Description Usage Arguments Author(s) See Also Examples
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
.
1 2 3 4 5 6 7 8 9 | ## S4 method for signature '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, ...)
|
x |
object of class
|
gatingTemplate |
name of the gatingTemplate csv file used to gate
|
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 |
back_gate |
names of the population(s) to back-gate, set to |
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 |
display |
numeric [0,1] to control the percentage of events to be
plotted. Specifying a value for |
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 |
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 |
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
|
Dillon Hammill, Dillon.Hammill@anu.edu.au
cyto_plot_gating_scheme,GatingHierarchy-method
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | library(CytoRSuiteData)
# Load in samples
fs <- Activation
gs <- GatingSet(fs)
# 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)
# 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
)
|
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