cyto_gate_extract: Extract Saved Gate(s) from gatingTemplate.

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Extract Saved Gate(s) from gatingTemplate.

Description

Extract Saved Gate(s) from gatingTemplate.

Usage

cyto_gate_extract(parent, alias, gatingTemplate = NULL, ...)

Arguments

parent	name of the parental population.
alias	name of the population for which the gate must be extracted.
gatingTemplate	name of the gatingTemplate csv file (e.g. "gatingTemplate.csv") where the gate(s) are saved.
...	not used.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoExploreRData)

# Bypass working directory check for external files
options("CytoExploreR_wd_check" = FALSE)

# 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)

# gatingTemplate
gtfile <- system.file("extdata",
  "Activation-gatingTemplate.csv",
  package = "CytoExploreRData"
)

# Extract T Cells gate
cyto_gate_extract("Live Cells", "T Cells", gatingTemplate = gtfile)

# Reset CytoExploreR_wd_check to default
options("CytoExploreR_wd_check" = TRUE)

DillonHammill/CytoExploreR documentation built on March 2, 2023, 7:34 a.m.