gs_gate_transform_interactive: Interactively adjust a gate from a GatingSet

In NKInstinct/gater: Interactive Cytometry Gating in R

Interactively adjust a gate from a GatingSet

Description

CAUTION: Experimental Function. Still probably has bugs.

Usage

gs_gate_transform_interactive(
  gs,
  node,
  sample = 1,
  dims = list("FSC-A", "SSC-A"),
  overlayGates = NULL
)

Arguments

gs	The GatingSet containing the gate you want to adjust
node	String specifying the (unambiguous) name of the node to adjust
sample	Numeric specifying which sample in the GatingSet to use for example purposes. Note that the adjusted gate will be applied to ALL samples, not just this one.
dims	List of characters specifying channel names or marker names to plot on x and y axis. Defaults to list("FSC-A", "SSC-A") mostly just to make the format clear.
overlayGates	(optional) string or character vector specifying names of gates to draw on the plot but NOT adjust, for ease of adjusting a gate in the vicinity of other gates. Leave NULL to not overlay any gates.

Details

Call gs_gate_transform_interactive to open a small Shiny app to allow for manual, interactive adjustments to gates. Currently only supports rectangleGates and polygonGates.

Value

NULL, but silently deletes the old gate, adds the new one, and recomputes the GatingSet.

Examples

path_to_fcs <- system.file("extdata", package = "flowGate")
fs <- read.flowSet(path = path_to_fcs,
                   pattern = ".FCS$",
                   full.names = TRUE)
gs <- GatingSet(fs)

if(interactive()) { # only run in interactive sessions
gs_gate_interactive(gs,
                    filterId = "Lymphocytes",
                    dims = list("FSC-H", "SSC-H"))
                    
# Adds a lymphocytes gate to the GatingSet (exactly as in gs_gate_interactive)
                    
gs_gate_transform_interactive(gs,
                              filterId = "Lymphocytes", 
                              dims = list("FSC-H", "SSC-H"))
}

# Opens a window to adjust the gate manually

NKInstinct/gater documentation built on March 18, 2023, 12:42 p.m.