cyto_plot_gating_scheme: Plot Cytometry Gating Strategies

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Plot Cytometry Gating Strategies

Description

cyto_plot_gating_scheme automatically plots the entire gating scheme and has full support for gate tracking and back-gating through gate_track and back_gate.

Usage

## S3 method for class 'GatingSet'
cyto_plot_gating_scheme(
  x,
  gatingTemplate = NULL,
  group_by = "name",
  back_gate = FALSE,
  gate_track = FALSE,
  show_all = FALSE,
  header,
  popup = FALSE,
  layout = NULL,
  point_col = NA,
  label_text_size = 0.8,
  gate_line_col = "red",
  legend = TRUE,
  legend_text = NULL,
  legend_text_size = 1.2,
  header_text_font = 2,
  header_text_size = 1,
  header_text_col = "black",
  border_line_width = NULL,
  border_line_col = "black",
  title_text_col = "black",
  ...
)

## S3 method for class 'GatingHierarchy'
cyto_plot_gating_scheme(
  x,
  gatingTemplate = NULL,
  back_gate = FALSE,
  gate_track = FALSE,
  show_all = FALSE,
  header,
  popup = FALSE,
  layout,
  point_col = NA,
  label_text_size = 0.8,
  gate_line_col = "red",
  legend = TRUE,
  legend_text,
  legend_text_size = 1.2,
  header_text_font = 2,
  header_text_size = 1,
  header_text_col = "black",
  border_line_width,
  border_line_col = "black",
  title_text_col = "black",
  ...
)

Arguments

x	object of class GatingHierarchy or GatingSet.
gatingTemplate	name of the gatingTemplate csv file used to gate x. If not supplied the gating scheme will be obtained directly from the GatingSet.
group_by	a vector of pData variables to sort and merge samples into groups prior to plotting, set to "name" by default to plot each sample separately.
back_gate	names of the population(s) to back-gate, set to FALSE by default to turn off back-gating. To back-gate all populations set this argument to "all".
gate_track	logical indicating whether gate colour should be tracked throughout gating scheme, set to TRUE by default.
show_all	logical indicating whether every population should be included in every plot in the gating scheme, set to FALSE by default.
header	character string to use as the header for the plot layout, set to "Gating Scheme" by default.
popup	logical indicating whether the gating scheme should be plotted in a pop-up window, set to FALSE by default.
layout	a vector of the length 2 indicating the dimensions of the grid for plotting c(#rows, #columns).
point_col	colour of points in 2D plots set to NA to use default red-blue colour scale. Control the colour of overlays by supplying multiple colours to this argument (e.g. c("blue","red")).
label_text_size	numeric to control the size of text in the plot labels, set to 0.8 by default.
gate_line_col	colour to use for gate borders, set to "red" by default.
legend	logical indicating whether a legend should be included when an overlay is supplied.
legend_text	vector of character strings to use for legend when an overlay is supplied.
legend_text_size	character expansion for legend text, set to 1.2 by default.
header_text_font	numeric to control the font of the header, set to 2 by default for bold font.
header_text_size	numeric to control the size of the header text, set to 1 by default.
header_text_col	colour to use for header text, set to "black" by default.
border_line_width	line width for plot border, set to 3 when gate_track is TRUE.
border_line_col	line colour for plot border, set to "black" by default.
title_text_col	colour to use for title text, set to "black" by default.
...	extra arguments passed to cyto_plot.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoExploreRData)

# Load in samples
fs <- Activation
gs <- GatingSet(fs)

# Apply compensation
gs <- cyto_compensate(gs)

# Transform fluorescent channels
gs <- cyto_transform(gs)

# Gate using cyto_gate_draw
gt <- Activation_gatingTemplate
gt_gating(gt, gs)

# Gating scheme
cyto_plot_gating_scheme(gs[[4]])

# Back-gating
cyto_plot_gating_scheme(gs[[32]],
  back_gate = TRUE
)

# Gate-tracking
cyto_plot_gating_scheme(gs[1:2],
  gate_track = TRUE
)

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