Function to save plot figures

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$number,
  width = 29.7 * 0.6,
  height = 21 * 0.6,
  dpi = 300,
  units = "cm",
  clean_up = TRUE,
  directory = file.path(getOption("cctu_output", default = "Output"), "Figures"),
  format = getOption("cctu_fig_format", default = c("png", "eps")),
  graphics_args = NULL,
  verbose = options()$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 "png", "eps", "ps", "pdf", "svg", "jpg" or "jpeg" to determine the file type to use. You can request multiple file types by providing a vector. The "png" format will always be produced and saved under directory, typically this is Output/Figures. All other formats will be saved under a sub-folder with the format name. See details for more information. You can set the default figure format by setting options(cctu_fig_format = c("png", "eps")) (default).
graphics_args: a list of named arguments to supply to graphics function. png for "png", postscript for "ps" or "eps", jpeg for "jpg" and "jpeg", pdf for "pdf"). If you have the ragg package installed, it will use agg_png for "png" and agg_jpeg for "jpg" and "jpeg" for better quality. The svglite is used for "svg" file.
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.
plot: the plot object to save. defaults to last_plot

Value

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

Details

## Saving a plot

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.

## Figure formats

You can request for multiple figure formats when saving a plot. You can save "png" (default), "eps", "ps", "pdf", "svg", "jpg" and/or "jpeg" formats. The "png" format will always be produced to produce final Word report. The "eps", "ps", "pdf" and "svg" are vector figures and you can post edit figures with tools like Inkscape. The "svg" is recommended if you want to modify the plots. You can then easily export "svg" to other formats, including "eps" and "ps", "pdf". The svglite is used to generate "svg" file.

Examples

if (FALSE) { # \dontrun{
#####################################
# 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)
} # }

Usage

Arguments

Value

Details

See also

Examples