CytoExploreR implementation of flowWorkspace asinh_Gml2 transformation which always returns a transformerList object and displays the result of the transformation(s) using cyto_plot. To combine different types of transformations have a look at cyto_transformer_combine. cyto_transform should be used to apply the transformations to the data.

# S3 method for GatingSet
cyto_transformer_arcsinh(
  x,
  channels = NULL,
  parent = "root",
  select = NULL,
  plot = TRUE,
  popup = FALSE,
  display = 25000,
  axes_limits = "machine",
  ...
)

# S3 method for GatingHierarchy
cyto_transformer_arcsinh(
  x,
  channels = NULL,
  parent = "root",
  select = NULL,
  plot = TRUE,
  popup = FALSE,
  display = 25000,
  axes_limits = "machine",
  ...
)

# S3 method for flowSet
cyto_transformer_arcsinh(
  x,
  channels = NULL,
  parent = "root",
  select = NULL,
  plot = TRUE,
  popup = FALSE,
  display = 25000,
  axes_limits = "machine",
  ...
)

# S3 method for flowFrame
cyto_transformer_arcsinh(
  x,
  channels = NULL,
  parent = "root",
  select = NULL,
  plot = TRUE,
  popup = FALSE,
  display = 25000,
  axes_limits = "machine",
  ...
)

Arguments

x

an object of class flowFrame, flowSet, GatingHierarchy or GatingSet.

channels

name(s) of channel(s)/marker(s) for which transformation functions must be generated. Set to all the fluorescent channels by default if no channels/markers are supplied.

parent

name of the parent population to use for generating the transformation(s).

select

list of selection criteria passed to cyto_select to select a subset of samples for cyto_plot.

plot

logical indicating whether the results of transformations should be plotted using cyto_plot.

popup

logical indicating whether the plots should be constructed in a pop-up window.

display

number or frequency of events to display in plots, set to 25000 events by default. See cyto_plot for details.

axes_limits

options include "auto", "data" or "machine" to use optimised, data or machine limits respectively. Set to "machine" by default to use entire axes ranges. Fine control over axes limits can be obtained by altering the xlim and ylim arguments.

...

additional arguments passed to asinh_Gml2 and cyto_plot.

Value

a transformerList object.

See also

Author

Dillon Hammill, Dillon.Hammill@anu.edu.au