Function reference • CytoExploreR

All functions
`cyto_apply()`	Apply a function over cytometry objects
`cyto_barcode()`	Barcode each file in a flowSet with a sample ID
`cyto_beads_sample()`	Sample GatingSet to bead count
`cyto_calibrate()`	Calibrate channel ranges for cyto_plot
`cyto_calibrate_reset()`	Remove current calibration settings
`cyto_channels()`	Extract channel names
`cyto_channels_extract()`	Extract channels associated with certain markers
`cyto_channels_restrict(<flowFrame>)` `cyto_channels_restrict(<flowSet>)` `cyto_channels_restrict(<GatingSet>)`	Restrict the channels of a cytometry object
`cyto_channel_match()`	Table Editor for Channel Match File Construction
`cyto_channel_select()`	Select Fluorescent Channel for Compensation Controls
`cyto_check()`	Check a flowFrame, flowSet, GatingHierarchy or GatingSet has been supplied
`cyto_clean()`	Apply flowAI anomaly detection to clean cytometry data
`cyto_compensate()`	Apply fluorescence compensation to samples
`cyto_convert()`	Convert between cytometry objects
`cyto_copy()`	Copy a cytoset, cytoframe or GatingSet
`cyto_details()`	Extract experiment details
`cyto_details_edit()`	Interactively edit cyto_details for a flowSet or GatingSet
`cyto_details_save()`	Save experiment details to csv file
`cyto_empty()`	Construct an empty flowFrame
`cyto_export()`	Export cytometry data for use in flowJo or Cytobank
`cyto_extract()`	Extract a valid flowFrame or flowSet
`cyto_filter()`	Filter samples based on experiment variables
`cyto_fluor_channels()`	Extract Fluorescent Channels
`cyto_gate_bool()`	Add boolean gate to GatingSet and gatingTemplate
`cyto_gate_convert(<rectangleGate>)` `cyto_gate_convert(<polygonGate>)` `cyto_gate_convert(<ellipsoidGate>)` `cyto_gate_convert(<quadGate>)` `cyto_gate_convert(<filters>)` `cyto_gate_convert(<list>)` `cyto_gate_prepare()`	Convert Between 1D and 2D Gate Objects
`cyto_gate_copy()`	Copy gates to other nodes in GatingSet and update gatingTemplate
`cyto_gate_draw(<GatingSet>)` `cyto_gate_draw(<flowSet>)` `cyto_gate_draw(<flowFrame>)`	Interactively draw and construct gate objects
`cyto_gate_edit()`	Edit Existing Gate(s).
`cyto_gate_extract()`	Extract Saved Gate(s) from gatingTemplate.
`cyto_gate_remove()`	Remove Gate(s) and Edit gatingTemplate csv File
`cyto_gate_rename()`	Rename Gates
`cyto_gate_transform(<rectangleGate>)` `cyto_gate_transform(<polygonGate>)` `cyto_gate_transform(<ellipsoidGate>)` `cyto_gate_transform(<quadGate>)` `cyto_gate_transform(<filters>)` `cyto_gate_transform(<list>)`	Transform gates objects
`cyto_gate_type()`	Get Gate Type from Saved Gate.
`cyto_gatingTemplate_active()`	Active gatingTemplate
`cyto_gatingTemplate_apply()`	Apply gates saved in gatingTemplate to a GatingHierarchy or GatingSet
`cyto_gatingTemplate_create()`	Create an empty gatingTemplate csv file
`cyto_gatingTemplate_edit()`	Interactively Edit a gatingTemplate
`cyto_gatingTemplate_generate(<GatingHierarchy>)` `cyto_gatingTemplate_generate(<GatingSet>)`	Generate a CytoExploreR gatingTemplate for a GatingHierarchy or GatingSet
`cyto_gatingTemplate_read()`	Read in a gatingTemplate object or gatingTemplate csv file
`cyto_gatingTemplate_select()`	Select a gatingTemplate for downstream analyses
`cyto_gatingTemplate_update()`	Convert CytoRSuite gatingTemplate to be compatible with CytoExoloreR
`cyto_gatingTemplate_write()`	Write gatingTemplate to csv file
`cyto_group_by()`	Group a flowSet or GatingSet by experiment variables
`cyto_load()`	Load .fcs files into ncdfFlowSet
`cyto_map()`	Create dimension-reduced maps of cytometry data
`cyto_markers(<GatingSet>)` `cyto_markers(<GatingHierarchy>)` `cyto_markers(<flowSet>)` `cyto_markers(<flowFrame>)`	Extract marker names
`cyto_markers_edit()`	Assign marker names to flowFrame or flowSet
`cyto_markers_extract()`	Extract marker names for certain channels
`cyto_merge_by(<GatingSet>)` `cyto_merge_by(<flowSet>)`	Merge a flowSet by experiment variables
`cyto_names<-`()	Replacement method for cyto_names
`cyto_names()`	Extract sample names
`cyto_names_parse()`	Parse file names into experiment details
`cyto_nodes()`	Extract Names of Gated Populations in GatingHierarchy or GatingSet
`cyto_nodes_ancestor()`	Get name of most recent common ancestor shared by nodes
`cyto_nodes_convert()`	Convert to unique node paths
`cyto_plot(<GatingSet>)` `cyto_plot(<GatingHierarchy>)` `cyto_plot(<flowSet>)` `cyto_plot(<flowFrame>)`	cyto_plot
`cyto_plot_compensation(<GatingSet>)` `cyto_plot_compensation(<GatingHierarchy>)` `cyto_plot_compensation(<flowSet>)` `cyto_plot_compensation(<flowFrame>)`	Visualise Compensation of Fluorescent Spillover in All Fluorescent Channels
`cyto_plot_complete()`	Indicate Completion of Custom cyto_plot Layout for Saving
`cyto_plot_contour()`	Add contour lines to cyto_plot
`cyto_plot_custom()`	Create custom cyto_plot
`cyto_plot_density()`	Add density distributions to empty plots
`cyto_plot_empty()`	Create an empty cyto_plot
`cyto_plot_explore(<GatingSet>)` `cyto_plot_explore(<GatingHierarchy>)` `cyto_plot_explore(<flowSet>)` `cyto_plot_explore(<flowFrame>)`	Explore Cytometry Data in Bivariate Plots
`cyto_plot_gate(<default>)` `cyto_plot_gate(<rectangleGate>)` `cyto_plot_gate(<polygonGate>)` `cyto_plot_gate(<ellipsoidGate>)` `cyto_plot_gate(<quadGate>)` `cyto_plot_gate(<filters>)` `cyto_plot_gate(<list>)`	Plot Gate Objects onto an Existing cyto_plot
`cyto_plot_gating_scheme(<GatingSet>)` `cyto_plot_gating_scheme(<GatingHierarchy>)`	Plot Cytometry Gating Strategies
`cyto_plot_gating_tree(<GatingHierarchy>)` `cyto_plot_gating_tree(<GatingSet>)` `cyto_plot_gating_tree(<gatingTemplate>)`	Plot Gating Trees
`cyto_plot_label(<GatingHierarchy>)` `cyto_plot_label(<flowFrame>)`	Add labels to cyto_plot
`cyto_plot_labeller()`	Add labels to existing cyto_plot
`cyto_plot_layout()`	Set Panel Layout for cyto_plot
`cyto_plot_new()`	Open new graphics device for cyto_plot
`cyto_plot_point()`	Add points and contour lines to empty cyto_plot
`cyto_plot_profile(<GatingSet>)` `cyto_plot_profile(<GatingHierarchy>)` `cyto_plot_profile(<flowSet>)` `cyto_plot_profile(<flowFrame>)`	Plot expression profile in all channels
`cyto_plot_record()`	Record an existing cyto_plot
`cyto_plot_reset()`	Reset all cyto_plot related settings
`cyto_plot_save()`	Save High Resolution cyto_plot Images
`cyto_plot_save_reset()`	Revert unwanted cyto_plot_save call
`cyto_plot_theme()`	Create custom themes for cyto_plot
`cyto_plot_theme_args()`	Get supported cyto_plot_theme arguments
`cyto_plot_theme_reset()`	Reset cyto_plot_theme to default settings
`cyto_sample()`	Sample a flowFrame or flowSet
`cyto_save()`	Write samples to FCS files in new folder or save GatingSet
`cyto_select()`	Select samples based on experiment variables
`cyto_setup()`	Load.fcs files into GatingSet and annotate with experiment details
`cyto_spillover_compute()`	Compute Spillover Matrix
`cyto_spillover_edit(<GatingSet>)` `cyto_spillover_edit(<flowSet>)`	Interactively Edit Spillover Matrices in Real-Time
`cyto_spillover_extract()`	Extract spillover matrix from cytometry object
`cyto_spillover_spread_compute()`	Compute Spillover Spreading Matrix
`cyto_split()`	Split samples merged with cyto_merge
`cyto_stats_compute(<GatingSet>)` `cyto_stats_compute(<GatingHierarchy>)` `cyto_stats_compute(<flowSet>)` `cyto_stats_compute(<flowFrame>)`	Compute, export and save statistics
`cyto_transform()`	Apply Transformations to Cytometry Data
`cyto_transformer_arcsinh(<GatingSet>)` `cyto_transformer_arcsinh(<GatingHierarchy>)` `cyto_transformer_arcsinh(<flowSet>)` `cyto_transformer_arcsinh(<flowFrame>)`	Definition(s) of arcsinh transformation(s)
`cyto_transformer_biex(<GatingSet>)` `cyto_transformer_biex(<GatingHierarchy>)` `cyto_transformer_biex(<flowSet>)` `cyto_transformer_biex(<flowFrame>)`	Definition(s) of biexponential transformation(s)
`cyto_transformer_combine()`	Combine cyto_transformer definitions
`cyto_transformer_extract()`	Extract transformers from a GatingHierarchy or GatingSet
`cyto_transformer_log(<GatingSet>)` `cyto_transformer_log(<GatingHierarchy>)` `cyto_transformer_log(<flowSet>)` `cyto_transformer_log(<flowFrame>)`	Definition(s) of Log Transformation(s)
`cyto_transformer_logicle(<GatingSet>)` `cyto_transformer_logicle(<GatingHierarchy>)` `cyto_transformer_logicle(<flowSet>)` `cyto_transformer_logicle(<flowFrame>)`	Definition(s) of logicle transformation(s)
`cyto_transform_extract()`	Extract Transformations from TransformerList
`data_editor()`	Interactive data editor
`fftRtsne()`	FIt-SNE Based on Kluger Lab FIt-SNE
`file_wd_check()`	Check if a file exists in the current working directory

Reference

All functions