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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