Remove Gate(s) and Edit gatingTemplate csv File

cyto_gate_remove(
  gs,
  parent = NULL,
  alias = NULL,
  channels = NULL,
  type = NULL,
  gatingTemplate = NULL,
  ...
)

Arguments

gs

an object of class GatingSet.

parent

name of the parent population from which to remove the gate. This argument is not necessary but is included to allow conversion of cyto_gate_draw code to cyto_gate_remove code by simply changing "draw" to "remove".

alias

name(s) of the population(s) to remove (e.g. "Single Cells"). By default all descendant populations will be removed as well.

channels

names of the channel(s) used to gate the population. This argument is not necessary but is included to allow conversion of cyto_gate_draw code to cyto_gate_remove code by simply changing "draw" to "remove".

type

gate type(s) used to for the gates to be removed. This argument is not necessary but is included to allow conversion of cyto_gate_draw code to cyto_gate_remove code by simply changing "draw" to "remove".

gatingTemplate

name of the gatingTemplate csv file (e.g. "gatingTemplate.csv").

...

additional cyto_gate_draw arguments that will be ignored.

Value

an object of class GatingSet with gate and children removed and updated gatingTemplate to reflect these changes.

Author

Dillon Hammill, Dillon.Hammill@anu.edu.au

Examples

if (FALSE) { library(CytoExploreRData) # Load in samples fs <- Activation gs <- GatingSet(fs) # Apply compensation gs <- cyto_compensate(gs) # Transform fluorescent channels gs <- cyto_transform(gs) # Gate using cyto_gate_draw gt <- Activation_gatingTemplate gt_gating(gt, gs) # Remove T Cells population - replace gatingTemplate name cyto_gate_remove(gs, "T Cells", gatingTemplate = "gatingTemplate.csv") }