Compute Spillover Spreading Matrix

Source: R/cyto_spillover_spread_compute.R

cyto_spillover_spread_compute computes the spillover spreading matrix as described by Nguyen et al. (2013) using gated and compensated compensation controls.

cyto_spillover_spread_compute(
  x,
  parent = NULL,
  axes_trans = NULL,
  channel_match = NULL,
  compensated = FALSE,
  spillover = NULL,
  spillover_spread = NULL,
  axes_limits = "machine",
  ...
)

Arguments

x

object of class flowSet or GatingSet containing compensated, transformed and gated compensation controls.
parent

name of the population to use for downstream calculations when a GatingSet object is supplied, set to the last gated population by default (e.g. "Single Cells").
axes_trans

object of class transformerList generated by a cyto_transformer which contains the transformer definitions to be used internally to transform the fluorescent channels of the samples as required.
channel_match

name of csv file to associate a fluorescent channel with each of the compensation controls. The channel_match file should contain a "name" column with the names of the compensation controls and a "channel" column to associate a fluorescent channel with each compensation control. Users need not generate this file by hand as it will be created following the channel selection process.
compensated

logical indicating whether the supplied compensation controls have been compensated. Compensation controls must be compensated prior to calculation of spillover spreading matrix. If compensated is set to FALSE, the compensation controls will be compensated internally using the supplied spillover matrix.
spillover

name of the output spillover matrix csv file to be used internally to compensate the compensation controls. If no spillover matrix is supplied spillover_spread_compute, the spillover matrix attached to compensation controls will be applied.
spillover_spread

name of the csv file to which the spillover spreading matrix will be saved, set to "date-Spillover-Spread-Matrix.csv" by default.
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 cyto_plot.

References

Nguyen R, Perfetto S, Mahnke YD, Chattopadhyay P & Roederer M, (2013). Quantifying spillover spreading for comparing instrument performance and aiding in multicolor panel design. Cytometry A, 83(3):306-15.

See also

cyto_spillover_compute

cyto_spillover_edit

Author

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