gate_extract: Extract Saved Gate(s) from gatingTemplate.

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

Description

Extract Saved Gate(s) from gatingTemplate.

Usage

gate_extract(parent, alias, gatingTemplate)

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.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoRSuiteData)

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

# Load in samples
fs <- Activation
gs <- GatingSet(fs)

# Apply compensation
gs <- compensate(gs, fs[[1]]@description$SPILL)

# Transform fluorescent channels
trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
gs <- transform(gs, trans)

# Gate using gate_draw
gt <- Activation_gatingTemplate
gating(gt, gs)

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

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

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

DillonHammill/cytoSuite documentation built on March 7, 2019, 10:09 a.m.