cyto_transformer_logicle: Definition(s) of logicle transformation(s)

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Definition(s) of logicle transformation(s)

Description

CytoExploreR implementation of flowCore logicle transformation which allows the use of multiple samples to estimate transformation parameters, 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.

Usage

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

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

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

## S3 method for class 'flowFrame'
cyto_transformer_logicle(
  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 estimateLogicle and cyto_plot.

Value

a transformerList object.

Author(s)

Dillon Hammill, [e-mail]

See Also

estimateLogicle

estimateLogicle

cyto_transformer_arcsinh

cyto_transformer_biex

cyto_transformer_combine

cyto_transform

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