cyto_plot_empty: Create an empty cyto_plot

In DillonHammill/CytoExploreR: Interactive Analysis of Cytometry Data

Create an empty cyto_plot

Description

cyto_plot_empty generates to base for cyto_plot by creating an empty plot with border, axes, axes_text and titles. Data is subsequently added to this base layer with cyto_plot_point or cyto_plot_density.

Usage

cyto_plot_empty(x, ...)

## S3 method for class 'flowFrame'
cyto_plot_empty(
  x,
  channels,
  axes_trans = NA,
  overlay = NA,
  gate = NA,
  xlim = NA,
  ylim = NA,
  axes_limits = "auto",
  axes_limits_buffer = 0.03,
  title,
  xlab,
  ylab,
  margins = NULL,
  density_modal = TRUE,
  density_smooth = 1.5,
  density_stack = 0.5,
  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,
  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",
  border_line_type = 1,
  border_line_width = 1,
  border_line_col = "black",
  border_fill = "white",
  border_fill_alpha = 1,
  legend = FALSE,
  legend_text,
  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,
  ...
)

Arguments

x	object of class flowFrame.
...	not in use.
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 transformList or transformerList generated by estimateLogicle which was used to transform the fluorescent channels of the supplied flowFrame. This transformation object will be used internally to ensure that the axes labels of the plot are appropriately transformed. The transformation object will NOT be applied to the flowFrame internally and should be applied to the flowFrame prior to plotting.
overlay	a list of flowFrames to overlay onto the plot.
gate	list of gate objects to be plotted, used internlaly to ensure gate co-ordinates are taken into account when computing axes limits.
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)).
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.
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.
xlab	x axis label.
ylab	y axis label.
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.
density_modal	logical indicating whether density should be normalised to mode and presented as a percentage. Set to TRUE by default.
density_smooth	smoothing parameter passed to density to adjust kernel density.
density_stack	numeric [0,1] indicating the degree of offset for overlaid populations, set to 0.5 by default. #' @param density_cols vector colours to draw from when selecting density fill colours if none are supplied to density_fill.
density_cols	vector colours to draw from when selecting density fill colours if none are supplied to density_fill.
density_fill	colour(s) used to fill polygons.
density_fill_alpha	numeric [0,1] used to control fill transparency, set to 1 by default to remove transparency.
density_line_type	line type(s) to use for border(s), set to solid lines by default.
density_line_width	line width for border.
density_line_col	colour(s) for border line, 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 colours to use for density gradient.
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.
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 indicating the font to use for axes, set to 1 for plain font by default. See ?par font for details.
axes_text_size	character expansion for axis text.
axes_text_col	colour of axis text.
axes_label_text_font	numeric indicating the font to use for title, set to 1 for plain font by default. See ?par font for details.
axes_label_text_size	character expansion for axis labels.
axes_label_text_col	colour of axis labels.
title_text_font	numeric indicating the font to use for title, set to 2 for bold font by default. See ?par font for details.
title_text_size	character expansion for plot title.
title_text_col	colour for plot title.
border_line_type	line type to use for plot border, set to 1 by default for a sold border.
border_line_width	line width for plot border, set to 1 by default.
border_line_col	line colour for plot border, set to "black" by default.
border_fill	colour to use for the plot background, set to "white" by default.
border_fill_alpha	transparency to use for border_fill colour, set to 1 by default to add no transparency.
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.

Author(s)

Dillon Hammill ([e-mail])

Examples

library(CytoExploreRData)

# Construct an empty 2D plot with black background
cyto_plot_empty(Activation[[32]],
  channels = c("FSC-A", "SSC-A"),
  border_fill = "black"
)

# Construct an empty 1D plot
cyto_plot_empty(Activation[[32]],
  channels = c("FSC-A"),
  overlay = Activation[1:2]
)

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