cyto_gatingTemplate_apply: Apply gates saved in gatingTemplate to a GatingHierarchy or...

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Apply gates saved in gatingTemplate to a GatingHierarchy or GatingSet

Description

A convenient wrapper for gatingTemplate and gt_gating to apply a gatingTemplate csv file to a GatingSet.

Usage

cyto_gatingTemplate_apply(x, gatingTemplate = NULL, ...)

Arguments

x	object of class GatingHierarchy or GatingSet.
gatingTemplate	name of the gatingTemplate csv file which contains the gates to be applied to x. This can alos be an object of class gatingTemplate if a GatingSet object is supplied.
...	additional arguments passed to gating.

Value

NULL and update the GatingHierarchy/ GatingSet in the global environment with the gates in the gatingTemplate.

Examples

## Not run: 
library(CytoExploreRData)

# 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(fs))
gs <- transform(gs, trans)

# Apply gatingTemplate in working directory to GatingSet
cyto_gatingTemplate_apply(gs, "gatingTemplate.csv")

## End(Not run)

DillonHammill/CytoExploreR documentation built on June 8, 2025, 3:05 a.m.