Plot Flow Cytometry Gating Strategies - GatingSet Method

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.

# S4 method for GatingSet
cyto_plot_gating_scheme(x, gatingTemplate = NULL,
  group_by, back_gate = FALSE, gate_track = FALSE, show_all = FALSE,
  display = NULL, header = NA, title = NULL, popup = FALSE,
  layout = NULL, point_col = NULL, density_stack = 0.5,
  density_fill = NULL, gate_line_col = NULL, border_line_col = NULL,
  border_line_width = NULL, legend = TRUE, legend_text = NULL,
  legend_text_size = 1.2, title_text_col = NULL,
  label_text_size = 0.8, ...)

Arguments

x	object of class 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 merge samples into groups prior to plotting, set to NULL by default to prevent merging. To merge all samples set this argument to TRUE or "all".
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.
display	numeric [0,1] to control the percentage of events to be plotted. Specifying a value for display can substantial improve plotting speed for less powerful machines.
header	character string to use as the header for the plot layout, set to "Gating Scheme" by default.
title	vector of titles to use above each plot.
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")).
density_stack	numeric [0,1] indicating the degree of offset for 1-D density distributions with overlay, set to 0.5 by default.
density_fill	fill colour for 1D density distributions. Control the colour of overlays by supplying multiple colours to this argument (e.g. c(NA,"red")).
gate_line_col	vector of colours to use for gates. Individual gate colours can only be controlled when gate_track is set to TRUE.
border_line_col	line colour for plot border, set to "black" by default.
border_line_width	line width for plot border, set to 3 when gate_track is TRUE.
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.
title_text_col	colour for plot title.
label_text_size	numeric to control the size of text in the plot labels, set to 0.8 by default.
...	extra arguments passed to cyto_plot, see cyto_plot,flowFrame-method for more details.

See also

cyto_plot_gating_scheme,GatingHierarchy-method

cyto_plot,flowFrame-method

Examples

library(CytoRSuiteData)

# Load in samples
fs <- Activation
gs <- GatingSet(fs)
#> .
#> .
#> .
#> .
#> done!

# Apply compensation
gs <- compensate(gs, fs[[1]]@description$SPILL)

# Transform fluorescent channels
trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
gs <- transform(gs, trans)

# Gate using gate_draw
gt <- Activation_gatingTemplate
gating(gt, gs)
#> Preprocessing for 'Cells'
#> Gating for 'Cells'
#> done.
#> Preprocessing for 'Single Cells'
#> Gating for 'Single Cells'
#> done.
#> Preprocessing for 'Live Cells'
#> Gating for 'Live Cells'
#> done.
#> Preprocessing for 'Dendritic Cells'
#> Gating for 'Dendritic Cells'
#> done.
#> Preprocessing for 'T Cells'
#> Gating for 'T Cells'
#> done.
#> Preprocessing for 'CD8 T Cells'
#> Gating for 'CD8 T Cells'
#> done.
#> Preprocessing for 'CD69+ CD8 T Cells'
#> Gating for 'CD69+ CD8 T Cells'
#> done.
#> Preprocessing for 'CD4 T Cells'
#> Gating for 'CD4 T Cells'
#> done.
#> Preprocessing for 'CD69+ CD4 T Cells'
#> Gating for 'CD69+ CD4 T Cells'
#> done.
#> finished.

# Gating scheme
cyto_plot_gating_scheme(gs)

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

# Gate-tracking
cyto_plot_gating_scheme(gs,
  gate_track = TRUE
)