gs_apply_gating_strategy: Sequentially apply a manual gating strategy to a GatingSet or...

In NKInstinct/gater: Interactive Cytometry Gating in R

Sequentially apply a manual gating strategy to a GatingSet or list

Description

This function allows for a "semi-automatic" approach to interactive manual gating of flow cytometry data. It leverages the purrr package to let you easily define a gating strategy and then apply it sequentially to a GatingSet. This will call gs_gate_interactive() once for each line in your gating strategy, applying it to your GatingSet as soon as you draw each prompted gate.

Usage

gs_apply_gating_strategy(gs, gating_strategy, ...)

Arguments

gs	A GatingSet or list of GatingSets.
gating_strategy	A tibble-formatted gating strategy (see examples below)
...	Other parameters to pass to gs_gate_interactive(). Note that only constant parameters should be supplied here—anything that varies should be included in the gating_strategy tibble.

Details

The gating strategy should be a tibble, with each column name corresponding to one parameter from gs_gate_interactive. Any parameters not specified in this tibble will either use their defaults from gs_gate_interactive or can be specified directly in the function call to gs_apply_gating_strategy. Typically, this gating strategy will have a column for 'filterId', 'dims', 'subset', and 'coords', but techinicaly only filterId is required. See examples below for an easy way to construct this strategy using tribble().

Value

the GatingSet or list of GatingSets with the gates in gating_strategy applied as specified.

Examples

fs <- flowCore::read.flowSet(
  path = system.file("extdata", package = "flowGate"), pattern = ".FCS$")

gs <- flowWorkspace::GatingSet(fs)

# Note - this is a very rudamentary GatingSet for example purposes only. 
# Please see the vignette accompanying this package or the flowWorkspace
# documentation # for a complete look at creating a GatingSet.

gating_strategy <- tibble::tribble(
~filterId,      ~dims,                       ~subset,        ~coords,
"Lymphocytes", list("FSC-H", "SSC-H"),       "root",         list(c(0, 3e5), c(0, 3e5)),
"CD45 CD15",   list("CD45 PE", "CD15 FITC"), "Lymphocytes",  list(c(0, 3e5), c(0, 2e5)),
)


if(interactive()){
gs_apply_gating_strategy(gs,
gating_strategy = gating_strategy,
bins = 512) # note that extra args for gs_gate_interactive can be supplied.
}

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