write_plot: Function to save plot figures

In shug0131/cctu: In-House Functions for Report Writing at Cambridge Clinical Trials Unit

Function to save plot figures

Description

One may not always use ggplot2 to draw plot, base plot function for example, this function is particularly useful in that situation.

Usage

write_plot(
  ...,
  plot_fn = plot,
  number = cctu_env$number,
  width = 29.7 * 0.6,
  height = 21 * 0.6,
  dpi = 300,
  units = "cm",
  clean_up = TRUE,
  directory = file.path(getOption("cctu_output", default = "Output"), "Figures"),
  format = c("png", "postscript", "jpeg"),
  graphics_args = NULL,
  verbose = options()$verbose,
  footnote = NULL,
  plot_args = NULL
)

Arguments

...	Arguments to be passed to the ploting function plot_fn below.
plot_fn	function to draw a plot. This can be simple print OR plot (default) OR a custom plot drawing function depending on how the plot was drawn. See the details and examples below.
number	the number used to as a suffix in the output filename, and to link to TableofTables. Default is to use the value in the cctu_env package environment that is set within attach_pop.
width	the width to save as
height	the height to save as
dpi	the resolution setting
units	either "cm" (the default) or "inches"
clean_up	logical to invoke the clean_up function at the end. Defaults to TRUE
directory	where to save the figures within path or current working directory. The Output directory can be over-riden with options("cctu_output").
format	either "jpg", "postscript", or "png" to determine the file type to use
graphics_args	a list of named arguments to supply to graphics function (png, postscript, jpeg)
verbose	logical to print information on changes to the global environment or external files. Defaults to options()$verbose.
footnote	character vector, can be used to add footnotes.
plot_args	Deprecated, kept here for backcompatibility. A named list arguments for plot_fn.

Details

The plot_fn can be a user defined function to draw plot. Let us assume the object p is your plot object. If you can see the plot by simply typing p on the console, then this should be print. If you can see the plot by simply typing plot(p) on the console, then this should be plot.

All parameters should be passed with names. Checkout the examples below.

Value

writes a copy of a plot to file fig_number.. edits the TableofTables object with the calling programe No return object.

See Also

write_table write_ggplot

Examples

## Not run: 
#####################################
# Below is a simple example ========#
#####################################
#
write_plot(plot_fn = plot, plot_args = list(x = iris[, 1], y = iris[, 2]))
# This is equivalent drawing the following plot and save it
plot(x = iris[, 1], y = iris[, 2])

# Below is user defined function plotting
# One can use this method to draw a complicated plot
new_plot <- function(x, y, h, v) {
  par(pty = "s", cex = 0.7) # adjust plot style
  plot(x, y)
  abline(h = h, v = v, lty = 2) # add some lines
}
write_plot(
  x = iris[, 1], y = iris[, 2], h = 2.5, v = 6.0,
  plot_fn = new_plot
)


####################################################
# To draw a KM-plot from survminer package ========#
####################################################

library("survival")
library("survminer")
fit <- survfit(Surv(time, status) ~ sex, data = lung)
# Drawing survival curves
p <- ggsurvplot(fit, data = lung)
write_plot(p, plot_fn = survminer:::print.ggsurvplot)
# The code above works because the p is a ggsurvplot object (check it with class(p))
# There's a printing function print.ggsurvplot to handle the printing of the KM-plot.
# But this function is not exported by survminer, so we need to use three colons.

#####################################
# Draw a consort diagram ===========#
#####################################

library(grid)
# Might want to change some settings
txt0 <- c("Study 1 (n=160)", "Study 2 (n=140)")
txt1 <- "Population (n=300)"
txt1_side <- "Excluded (n=15):\n\u2022 MRI not collected (n=15)"

# supports pipeline operator
g <- add_box(txt = txt0) |>
  add_box(txt = txt1) |>
  add_side_box(txt = txt1_side) |>
  add_box(txt = "Randomized (n=200)")
# Since you can draw the plot g with plot(g), the ploting function is plot
# The plotting function is \code{plot.consort}, so simple plot or plot.consort works
write_plot(g, plot_fn = plot)
# Or just
write_plot(g)

## End(Not run)

shug0131/cctu documentation built on Feb. 15, 2025, 3:27 p.m.