Plot Gating Trees

cyto_plot_gating_tree provides a simpler visualisation of the gating scheme for GatingHierarchy, GatingSet and gatingTemplate objects. The GatingHierachy method is also capable of displaying population statistics such as frequency of parent or count.

# S3 method for GatingHierarchy
cyto_plot_gating_tree(x, stat = NULL, ...)

# S3 method for GatingSet
cyto_plot_gating_tree(x, ...)

# S3 method for gatingTemplate
cyto_plot_gating_tree(x, ...)

Arguments

x	object of class GatingHierarchy, GatingSet or gatingTemplate.
stat	used in GatingHierachy method to add either "percent" or "count" statistics onto the gating tree, set to NULL by default to exclude statistics.
...	not in use.

Author

Dillon Hammill (Dillon.Hammill@anu.edu.au)

Examples

library(CytoExploreRData)

# Load in samples
fs <- Activation

# Add samples to GatingSet
gs <- GatingSet(fs)

# Apply compensation
gs <- cyto_compensate(gs)

# Transform fluorescent channels
gs <- cyto_transform(gs, select = "Stim-D", trans_type = "logicle")

# Gating
gt <- Activation_gatingTemplate
cyto_gatingTemplate_apply(gs, gt)
#> 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.
#> A GatingSet with 33 samples

# Visualise gating tree using gatingTemplate
cyto_plot_gating_tree(gt)

# Visualise gating tree for GatingSet (same output as gatingTemplate)
cyto_plot_gating_tree(gs)

# Visualise gating tree for GatingHierarchy
cyto_plot_gating_tree(gs[[32]], stat = "percent")
cyto_plot_gating_tree(gs[[32]], stat = "count")