cyto_plot: cyto_plot

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

cyto_plot

Description

Explore and visualise cytometry data.

Usage

## S3 method for class 'GatingSet'
cyto_plot(
  x,
  parent,
  alias = NA,
  channels,
  axes_trans = NA,
  group_by = "name",
  overlay = NA,
  gate = NA,
  display = 25000,
  layout,
  margins = NULL,
  popup = FALSE,
  select = NULL,
  xlim = NA,
  ylim = NA,
  xlab,
  ylab,
  title,
  negate,
  density_modal = TRUE,
  density_smooth = 0.6,
  density_stack = 0,
  density_layers = NA,
  density_cols = NA,
  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_scale = NA,
  point_cols = NA,
  point_col = NA,
  point_col_alpha = 1,
  contour_lines = 0,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  axes_limits = "auto",
  axes_limits_buffer = 0.03,
  axes_text = c(TRUE, TRUE),
  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 = NA,
  legend_text_font = 1,
  legend_text_size = 1,
  legend_text_col = "black",
  legend_line_type = NA,
  legend_line_width = NA,
  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",
  gate_fill = "white",
  gate_fill_alpha = 0,
  label,
  label_text = NA,
  label_stat = "",
  label_position = "auto",
  label_text_x = NA,
  label_text_y = NA,
  label_text_font = 2,
  label_text_size = 0.8,
  label_text_col = "black",
  label_fill = "white",
  label_fill_alpha = 0.6,
  border_line_type = 1,
  border_line_width = 1,
  border_line_col = "black",
  border_fill = "white",
  border_fill_alpha = 1,
  ...
)

## S3 method for class 'GatingHierarchy'
cyto_plot(
  x,
  parent,
  alias = NA,
  channels,
  axes_trans = NA,
  overlay = NA,
  gate = NA,
  axes_limits = "auto",
  display = 25000,
  margins = NULL,
  popup = FALSE,
  xlim = NA,
  ylim = NA,
  xlab,
  ylab,
  title,
  negate,
  density_modal = TRUE,
  density_smooth = 0.6,
  density_stack = 0,
  density_cols = NA,
  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_scale = NA,
  point_cols = NA,
  point_col = NA,
  point_col_alpha = 1,
  contour_lines = 0,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  axes_limits_buffer = 0.03,
  axes_text = c(TRUE, TRUE),
  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 = NA,
  legend_text_font = 1,
  legend_text_size = 1,
  legend_text_col = "black",
  legend_line_type = NA,
  legend_line_width = NA,
  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",
  gate_fill = "white",
  gate_fill_alpha = 0,
  label,
  label_text,
  label_stat,
  label_position = "auto",
  label_text_x = NA,
  label_text_y = NA,
  label_text_font = 2,
  label_text_size = 1,
  label_text_col = "black",
  label_fill = "white",
  label_fill_alpha = 0.6,
  border_line_type = 1,
  border_line_width = 1,
  border_line_col = "black",
  border_fill = "white",
  border_fill_alpha = 1,
  ...
)

## S3 method for class 'flowSet'
cyto_plot(
  x,
  channels,
  axes_trans = NA,
  group_by = "name",
  overlay = NA,
  gate = NA,
  axes_limits = "auto",
  display = 25000,
  layout,
  margins = NULL,
  popup = FALSE,
  select = NULL,
  xlim = NA,
  ylim = NA,
  xlab,
  ylab,
  title,
  negate = FALSE,
  density_modal = TRUE,
  density_smooth = 0.6,
  density_stack = 0,
  density_layers = NA,
  density_cols = NA,
  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_scale = NA,
  point_cols = NA,
  point_col = NA,
  point_col_alpha = 1,
  contour_lines = 0,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  axes_limits_buffer = 0.03,
  axes_text = c(TRUE, TRUE),
  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 = NA,
  legend_text_font = 1,
  legend_text_size = 1,
  legend_text_col = "black",
  legend_line_type = NA,
  legend_line_width = NA,
  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",
  gate_fill = "white",
  gate_fill_alpha = 0,
  label,
  label_text = NA,
  label_stat,
  label_position = "auto",
  label_text_x = NA,
  label_text_y = NA,
  label_text_font = 2,
  label_text_size = 0.8,
  label_text_col = "black",
  label_fill = "white",
  label_fill_alpha = 0.6,
  border_line_type = 1,
  border_line_width = 1,
  border_line_col = "black",
  border_fill = "white",
  border_fill_alpha = 1,
  ...
)

## S3 method for class 'flowFrame'
cyto_plot(
  x,
  channels,
  axes_trans = NA,
  overlay = NA,
  gate = NA,
  axes_limits = "auto",
  display = 25000,
  margins = NULL,
  popup = FALSE,
  xlim = NA,
  ylim = NA,
  xlab,
  ylab,
  title,
  negate = FALSE,
  density_modal = TRUE,
  density_smooth = 0.6,
  density_stack = 0,
  density_cols = NA,
  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_scale = NA,
  point_cols = NA,
  point_col = NA,
  point_col_alpha = 1,
  contour_lines = 0,
  contour_line_type = 1,
  contour_line_width = 1,
  contour_line_col = "black",
  contour_line_alpha = 1,
  axes_limits_buffer = 0.03,
  axes_text = c(TRUE, TRUE),
  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 = NA,
  legend_text_font = 1,
  legend_text_size = 1,
  legend_text_col = "black",
  legend_line_type = NA,
  legend_line_width = NA,
  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",
  gate_fill = "white",
  gate_fill_alpha = 0,
  label,
  label_text,
  label_stat,
  label_position = "auto",
  label_text_x = NA,
  label_text_y = NA,
  label_text_font = 2,
  label_text_size = 1,
  label_text_col = "black",
  label_fill = "white",
  label_fill_alpha = 0.6,
  border_line_type = 1,
  border_line_width = 1,
  border_line_col = "black",
  border_fill = "white",
  border_fill_alpha = 1,
  ...
)

Arguments

x	object of class flowFrame, flowSet, GatingHierarchy or GatingSet.
parent	name of the population to plot when a GatingHierarchy or GatingSet object is supplied.
alias	name of the gated population(s) to gated in the plot when a GatingHierarchy or GatingSet object is supplied. Setting alias to "" will automatically plot any gates contructed in the supplied channels. alias is equivalent to the gate argument for flowFrame and flowSet objects.
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 transformerList which was used to transform the channels of the supplied flowFrame. cyto_plot does not support in-line transformations and as such the transformations should be applied to the data prior to plotting. The transformerList is used internally to ensure that the axes on the constructed plots are appropriately labelled.
group_by	a vector of pData variables to sort and merge samples into groups prior to plotting, set to "name" by default to prevent merging. To merge all samples set this argument to TRUE or "all".
overlay	name(s) of the populations to overlay or a flowFrame, flowSet, list of flowFrames, list of flowSets or list of flowFrame lists containing populations to be overlaid onto the plot(s). This argument can be set to "children" or "descendants" when a GatingSet or GatingHierarchy to overlay all respective nodes.
gate	gate objects to be plotted, can be either objects of class rectangleGate, polygonGate, ellipsoidGate, quadGate or filters. Lists of these supported gate objects are also supported.
display	numeric to control the number or percentage of events to display. Values [0,1] indicate the percentage of events to display (i.e. value of 1 will display all events), whilst values larger than 1 indicate the number of events to display. The default value for display is set to 25000 to display 25000 events only.
layout	a vector of the length 2 indicating the dimensions of the grid for plotting c(#rows, #columns).
margins	a vector of length 4 to control the margins around the bottom, left, top and right of the plot, set to NULL by default to let 'cyto_plot' compute optimal margins.
popup	logical indicating whether the plot should be constructed in a pop-up window, set to FALSE by default. popup will open OS-specific graphic device prior to plotting. Mac users will need to install XQuartz for this functionality.
select	named list containing experimental variables to be used to select samples using cyto_select when a flowSet or GatingSet is supplied. Refer to cyto_select for more details.
xlim	lower and upper limits of x axis (e.g. c(0,250000)).
ylim	lower and upper limits of y axis (e.g. c(0,250000)).
xlab	x axis label.
ylab	y axis label.
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 NA.
negate	logical indicating whether a label should be included for the negated population when gate objects are supplied, set to FALSE by default.
density_modal	logical indicating whether density should be normalised to mode and presented as a percentage for 1-D plots. Set to TRUE by default.
density_smooth	smoothing parameter passed to density to adjust kernel density for 1-D plots.
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_cols	vector colours to draw from when selecting density fill colours if none are supplied to density_fill.
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 lty for alternatives.
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 "black" by default.
point_shape	shape(s) to use for points in 2-D scatterplots, set to "." by default to maximise plotting speed. See pch for alternatives.
point_size	numeric to control the size of points in 2-D scatter plots set to 2 by default.
point_col_scale	vector of ordered colours to use for the density colour gradient of points.
point_cols	vector colours to draw from when selecting colours for points if none are supplied to point_col.
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_col_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 1 to draw solid lines by default. See lty for alternatives.
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 "black" by default.
contour_line_alpha	numeric [0,1] to control the transparency of contour lines, set to 1 by default to remove transparency.
axes_limits	options include "auto", "data" or "machine" to use optimised, data or machine limits respectively. Set to "auto" by default to use optimised axes ranges. Fine control over axes limits can be obtained by altering the xlim and ylim arguments.
axes_limits_buffer	decimal indicating the percentage of buffering to add to either end of the axes limits, set to 0.03 by default.
axes_text	logical vector of length 2 indicating whether axis text should be included for the x and y axes respectively, set to c(TRUE,TRUE) by default to display axes text on both axes.
axes_text_font	numeric to control the font of axes text, set to 1 for plain font by default. See font for alternatives.
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 "black" by default.
axes_label_text_font	numeric to control the font axes labels, set to 1 for plain font by default. See font for alternatives.
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 "black" by default.
title_text_font	numeric to control the font of title text, set to 2 for bold font by default. See font for alternatives.
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 "black" by default.
legend	can be either "line" or "fill" to indicate whether a legend should be constructed based on the density "line" or "fill", set to FALSE by default to remove the legend.
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 font for alternatives.
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 "black" by default.
legend_line_type	numeric to control the line type for line legends, set to 1 by default. Refer to lty in par for alternatives.
legend_line_width	numeric to control the line width in line legend, set to 1 by default. Refer to lwd in par for alternatives.
legend_line_col	colour(s) to use for the lines in 1-D plot legends when legend is set to "line".
legend_box_fill	fill colour(s) to use for the boxes in 1-D plot legends when legend is set to "fill".
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 1 to draw solid lines by default. See lty for alternatives.
gate_line_width	numeric to control the line width(s) of gates, set to 2.5 by default.
gate_line_col	colour(s) to use for gates, set to "red" by default.
gate_fill	fill colour(s) to use for gates, set to "white by default.
gate_fill_alpha	numeric to control the fill transparency of gates, set to 0 by default to remove fill colour(s).
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 argument. The default statistic is "percent" for gated data. This argument must be set to TRUE in order to add labels with gates.
label_text	vector of population names to use in the labels.The exclude the population names set this argument to NA.
label_stat	indicates the type of statistic to include in the plot labels, can be "percent", "count", "mean", "median", "mode" or "geo mean", set to "percent" for gated data or NA to exclude statistics for un-gated data. Currently, only "percent" and "count" are supported for 2-D scatter plots.
label_position	either "auto" or "manual". The "auto" option (default) positions labels will be placed in the center of gates and offset if necessary. The "manual" option will allow label positioning by mouse click. Label positions are set on a per gate basis, all samples in the same group will have the same label positions. To individually label plots users must manually supply the co-ordinates to label_text_x and label_text_y.
label_text_x	vector of x co-ordinate(s) to manually adjust the position plot label(s) on the plot. To interactively position labels set either label_text_x or label_text_y to "select".
label_text_y	vector of y co-ordinate(s) to manually adjust the position plot label(s) on the plot. To interactively position labels set either label_text_x or label_text_y to "select".
label_text_font	numeric to control the font of text in plot labels, set to 2 for bold font by default. See font for alternatives.
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 "black" by default.
label_fill	fill colour(s) to use for labels, set to "white" by default.
label_fill_alpha	numeric to control background fill transparency of label, 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 1 by default for a solid border. See lty for alternatives.
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.
border_fill	border_fill fill colour to use inside the plot border (i.e. background colour), set to "white" by default.
border_fill_alpha	transparency to use for border_fill colour, set to 1 by default for no transparency.
...	additional arguments not currently in use.

Author(s)

Dillon Hammill, [e-mail]

Examples

library(CytoExploreRData)

# Load samples into GatingSet
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)

# Apply gatingTemplate
gt <- Activation_gatingTemplate
gt_gating(gt, gs)

# 2-D scatter plot with overlay & Gates
cyto_plot(gs[1:9],
  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[1:9],
  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")
)

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