Visualize Cytometry data with ggplot


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Documentation for package ‘ggcyto’ version 1.8.2

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%+%-method replace current cytometry data
+-method overloaded '+' method for ggcyto.gs
+-method overloaded '+' method for ggcyto
+-method overloaded '+' method for ggcyto_gate_layout
+.ggcyto_flowSet overloaded '+' method for ggcyto
+.ggcyto_GatingLayout overloaded '+' method for ggcyto_gate_layout
+.ggcyto_GatingSet overloaded '+' method for ggcyto.gs
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.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)
compute_stats compute the statistics of the cell population defined by gates
flowCore_asinht_trans Inverse hyperbolic sine transformation(flowCore version).
fortify 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.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.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
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_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.flowSet Create a new ggcyto plot from a flowSet
ggcyto.GatingHierarchy Create a new ggcyto plot from a GatingSet
ggcyto.GatingSet Create a new ggcyto plot from a GatingSet
ggcyto.GatingSetList Create a new ggcyto plot from a GatingSet
ggcyto.ncdfFlowList Create a new ggcyto plot from a flowSet
ggcyto_arrange Arrange a list of ggplot objects into gtable
ggcyto_par_default Return The default ggcyto settings
ggcyto_par_set Set some default parameters for ggcyto
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
labs_cyto Change axis labels and legend titles
marginalFilter Generate a marginal gate.
merge.quad.gates extend the original flowWorkspace:::.mergeGates function to restore quadGate when applicable
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
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_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_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
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.
transform-method transform methods for gates
transform_gate transform methods for gates
transform_gate.ellipsoidGate transform methods for gates
transform_gate.polygonGate transform methods for gates
transform_gate.quadGate transform methods for gates
transform_gate.rectangleGate transform methods for gates