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()

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()

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()

plot the gating scheme

plot()

plot the flowClust gating results

plot()

plot a fcFilterList