Man pages for VoisinneG/flowR
R-shiny interface for the analysis of flow cytometry data
| add_columns_from_metadata | Add metadata columns |
| add_gate | Add a gate layer to plot |
| add_gates_flowCore | Add gates from a gating hierarchy to a GatingSet |
| add_gate_to_plot | Add a gate layer to plot |
| asinh_trans | Scaled hyperbolic arc-sine transformation |
| asinh_transform | Scaled hyperbolic arc-sine function |
| build_flowset_from_df | Build a flowSet from a data.frame |
| call_plot_function | Generates a plot from data |
| ClusteringUI | Automatic cluster identification |
| CompensationUI | Visualize, import, export and edit compensation matrices... |
| ComputeSpillUI | Compute spillover matrix |
| copy_gate | Copy a gate and its children as children of another parent... |
| dim_reduction | Perform dimensionality reduction |
| Dim_reductionUI | Perform dimensionality reduction using t-SNE or UMAP |
| ellipse_path | Return coordinates of points along an ellipse defined by its... |
| exampleModuleUI | exampleModuleUI and exampleModule |
| find_all_parent_gates | find, in a recursive manner, all parent gates of a given Gate... |
| flowR_server | flowR app main server function |
| flowR_ui | flowR app main ui function |
| format_info | Suppresses the function name from its description as returned... |
| format_plot | Format a ggplot object |
| GatingSetsUI | Manage and visualize GatingSets and their hierarchy |
| GatingUI | Edit, visualize and show statistics from a gating hierarchy |
| get_all_ancestors | Return all ancestors from a set of nodes in a tree |
| get_all_descendants | Return all descendants from a set of nodes in a tree |
| get_cluster | Identify clusters |
| get_data_gs | Return data from a GatingSet |
| get_gate_coordinates | Return coordinates of flowCore gate. |
| get_gates_from_gs | Build a gating hierarchy from a GatingSet |
| get_gates_from_ws | Extract all gates from a FlowJO workspace |
| get_gates_from_ws_diva | Extract all gates from a Diva xml workspace |
| get_groups_from_ws | Return the names of all 'groups' from a FlowJO workspace |
| get_package_functions_info | get description of package's functions |
| get_parameters_gs | Get parameters from a GatingSet |
| get_plot_data | Return data used for plotting a GatingSet |
| get_plot_data_range | Get data ranges from a plot |
| getPopStatsPlus | Return statistics for all subsets ans samples in a GatingSet |
| get_spillover_matrices_from_ws | Extract spillover matrices from a FlowJO workspace |
| get_spillover_matrices_from_ws_diva | Extract spillover matrices from a Diva xml workspace |
| get_templates_from_ws_diva | Return the names of all 'templates' from a Diva xml workspace |
| gh_get_gate_names | Get all gate names from a GatingHierarchy |
| gs_get_fs_subset | Return a flowSet from a given subset in a GatingSet |
| ImportSpillUI | Import spillover matrix |
| ImportUI | Import data and build a GatingSet |
| MetadataUI | Import, export and edit metadata associated with a GatingSet |
| ModulesUI | Search, select and load modules |
| parseCompensationDiva | Return the spillover coefficients associated with a... |
| parseGate | Return relevant info from a Gate xml_node |
| parseGateDiva | Return relevant info from a 'gate' xml_node from a Diva xml... |
| parseGroupNodes | Return the name and IDs of samples in a GroupNode xml_node... |
| parseSampleNodes | Return the name and ID of a SampleNode xml_node from a FlowJO... |
| parseSpillover | Return the spillover coefficients associated with a spillover... |
| parseSpilloverMatrix | Return the spillover matrix associated with a spilloverMatrix... |
| parseSpilloverMatrixDiva | Return the spillover matrix associated with a... |
| parseTemplatesNodesDiva | Return the name of 'template' xml_node from a Diva xml... |
| patternSelectionInput | Select variables based on pattern (or a regular expression) |
| plot_bar | Generates a bar plot |
| plot_contour | Generates a contour plot |
| plotCytoUI | Build plots from a GatingSet |
| plot_dots | Generates a dot plot |
| plot_gate | Plot a gate from a GatingSet |
| plotGatingHierarchy | plotGatingHierarchy |
| plotGatingSetInput | Build plots from a GatingSet |
| plot_gh | Plot all gates for a given sample of a GatingSet |
| plot_gs | Plot a GatingSet |
| plot_gs_ggcyto | Plot a GatingSet |
| plot_heatmap | Generates a heatmap |
| plot_hexagonal | Generates a hexagonal heatmap of 2d bin counts (see... |
| plot_histogram | Generates an histogram or a density plot |
| plot_pca | Perform a PCA and plot the result |
| plot_stat | Plot aggregated data from a GatingSet |
| plotStatInput | plotStatInput and plotStat |
| plotStatUI | plotStat server function |
| plot_tile | Generates a tile plot |
| PlottingUI | Build, display and save plots from a gating set |
| plot_tree | Build a tree graph from a named list |
| run_flowR | Run flowR GUI |
| scale_values | scale column of a data frame |
| selectionInput | Select samples and subsets from a GatingSet |
| simpleDisplayUI | A shiny Module to display and save plots |
| StatsUI | Compute and visualize sample/subset statistics from a... |
| SubsampleUI | Subsample a GatingSet |
| transform_gates | Transform gates coordinates and modify names of parameters. |
| TransformUI | Edit flow parameter transformation and description |
