Plots Cell Survival Curves using ggplot — ggplotCSCurve • CellSurvAssay

This function helps to plot the cell survival curves using ggplot, and is the recommended way to plot this curves over plotCSCurve. A single function plots the curves, both for a single or multiple cell type(s), and allows most of the options necessary to customize the figures for publication.

Usage

ggplotCSCurve(
  data,
  ...,
  method = "ml",
  PEmethod = "fit",
  colors = NULL,
  title = "",
  title_size = 20,
  title_color = "black",
  title_face = "bold",
  title_align = "center",
  subtitle = "",
  sub_size = 15,
  sub_color = "black",
  sub_face = "italic",
  sub_align = "center",
  xlab = "Dose (Gy)",
  xlab_size = 16,
  xlab_color = "black",
  xlab_face = "bold",
  rem_minor_x = "yes",
  emph_major_x = "no",
  major_x_col = "gray",
  major_x_width = 1,
  ylab = "Surviving Fraction",
  ylab_size = 16,
  ylab_color = "black",
  ylab_face = "bold",
  rem_minor_y = "yes",
  emph_major_y = "no",
  major_y_col = "gray",
  major_y_width = 1,
  legend_title = "",
  ltitle_size = 20,
  ltitle_color = "black",
  ltitle_face = "bold",
  ltitle_align = "left",
  legend_pos = "inside",
  legend_back = "",
  legend_border = "",
  legend_border_width = 0,
  ltext_size = 18,
  ltext_color = "black",
  ltext_face = "bold",
  xtext_size = 14,
  xtext_color = "black",
  xtext_face = "bold",
  ytext_size = 14,
  ytext_color = "black",
  ytext_face = "bold",
  point_shape = 16,
  point_size = 3.5,
  segment_type = 1,
  segment_width = 1,
  curve_width = 1.5,
  curve_type = 1,
  theme = ggplot2::theme_bw(),
  ylim = NULL,
  ybreaks = ggplot2::waiver(),
  save = "no",
  plot_width = 5,
  plot_height = 4,
  units = "in",
  save_path = getwd(),
  save_filename = "myplot.pdf"
)

Arguments

data: A data frame containing at least the following five columns: "cline", "Exp", "dose", "ncells", and "ncolonies".
...: The name of the cell type(s)/group(s). If entering multiple cell types, separate each by a comma.
method: Method used for the fit. It's "ml" (maximum likelihood) by default. Can be "ls" (least squares) or "franken" (weighted least squares as described by Franken eta al.(2006)).
PEmethod: Controls the value of the plating efficiencies. The default method, "fit", calculates fitted plating efficiencies as model parameters, while "fix" uses fixed ones calculated from the observed zero dose data.
colors: A vector of strings denoting the colors of the curves. Size of the vector should be equal to or more than the number of cell types entered. If no colors are chosen by the user, the function chooses them by random and they might change with each plotting.
title: A string denoting the title of the plot. Default is "".
title_size: An integer denoting the font size of the title. Default is 20.
title_color: A string denoting the color of the font of the title. Default is "black".
title_face: A string denoting the type of font face. Accepts "bold", "italic", or "bold.italic". Default is "bold".
title_align: A string denoting the justification (alignment) of the plot title. Accepts "center", "left", or "right". Default is "center".
subtitle: A string denoting the subtitle of the plot; default is "".
sub_size, sub_color, sub_face, sub_align: Used to customize the font size, color, face, and alignment of the subtitle respectively, like the plot title. Default values of these are 15, "black", "italic", and "center" respectively.
xlab: A string denoting the label of X-axis; default is "Dose (Gy)".
xlab_size, xlab_color, xlab_face: Used to customize the font size, color, face, and alignment of the label of the X-axis respectively, like the plot title. Default values of these are 16, "black", and "bold" respectively.
rem_minor_x: If "no", keeps the minor grids in the X-axis. Default is "yes".
emph_major_x: If "yes", allows to emphasize and customize the major grids in the X-axis. Default is "no".
major_x_col, major_x_width: Allows the change of the color and width of the major grids in the X-axis, when emph_major_x = "yes". Default values of these are "gray" and 1 respectively.
ylab: A string denoting the label of y-axis; default is "Surviving Fraction".
ylab_size, ylab_color, ylab_face: Used to customize the font size, color, face, and alignment of the label of the Y-axis respectively, like the plot title. Default values of these are 16, "black", and "bold" respectively.
rem_minor_y: If "no", keeps the minor grids in the Y-axis. Default is "yes".
emph_major_y: If "yes", allows to emphasize and customize the major grids in the Y-axis. Default is "no".
major_y_col, major_y_width: Allows the change of the color and width of the major grids in the Y-axis, when emph_major_y = "yes". Default values of these are "gray" and 1 respectively.
legend_title: A string denoting the title of the legend; default is "".
ltitle_size, ltitle_color, ltitle_face, ltitle_align: Used to customize the font size, color, face, and alignment of the legend title respectively, like the plot title. Default values of these are 20, "black", "bold", and "left" respectively.
legend_pos: A string denoting the position of the legend. "inside" is default, and places the legend at the bottom left of the figure. Also accepts "outside" (places the legend outside the figure on the right) and "none" (removes the legend).
legend_back: A string denoting the color of the legend background. Default is "".
legend_border: A string denoting the color of the legnd border. Default is "".
legend_border_width: An integer denoting the width of the legend border. Default is 0.
ltext_size, ltext_color, ltext_face: To change the font size, color, and face of the legend texts. Default values of these are 18, "black", and "bold" respectively.
xtext_size, xtext_color, xtext_face: To change the font size, color, and face of x axis ticks.Default values of these are 14, "black", and "bold" respectively.
ytext_size, ytext_color, ytext_face: To change the font size, color, and face of y axis ticks. Default values of these are 14, "black", and "bold" respectively.
point_shape: An integer denoting the shape of the points in the plot. Default is 16.
point_size: An integer denoting the size of the points in the plot. Default is 3.5.
segment_type: An integer denoting the type of the straight line segments in the plot. Default is 1.
segment_width: An integer denoting the width of straight line segments in the plot. Default is 1.
curve_width: An integer denoting the width of curved line segments in the plot. Default is 1.5.
curve_type: An integer denoting the type of curved line segments in the plot. Default is 1.
theme: The name of the theme to be used in the plot. It should be preceded by the name of the package in the form: package::theme(). Default is ggplot2::theme_bw().
ylim: A vector denoting the limits of the y-axis. Defaults are chosen automatically by ggplot().
ybreaks: A vector denoting the y-axis breaks/ticks. Defaults are chosen automatically by ggplot().
save: To save the plot. save = "yes" saves the plot in the specified path and format.
plot_width: A number denoting the width of the plot. Default is 5.
plot_height: A number denoting the height of the plot. Default is 4.
units: A string denoting the units of the height and width of the plot mentioned. Accepts "in", "cm", "mm", or "px". Default is "in".
save_path: Path where the plot is to be saved. Default is the current working directory obtained by getwd().
save_filename: File name with extension for the plot. Accepts most of the common extensions, including .pdf, .jpeg, and .png.

Value

A ggplot object.

Examples

datatab <- CASP8_data

# Single curve

ggplotCSCurve(datatab, "shCASP8-NT")


ggplotCSCurve(datatab, "control-B", colors = "black", xlab = "X-axis", ylab = "Y-axis",
title = "Single Plot", point_shape = 1, point_size = 2, segment_width = 1, segment_type = 1,
curve_width = 1, curve_type = 1, legend_title = "Cell types", ylim = c(0.008, 1.05),
ybreaks = c(0.01, 0.05, 0.20, 0.50, 1), theme = ggplot2::theme_classic())


# Multiple Curves

ggplotCSCurve(datatab, "shCASP8-NT", "shCASP8-B", "shCASP8-B+Z", "shCASP8-B+Z+N")


ggplotCSCurve(datatab, "shCASP8-NT", "shCASP8-B", "shCASP8-B+Z", "shCASP8-B+Z+N",
colors = c("darkgreen", "green", "orange", "magenta"), xlab = "X-axis", ylab = "Y-axis",
title = "Multiple Curves", point_shape = 15, point_size = 1, segment_width = 1, segment_type = 1,
curve_width = 1, curve_type = 1, legend_title = "Cell types", theme = ggplot2::theme_dark(),
legend_back = "white", legend_border = "white", legend_border_width = 0.5)


if (FALSE) {
# Save a plot
ggplotCSCurve(datatab, "shCASP8-NT", "shCASP8-B", "shCASP8-B+Z", "shCASP8-B+Z+N", save = "yes")
}

Plots Cell Survival Curves using `ggplot`

Usage

Arguments

Value

See also

Examples