Visualise Compensation of Fluorescent Spillover in All Fluorescent Channels

cyto_plot_compensation plots each compensation control in all fluorescent channels to make it easy to identify any potential compensation issues. The unstained control is automatically overlaid onto the plot as a refernce if supplied.

# S3 method for GatingSet
cyto_plot_compensation(
  x,
  parent = NULL,
  channel_match = NULL,
  compensate = FALSE,
  spillover = NULL,
  axes_trans = NA,
  axes_limits = "machine",
  overlay = TRUE,
  layout = NULL,
  popup = FALSE,
  title = NA,
  header = NULL,
  header_text_font = 2,
  header_text_size = 1,
  header_text_col = "black",
  density_stack = 0,
  density_fill = c("grey", "blue"),
  density_fill_alpha = 0.5,
  ...
)

# S3 method for GatingHierarchy
cyto_plot_compensation(
  x,
  parent = NULL,
  channel_match = NULL,
  compensate = FALSE,
  spillover = NULL,
  axes_trans = NA,
  axes_limits = "machine",
  layout = NULL,
  popup = FALSE,
  title = NA,
  header,
  header_text_font = 2,
  header_text_size = 1,
  header_text_col = "black",
  density_stack = 0,
  density_fill = c("grey", "blue"),
  density_fill_alpha = 0.5,
  ...
)

# S3 method for flowSet
cyto_plot_compensation(
  x,
  channel_match = NULL,
  compensate = FALSE,
  spillover = NULL,
  axes_trans = NA,
  axes_limits = "machine",
  overlay = TRUE,
  layout = NULL,
  popup = FALSE,
  title = NA,
  header = NULL,
  header_text_font = 2,
  header_text_size = 1,
  header_text_col = "black",
  density_stack = 0,
  density_fill = c("grey", "blue"),
  density_fill_alpha = 0.5,
  ...
)

# S3 method for flowFrame
cyto_plot_compensation(
  x,
  channel_match = NULL,
  compensate = FALSE,
  spillover = NULL,
  axes_trans = NA,
  axes_limits = "machine",
  layout = NULL,
  popup = FALSE,
  title = NA,
  header = NULL,
  header_text_font = 2,
  header_text_size = 1,
  header_text_col = "black",
  density_stack = 0,
  density_fill = c("grey", "blue"),
  density_fill_alpha = 0.5,
  ...
)

Arguments

x	object of class `flowFrame` or `flowSet`, `GatingHierarchy` or `GatingSet` containing gated compensation controls.
parent	indicates the name of the parent population to extract fro plotting to plot for GatingSet objects. Users can specify a parent for each compensation control either as a vector or by adding a parent column to `cyto_details(x)`.
channel_match	name of the fluorescent channel associated with the `flowFrame`. A `channel_match` csv file may also be supplied. If not supplied users will need to select the channel from a dropdown menu.
compensate	logical indicating whether the samples should be compensated prior to plotting, set to FALSE by default. If no spillover matrix is supplied to the spillover argument the spillover matrix will extracted from the samples.
spillover	name of spillover matrix csv file including .csv file extension to apply to sample when `compensate` is TRUE. If no `spillover` is supplied the spillover matrix will be extracted directly from the data and applied to the sample when `compensate` is TRUE.
axes_trans	object of class `transformerList` generated by a `cyto_transform` which contains the transformer definitions that were used to transform the channels of the supplied flowFrame, flowSet, GatingHierarchy or GatingSet.
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.
overlay	logical indicating whether the unstained control should be overlaid onto the plot if supplied in the flowSet or GatingSet, set to `TRUE` by default.
layout	vector of grid dimensions `c(#rows,#columns)` for each plot.
popup	logical indicating whether plots should be constructed in a pop-up window.
title	text to include above each plot, set to NA by default to remove titles.
header	title to use for the plots, set to the name of the sample by default. Turn off the header by setting this argument to NA.
header_text_font	font to use for header text, set to 2 by default.
header_text_size	text size for header, set to 1 by default.
header_text_col	colour for header text, set to "black" by default.
density_stack	numeric passsed to cyto_plot to control the degree of stacking for density distributions, set to 0 by default.
density_fill	vector of colours passed to cyto_plot to control the fill colours of density distributions, set to c("grey","blue") by default.
density_fill_alpha	numeric passed to cyto_plot to control the fill transparency of density distributions, set to 0.5 by default.
...	additional arguments passed to `cyto_plot`.

Author

Dillon Hammill (Dillon.Hammill@anu.edu.au)

Examples

library(CytoExploreRData)

# Bypass directory check for external files
options("CytoExploreR_wd_check" = FALSE)

# Load in compensation controls
gs <- GatingSet(Compensation)

# Gate single cells using cyto_gate_draw
gt <- Compensation_gatingTemplate
gt_gating(gt, gs)
#> Preprocessing for 'Cells'
#> Gating for 'Cells'
#> done!
#> done.
#> Preprocessing for 'Single Cells'
#> Gating for 'Single Cells'
#> done!
#> done.
#> finished.

# Extract flowSet for plotting
fs <- cyto_extract(gs, "Single Cells")

# Channel match file
cmfile <- system.file("extdata",
  "Compensation-Channels.csv",
  package = "CytoExploreRData"
)

# Compensation plots - flowFrame
cyto_plot_compensation(fs[[1]],
  channel_match = cmfile,
  display = 1000
)

# Compensation plots - flowSet
cyto_plot_compensation(fs,
  channel_match = cmfile,
  compensate = TRUE,
  display = 1000
)

# Compensation plots - GatingHierarchy
cyto_plot_compensation(gs[[1]],
  parent = "Single Cells",
  channel_match = cmfile,
  display = 1000,
  contour_lines = 10
)

# Compensation plots - GatingSet
cyto_plot_compensation(gs,
  parent = "Single Cells",
  channel_match = cmfile,
  display = 1000
)

# Return "CytoExploreR_wd_check" to default
options("CytoExploreR_wd_check" = TRUE)

Visualise Compensation of Fluorescent Spillover in All Fluorescent Channels

Arguments

See also

Author

Examples