Skip to contents

The helper script of a study's figure programs

Source: R/fig_setup.R
tfl_fig_setup_code.Rd

tfl_fig_setup_code() writes the figure style standard (tfl_fig_style()) as data – tfl_settings, tfl_palettes, tfl_markers – followed by helpers in plain ggplot2:

Usage

tfl_fig_setup_code(style = tfl_fig_style(), date = Sys.Date())

tfl_check_fig(plot, levels = NULL, quiet = FALSE)

Arguments

style

A figure style (tfl_fig_style()).

date

The date stamped in the banner.

plot

A ggplot (or a patchwork of them).

levels

The values the legend must show, in this order.

quiet

TRUE leaves out the summary message.

Value

tfl_fig_setup_code(): the script, one element per line. tfl_check_fig(): invisibly, a list: problems (each also a warning starting "Figure check:"), notes, fingerprint (an md5 of the drawn data, to tell whether a figure changed between two runs).

Details

  • theme_tfl(type) – the standard's theme, font sizes, lines and ticks;

  • scale_colour_tfl(palette) / scale_fill_tfl() / tfl_colours() – the standard's palettes (an ordered one given more groups than it has colours repeats them, with a warning);

  • tfl_shapes(values) / tfl_linetypes(values) – the arms' shapes and line types of the standard (treatment_shapes, treatment_linetypes; NULL when it has none);

  • tfl_marker(name) – an event or symbol marker (Death, censor ...);

  • tfl_save(plot, file, type) – ggsave() at the standard's size;

  • tfl_km_risk(ard, fit) – a KM figure's number at risk from the KM table's ARD (cardx::ard_survival_survfit(times = )), checked against the curve;

  • tfl_check(plot, levels = ) – the checks of tfl_check_fig().

A figure program sources it (source("programs/tfl/fig_setup.R")) and ends with tfl_check(plot). tfl_check_fig() runs the same checks from R, against the style in use.