Visualize Cytometry data with ggplot

Documentation for package ‘ggcyto’ version 1.32.0

Help Pages

-- 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