View source: R/cyto_plot_gating_tree.R
cyto_plot_gating_tree | R Documentation |
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 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, ...)
x |
object of class |
stat |
used in |
... |
not in use. |
Dillon Hammill (Dillon.Hammill@anu.edu.au)
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")
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