Extract Saved Gate(s) from gatingTemplate.

Extract Saved Gate(s) from gatingTemplate.

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

Dillon Hammill, Dillon.Hammill@anu.edu.au

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)
#> Preprocessing for 'Cells'
#> Gating for 'Cells'
#> done!
#> done.
#> Preprocessing for 'Single Cells'
#> Gating for 'Single Cells'
#> done!
#> done.
#> Preprocessing for 'Dead Cells'
#> Gating for 'Dead Cells'
#> done!
#> done.
#> Live Cells gating...
#> done!
#> done.
#> Preprocessing for 'T Cells'
#> Gating for 'T Cells'
#> done!
#> done.
#> Preprocessing for 'CD8 T Cells'
#> Gating for 'CD8 T Cells'
#> done!
#> done.
#> Preprocessing for 'CD69+ CD8 T Cells'
#> Gating for 'CD69+ CD8 T Cells'
#> done!
#> done.
#> Preprocessing for 'CD4 T Cells'
#> Gating for 'CD4 T Cells'
#> done!
#> done.
#> Preprocessing for 'CD69+ CD4 T Cells'
#> Gating for 'CD69+ CD4 T Cells'
#> done!
#> done.
#> Preprocessing for 'Dendritic Cells'
#> Gating for 'Dendritic Cells'
#> done!
#> done.
#> finished.

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

# Extract T Cells gate
cyto_gate_extract("Live Cells", "T Cells", gatingTemplate = gtfile)
#> [[1]]
#> A list of 1 filters applied to a flowFrame.
#> 

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