toxplot: toxplot

In raredd/plotr: More plotting functions and examples

toxplot

Description

Draw a toxicity summary plot.

Usage

toxplot(
  ftable,
  total,
  digits = 0L,
  headers = NULL,
  xlim = NULL,
  order = c("none", "decreasing", "increasing"),
  label.bars = c("n", "percent", "none"),
  col.bars = NULL,
  digits.bars = digits,
  widths = c(1, 1, 2),
  space = 1,
  xaxis.at = NULL,
  col.bg = "grey",
  alpha.bg = c(0.25, 0.5),
  legend = TRUE,
  args.legend = list(),
  ...
)

Arguments

ftable	a two- or three-dimensional ftable
total	total number of patients (for percentages)
digits	number of places past the decimal to keep for percentages
headers	a vector of labels for text column headers
xlim	the x-axis limits for the bar plot
order	optional ordering for the rows, one of "none" (default), "decreasing", or "increasing"; note that 3-d tables should not be re-ordered
label.bars	optional text on each bar, one of "n" (default), "percent", or "none"
col.bars	a vector of colors for each column of ftable
digits.bars	number of places past the decimal to keep for label.bars text
widths	the relative width of each column
space	additional space between final text column and bar plot
xaxis.at	x-axis tick positions
col.bg, alpha.bg	background color for text columns with alternating alpha.bg transparency
legend	logical; if TRUE, a legend for the col.bars is shown
args.legend	an optional named list of arguments passed to legend
...	additional graphical parameters passed to par

Examples

## example from rawr::tabler_by
set.seed(1)

f <- function(x, ...) sample(x, 100, replace = TRUE, ...)
tox <- data.frame(
  id = rep(1:10, 10), phase = 1:2,
  code = f(rawr::ctcae_v4$tox_code[1:100]),
  grade = f(1:3, prob = c(.6, .3, .1)),
  stringsAsFactors = FALSE
)
tox <- cbind(tox, rawr::match_ctc(tox$code)[, c('tox_cat', 'tox_desc')])

t1 <- ftable(
  Category = tox$tox_cat,
  Description = tox$tox_desc,
  Grade = tox$grade
)
t2 <- ftable(
  Description = tox$tox_desc,
  Grade = tox$grade
)
n <- 25


## basic usage
toxplot(t1, n) ## three column
toxplot(t2, n) ## two column


toxplot(
  t2, n, widths = c(1, 3), label.bars = 'percent',
  headers = c('Toxicity description', 'N (%)'),
  order = 'dec', xlim = c(0, 10), xaxis.at = c(0, 5, 10),
  args.legend = list(x = 'bottomright', horiz = FALSE, cex = 2)
)

raredd/plotr documentation built on Nov. 19, 2023, 4:09 a.m.