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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 |