcyto plot.
geom_gate.filter | Add a gate layer to a ggcyto plot.
geom_gate.filterList | Add a gate layer to a ggcyto plot.
geom_gate.filters | Add a gate layer to a ggcyto plot.
geom_gate.filtersList | Add a gate layer to a ggcyto plot.
geom_gate.list | Add a gate layer to a ggcyto plot.
geom_gate.logical | Add a gate layer to a ggcyto plot.
geom_gate.logicalFilterResult | Add a gate layer to a ggcyto plot.
geom_gate.quadGate | Add a gate layer to a ggcyto plot.
geom_hvline | Vertical or horizontal line.
geom_multi_range | Draw multi-ranges as multiple rectangles on 1D or 2D plot
geom_overlay | Overlay a population on an existing ggcyto plot analogous to backgating.
geom_overlay.character | Overlay a population on an existing ggcyto plot analogous to backgating.
geom_overlay.default | Overlay a population on an existing ggcyto plot analogous to backgating.
geom_overlay.flowFrame | Overlay a population on an existing ggcyto plot analogous to backgating.
geom_overlay.flowSet | Overlay a population on an existing ggcyto plot analogous to backgating.
geom_overlay.ncdfFlowList | Overlay a population on an existing ggcyto plot analogous to backgating.
geom_stats | Add a popluation statistics layer to a ggcyto plot.
getFlowFrame | extract flowFrame data structure from the given R object
getFlowFrame.flowSet | extract flowFrame data structure from the given R object
getFlowFrame.GatingHierarchy | extract flowFrame data structure from the given R object
getFlowFrame.GatingSet | extract flowFrame data structure from the given R object
getFlowFrame.GatingSetList | extract flowFrame data structure from the given R object
getFlowFrame.ncdfFlowList | extract flowFrame data structure from the given R object
ggcyto | Plot cytometry data using the ggcyto API
ggcyto-class | Plot cytometry data using the ggcyto API
ggcyto.default | Plot cytometry data using the ggcyto API
ggcyto.flowSet | Plot cytometry data using the ggcyto API
ggcyto.GatingHierarchy | Plot cytometry data using the ggcyto API
ggcyto.GatingSet | Plot cytometry data using the ggcyto API
ggcyto.GatingSetList | Plot cytometry data using the ggcyto API
ggcyto_add | overloaded '+' method for ggcyto
ggcyto_arrange | Arrange a list of ggplot objects into gtable
ggcyto_flowSet-class | Plot cytometry data using the ggcyto API
ggcyto_GatingLayout-class | Plot cytometry data using the ggcyto API
ggcyto_GatingSet-class | Plot cytometry data using the ggcyto API
ggcyto_par_default | Return The default ggcyto settings
ggcyto_par_set | Set some default parameters for ggcyto

## -- I --

is.ggcyto | Reports whether x is a ggcyto object
is.ggcyto_flowSet | Reports whether x is a ggcyto_flowSet object
is.ggcyto_par | Reports whether x is a ggcyto_par object

## -- L --

labs_cyto | Change axis labels and legend titles

## -- M --

marginalFilter | Generate a marginal gate.
merge.quad.gates | extend the original flowWorkspace:::.mergeGates function to restore quadGate when applicable

## -- P --

plot.ggcyto | Draw ggcyto on current graphics device.
print-method | Draw ggcyto on current graphics device.
print.ggcyto | Draw ggcyto on current graphics device.
print.ggcyto_GatingLayout | print method for ggcyto_gate_layout class

## -- R --

replace_data | replace current cytometry data
rescale_gate | rescale methods for gates
rescale_gate.ellipsoidGate | rescale methods for gates
rescale_gate.polygonGate | rescale methods for gates
rescale_gate.quadGate | rescale methods for gates
rescale_gate.rectangleGate | rescale methods for gates

## -- S --

scales_flowjo_biexp | Add a flowJo biexponential scale to the x or y axes of a ggcyto plot.
scales_flowjo_fasinh | Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_x_flowCore_fasinh | Add a flowCore inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_x_flowJo_biexp | Add a flowJo biexponential scale to the x or y axes of a ggcyto plot.
scale_x_flowjo_biexp | Add a flowJo biexponential scale to the x or y axes of a ggcyto plot.
scale_x_flowJo_fasinh | Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_x_flowjo_fasinh | Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_x_logicle | Add a logicle scale to the x or y axes of a ggcyto plot.
scale_y_flowCore_fasinh | Add a flowCore inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_y_flowJo_biexp | Add a flowJo biexponential scale to the x or y axes of a ggcyto plot.
scale_y_flowjo_biexp | Add a flowJo biexponential scale to the x or y axes of a ggcyto plot.
scale_y_flowJo_fasinh | Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_y_flowjo_fasinh | Add a flowJo inverse hyperbolic sine scale to the x or y axes of a ggcyto plot.
scale_y_logicle | Add a logicle scale to the x or y axes of a ggcyto plot.
show-method | Draw ggcyto on current graphics device.
show-method | print method for ggcyto_gate_layout class
show.ggcyto | Draw ggcyto on current graphics device.
show.ggcyto_GatingLayout | print method for ggcyto_gate_layout class
stats_null | clear all the geom_stats() layer previously added
stat_position | Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot.
stat_position.filter | Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot.
stat_position.filterList | Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot.
stat_position.list | Compute the positions of the population statistics based on the geometic gate centroid for a ggcyto plot.

## -- T --

transform | rescale methods for gates
transform-gate | rescale methods for gates
transform-method | rescale methods for gates

## -- misc --

%+% | replace current cytometry data
%+%-method | replace current cytometry data
+ | overloaded '+' method for ggcyto
+-method | overloaded '+' method for ggcyto
+.ggcyto_flowSet | overloaded '+' method for ggcyto
+.ggcyto_GatingLayout | overloaded '+' method for ggcyto
+.ggcyto_GatingSet | overloaded '+' method for ggcyto
+.ggcyto_ncdfFlowList | overloaded '+' method for ggcyto