cyto_plot_compensation-GatingSet-method: Plot Compensation in All Fluorescent Channels - GatingSet...

In DillonHammill/cytoSuite: Compensation, Gating & Visualisation Toolkit for Analysis of Flow Cytometry Data

Description

Plot each compensation control in all fluorescent channels to identify any potential compensation issues. The unstained control is overlaid in black as a reference.

Usage

## S4 method for signature 'GatingSet'
cyto_plot_compensation(x, parent = NULL,
  channel_match = NULL, compensate = FALSE, spillover = NULL,
  axes_trans = NULL, overlay = TRUE, layout, popup = FALSE,
  title = NA, header = NA, header_text_font = 2,
  header_text_size = 1, header_text_col = "black", ...)

Arguments

x	object of class GatingSet containing gated compensation controls and an unstained control.
parent	name of the population to plot.
channel_match	name of a csv file with two columns, the first called "name" lists the names of each compensation control and the second "channel" lists the fluorescent channel associated with each of the compensation controls. Use "Unstained" in the channel column for the universal unstained control. No need to construct this file manually as users will be guided through this process if the channel_match is missing.
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_file argument the spillover matrix will extracted from the samples.
spillover	name of spillover matrix csv file including .csv file extension to apply to samples when compensate is TRUE. If no spillover is supplied the spillover matrix will be extracted directly from the GatingSet and applied to the samples when compensate is TRUE.
axes_trans	object of class transformList or transformerList generated by estimateLogicle which was used to transform the fluorescent channels of the supplied flowFrame. This transform object will be used internally to ensure axes labels of the plot are appropriately transformed. The transform object will NOT be applied to the flowFrame internally and should be applied to the flowFrame prior to plotting.
overlay	logical indicating whether the unstained control should be overlaid onto the plot if supplied in the flowSet, 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	vector of titles to use for the plots, set to the name of the sample by default.
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.
...	additional arguments passed to cyto_plot,flowFrame-method.

Author(s)

Dillon Hammill ([e-mail])

See Also

cyto_plot,flowFrame-method

Examples

library(CytoRSuiteData)

# Don't run - bypass directory check for external files
options("CytoRSuite_wd_check" = FALSE)

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

# Gate single cells using gate_draw
gt <- Compensation_gatingTemplate
gating(gt, gs)

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

# Compensation plots
cyto_plot_compensation(gs,
  parent = "Single Cells",
  channel_match = cmfile
)

# Don't run - return "CytoRSuite_wd_check" to default
options("CytoRSuite_wd_check" = TRUE)

DillonHammill/cytoSuite documentation built on March 7, 2019, 10:09 a.m.