cyto_plot_gating_tree: Plot Gating Trees

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Plot Gating Trees

Description

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.

Usage

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

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

## S3 method for class '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(s)

Dillon Hammill ([e-mail])

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)

# 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")

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