cyto_transform | R Documentation |
Apply Transformations to Cytometry Data
cyto_transform(x, trans = NULL, ...) ## Default S3 method: cyto_transform( x, trans = NULL, type = "logicle", channels = NULL, parent = "root", select = NULL, inverse = FALSE, plot = TRUE, popup = FALSE, axes_limits = "machine", ... ) ## S3 method for class 'transformList' cyto_transform( x, trans = NULL, plot = TRUE, popup = FALSE, axes_limits = "machine", ... ) ## S3 method for class 'transformerList' cyto_transform( x, trans = NULL, inverse = FALSE, plot = TRUE, popup = FALSE, axes_limits = "machine", ... )
x |
object of class |
trans |
object of class
|
... |
additional arguments passed to |
type |
type of transformation to apply when no trans object is supplied,
options include |
channels |
names of the channels to transform, set to all the
fluorescent channels by default. Only required when no |
parent |
name of the parent population of |
select |
list of selection criteria passed to |
inverse |
logical indicating whether the inverse transformations should
be applied. Currently only supported for |
plot |
logical indicating whether the result of the transformations
should be plotted using |
popup |
logical indicating whether plots should be constructed in a popup window, set to FALSE by default. |
axes_limits |
options include |
object of class flowFrame
, flowSet
,
GatingHierarchy
or GatingSet
with transformations applied.
Dillon Hammill, Dillon.Hammill@anu.edu.au
cyto_transformer_log
cyto_transformer_arcsinh
cyto_transformer_biex
cyto_transformer_logicle
cyto_transformer_combine
# Load in CytoExploreRData to access data library(CytoExploreRData) # Activation flowSet fs <- Activation # Automatically transform flowSet fs_trans <- cyto_transform(fs, type = "arcsinh") # Manually construct & apply transformations trans <- cyto_transformer_biex(fs) fs_trans <- cyto_transform(fs, trans) # Add fs to GatingSet gs <- GatingSet(fs) # Automatically transform GatingSet gs_trans <- cyto_transform(gs, type = "logicle") # Manually construct & apply transformations trans <- cyto_transformer_logicle(gs) gs_trans <- cyto_transform(gs, trans)
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