Description Usage Arguments Author(s) See Also Examples
Explore & visualise a GatingSet.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | ## S4 method for signature 'GatingSet'
cyto_plot(x, parent, alias = NULL, channels,
axes_trans = NULL, group_by = FALSE, overlay = NULL, gate = NA,
limits = "machine", display = NULL, layout = NULL, popup = FALSE,
xlim = NULL, ylim = NULL, title, xlab = NA, ylab = NA,
density_modal = TRUE, density_smooth = 1.5, density_stack = 0,
density_layers = length(x), density_fill = NA,
density_fill_alpha = 1, density_line_type = 1,
density_line_width = 1, density_line_col = "black",
point_shape = ".", point_size = 2, point_col = NA,
point_alpha = 1, contour_lines = 0, contour_line_type = 1,
contour_line_width = 1, contour_line_col = "black",
axes_text_font = 1, axes_text_size = 1, axes_text_col = "black",
axes_label_text_font = 1, axes_label_text_size = 1.1,
axes_label_text_col = "black", title_text_font = 2,
title_text_size = 1.1, title_text_col = "black", legend = FALSE,
legend_text, legend_text_font = 1, legend_text_size = 1,
legend_text_col = "black", legend_line_col = NA,
legend_box_fill = NA, legend_point_col = NA, gate_line_type = 1,
gate_line_width = 2.5, gate_line_col = "red", label = TRUE,
label_text = NA, label_stat = "percent", label_text_font = 2,
label_text_size = 1, label_text_col = "black", label_box_x = NA,
label_box_y = NA, label_box_alpha = 0.6, border_line_type = 1,
border_line_width = 1, border_line_col = "black", ...)
|
x |
object of class
|
parent |
name of the population containing the events to plot. |
alias |
name of the gated population for which the gate should be drawn on the plot. |
channels |
name of the channel(s) or marker(s) to be used to construct the plot. The length of channels determines the type of plot to be constructed, either a 1-D density distribution for a single channel or a 2-D scatterplot with blue-red colour scale for two channels. |
axes_trans |
object of class
|
group_by |
a vector of pData variables to sort and merge samples into
groups prior to plotting, set to NULL by default to prevent merging. To
merge all samples set this argument to |
overlay |
name(s) of the populations to overlay or a |
gate |
gate object(s) to be added to plot. For |
limits |
indicates whether the axes limits should be based on the
|
display |
numeric [0,1] to control the percentage of events to be
plotted. Specifying a value for |
layout |
a vector of the length 2 indicating the dimensions of the grid
for plotting |
popup |
logical indicating whether the plot should be constructed in a
pop-up window, set to FALSE by default. |
xlim |
lower and upper limits of x axis (e.g. c(0,5)). |
ylim |
lower and upper limits of y axis (e.g. c(0,5)). |
title |
title to use for the plot, set to the name of the sample by
default. Title can be removed by setting this argument to |
xlab |
x axis label. |
ylab |
y axis label. |
density_modal |
logical indicating whether density should be normalised
to mode and presented as a percentage for 1-D plots. Set to |
density_smooth |
smoothing parameter passed to
|
density_stack |
numeric [0,1] indicating the degree of offset for 1-D density distributions with overlay, set to 0.5 by default. |
density_layers |
numeric indicating the number of samples to stack in each plot, set to all samples by default. |
density_fill |
fill colour(s) for 1-D density distributions. |
density_fill_alpha |
numeric [0,1] used to control 1-D density fill colour transparency, set to 1 by default for solid colours. |
density_line_type |
line type(s) to use for 1-D density lines, set to 1
by default to use solid lines. See |
density_line_width |
numeric to control line width(s) for 1-D density lines, set to 1 by default. |
density_line_col |
colour(s) for 1-D density lines, set to
|
point_shape |
shape(s) to use for points in 2-D scatterplots, set to
|
point_size |
numeric to control the size of points in 2-D scatter plots set to 2 by default. |
point_col |
colour(s) to use for points in 2-D scatter plots, set to NA by default to use a blue-red density colour scale. |
point_alpha |
numeric [0,1] to control point colour transparency in 2-D scatter plots, set to 1 by default to use solid colours. |
contour_lines |
numeric indicating the number of levels to use for contour lines in 2-D scatter plots, set to 0 by default to turn off contour lines. |
contour_line_type |
integer [0,6] to control the line type of contour
lines in 2-D scatter plots, set to |
contour_line_width |
numeric to control line width(s) for contour lines in 2-D scatter plots, set to 2 by default. |
contour_line_col |
colour(s) to use for contour lines in 2-D scatter
plots, set to |
axes_text_font |
numeric to control the font of axes text, set to 1 for
plain font by default. See |
axes_text_size |
numeric to control the size of axes text, set to 1 by default. |
axes_text_col |
colour to use for axes text, set to |
axes_label_text_font |
numeric to control the font axes labels, set to 1
for plain font by default. See |
axes_label_text_size |
numeric to control the text size of axes labels, set to 1.1 by default. |
axes_label_text_col |
colour to use for axes labels text, set to
|
title_text_font |
numeric to control the font of title text, set to 2
for bold font by default. See |
title_text_size |
numeric to control the text size of the plot title, set to 1.1 by default. |
title_text_col |
colour to use for plot title text, set to
|
legend |
can be either |
legend_text |
vector of labels to use in the legend. |
legend_text_font |
numeric to control the font of legend text, set to 1
for plain font by default. See |
legend_text_size |
numeric to control the size of text in the legend, set to 1 by default. |
legend_text_col |
colour(s) to use for text in legend, set to
|
legend_line_col |
colour(s) to use for the lines in 1-D plot legends
when legend is set to |
legend_box_fill |
fill colour(s) to use for the boxes in 1-D plot
legends when legend is set to |
legend_point_col |
colour(s) to use for points in 2-D scatter plot legend. |
gate_line_type |
integer [0,6] to control the line type of gates, set to
|
gate_line_width |
numeric to control the line width(s) of gates, set to
|
gate_line_col |
colour(s) to use for gates, set to |
label |
logical indicating whether gated populations should be labelled.
To include the names of the populations in these labels, supply the
population names to the |
label_text |
vector of population names to use in the labels. Set to
|
label_stat |
indicates the type of statistic to include in the plot
labels, can be |
label_text_font |
numeric to control the font of text in plot labels,
set to 2 for bold font by default. See |
label_text_size |
numeric to control the size of text in the plot labels, set to 1 by default. |
label_text_col |
colour(s) to use for text in plot labels, set to
|
label_box_x |
vector of x co-ordinate(s) to manually adjust the position plot label(s) on the plot. |
label_box_y |
vector of y co-ordinate(s) to manually adjust the position plot label(s) on the plot. |
label_box_alpha |
numeric to control background fill transparency of label boxes, set to 0.6 by default to introduce some transparency. |
border_line_type |
integer [0,6] to control the line type of plot
border, set to |
border_line_width |
numeric to control line width for the plot border, set to 1 by default. |
border_line_col |
colour to use for the plot border, set to "black" by default. |
... |
additional arguments passed to |
Dillon Hammill, Dillon.Hammill@anu.edu.au
cyto_plot,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 30 31 32 | library(CytoRSuiteData)
# Load samples into GatingSet
fs <- Activation
gs <- GatingSet(fs)
# Apply coompensation
gs <- compensate(gs, fs[[1]]@description$SPILL)
# Transform fluorescent channels
trans <- estimateLogicle(gs[[4]], cyto_fluor_channels(gs))
gs <- transform(gs, trans)
# Apply gatingTemplate
gt <- Activation_gatingTemplate
gating(gt, gs)
# 2-D scatter plot with overlay & Gates
cyto_plot(gs,
parent = "CD4 T Cells",
alias = "CD69+ CD4 T Cells",
channels = c("Alexa Fluor 647-A", "7-AAD-A"),
overlay = "CD8 T Cells"
)
# 2-D Scatter Plots with Back-Gating & Gates
cyto_plot(gs,
parent = "T Cells",
alias = c("CD4 T Cells", "CD8 T Cells"),
channels = c("Alexa Fluor 488-A", "Alexa Fluor 700-A"),
overlay = c("CD69+ CD4 T Cells", "CD69+ CD8 T Cells")
)
|
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