Function reference • openCyto

The gatingTemplate class The gatingTemplate class represents a gating strategy to be applied to a GatingSet, including specifications for automated gating methods and names for resulting subpopulations
`gatingTemplate()`	a class storing the gating method and population information in a graphNEL object
`gt_gating()`	Applies a gatingTemplate to a GatingSet.
`gt_get_nodes()`	get nodes from gatingTemplate object
`gt_get_gate()`	get gating method from the node
`gt_get_children()`	get children nodes
`gt_get_parent()`	get parent nodes
`gt_toggle_helpergates()` `gt_get_helpergates()` `gt_delete_helpergates()`	toggle/delete the hidden flag of the helper gates
`as.data.table(<gatingTemplate>)`	convert a gatingTemplate object to a data.table
Data-driven methods for generating gates (auto-gating) Use the expression data from a flowFrame to determine gate boundaries and generate gate objects
`gate_flowclust_1d()`	Applies flowClust to 1 feature to determine a cutpoint between the minimum cluster and all other clusters.
`gate_flowclust_2d()`	Automatic identification of a population of interest via flowClust based on two markers
`prior_flowclust()`	Elicits data-driven priors from a flowSet object for specified channels
`gate_mindensity()`	Determines a cutpoint as the minimum point of a kernel density estimate between two peaks
`gate_mindensity2()`	An improved version of mindensity used to determines a cutpoint as the minimum point of a kernel density estimate between two peaks.
`gate_quad_sequential()`	sequential quadrant gating function
`gate_quad_tmix()`	quadGate based on flowClust::tmixFiler
`gate_quantile()`	Determine the cutpoint by the events quantile.
`gate_tail()` `.cytokine_cutpoint()`	Gates the tail of a density using the derivative of a kernel density estimate
`tautstring()` `gate_tautstring()`	Taut String Density Estimator Gating
Building a gatingTemplate interactively Interactively apply gating methods sequentially as if they were in a gatingTemplate or generate a gatingTemplate based on gating that has already been performed
`gs_add_gating_method()`	apply a gating method to the `GatingSet`
`gs_remove_gating_method()`	Reverse the action of gating methods applied via `gs_add_gating_method`
`gs_add_gating_method_init()`	Clear history of `gs_add_gating_method` calls for a given `GatingSet` or `GatingSetList`
`gh_generate_template()`	generate a partially complete csv template from the existing gating hierarchy
Adding more gating methods Register additional gating methods for use in the openCyto framework
`register_plugins()`	Register a gating or preprocessing function with OpenCyto
`gt_list_methods()`	Print a list of the registered gating methods
Visualizing gatingTemplates and flowClust results
`plot(<gatingTemplate>,<missing>)`	plot the gating scheme
`plot(<fcTree>,<character>)`	plot the flowClust gating results
`plot(<fcFilterList>,<ANY>)`	plot a `fcFilterList`

Reference

The gatingTemplate class

Data-driven methods for generating gates (auto-gating)

Building a gatingTemplate interactively

Adding more gating methods

Visualizing gatingTemplates and flowClust results