cyto_plot_compensation: Visualise Compensation of Fluorescent Spillover in All...

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Visualise Compensation of Fluorescent Spillover in All Fluorescent Channels

Description

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.

Usage

## S3 method for class '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 class '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 class '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 class '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(s)

Dillon Hammill ([e-mail])

See Also

cyto_spillover_compute

cyto_spillover_edit

cyto_spillover_spread_compute

cyto_plot

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)

# 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)

DillonHammill/CytoExploreR documentation built on March 2, 2023, 7:34 a.m.