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
.
cyto_plot_empty(x, ...) # S3 method for 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, ... )
x | object of class |
---|---|
... | 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
|
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 |
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 |
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 |
density_smooth | smoothing parameter passed to
|
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
|
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
|
axes_text_font | numeric indicating the font to use for axes, set to 1
for plain font by default. See |
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 |
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 |
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 |
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_type | numeric to control the line type for line legends,
set to 1 by default. Refer to |
legend_line_width | numeric to control the line width in line legend,
set to 1 by default. Refer 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. |
Dillon Hammill (Dillon.Hammill@anu.edu.au)
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] )