river: River plots

In raredd/rawr: rawr miscellaneous

River plots

Description

Summarize a timeline for individuals over the course of a study.

river shows the trajectory of multiple subjects. Time on treatment is represented by a green line; progression as a red dot; censored or death as an "x" in blue or red, respectively; and responses colored with bands. Subjects continuing are shown with an arrow.

river2 shows the trajectory for a single patient with additional toxicity information represented by another series of bands colored by grade. Optionally, the trajectory for a single patient from river may be shown rather than with an arrow; see examples.

Usage

river(
  data,
  bar_data,
  id = NULL,
  at = seq_along(id),
  legend = TRUE,
  args.legend = list(),
  xlim = NULL,
  ylim = NULL,
  rev = FALSE,
  stagger = TRUE,
  col = NULL,
  axes = TRUE,
  label = TRUE,
  bar.width = 0.25,
  bar.alpha = 0.5,
  col.seg = c(1L, 3L),
  col.arrows = 1L,
  pch.pt = c(16L, 4L, 4L),
  cex.pt = 1.5,
  col.pt = c(2L, 2L, 4L),
  panel.first = NULL,
  panel.last = NULL,
  ...
)

river2(
  data,
  bar_data,
  bar_data2,
  id,
  legend = TRUE,
  args.legend = list(),
  xlim = NULL,
  ylim = NULL,
  rev = FALSE,
  stagger = FALSE,
  split = FALSE,
  col = NULL,
  col2 = NULL,
  axes = TRUE,
  bar.width = 0.25,
  bar.alpha = 0.5,
  ...
)

check_river_format(data, bar_data)

Arguments

data, bar_data, bar_data2	data frames; these should have a specific format, see details, examples, or run check_river_format()
id, at	optional parameters specifying individuals (rows) from data to plot and their positions along the y-axis; if not given, time lines are plotted sequentially
legend	logical; if TRUE, a legend using the unique values of data$status is drawn
args.legend	a named list of arguments passed to legend
xlim, ylim	x- and y-axis limits
rev	logical; if TRUE, observations will be plotted from top to bottom
stagger	logical; if FALSE, start dates will be fixed at 0 rather than relative to the first start date if TRUE (default)
col, col2	vectors of colors for responses (river) or toxicity grades river2, respectively
axes	logical; if TRUE, x-axes are drawn
label	logical; if TRUE, IDs are shown for each line
bar.width, bar.alpha	width and alpha transparency for bars
col.seg	colors for timeline/on-treatment
col.arrows	the color for on-going arrows or use NA to suppress
pch.pt, cex.pt, col.pt	the plotting character, size, and color for progression, death, and censoring points, respectively
panel.first, panel.last	expression evaluated before and after plotting
...	graphical parameters passed to par
split	logical; if TRUE, rows of bar_data2 will be plotted individually

Details

data, bar_data, and bar_data2 data frames need to have a minimum number of variables in a specific order, some of which should be Date formats (or can be coerced to dates, e.g., integers).

check_river_format() without any arguments will give a summary of the required formats.

Note that date columns can also be given as integers to be coerced to dates as seen in the examples. In this case, check_river_format will do the coersion to date before plotting. However, these two methods are interchangeable, but using integers rather than dates assume the data have a common starting time.

data should have 10 columns (any additional will be ignored) in the following order: ID; dates of registration, start of treatment, end of treatment, progression, off treatment, and survival status; status indicator; and dates of last contact and off study. That is, these should be in approximate chronological order.

bar_data and bar_data2 provide additional information to supplement data and may contain multiple records per ID.

bar_data is intended to represent response assessments and therefore should have three columns: ID, date of assessment, and assessment. Any additional columns are ignored. Assessment data should be a factor variable with proper level ordering or will be coerced.

bar_data2 is intended to represent toxicity assessments and therefore should have five columns: ID, start date, end date, grade, and description. Any additional columns are ignored. Grade should be a factor variable with proper level ordering or will be coerced. Descriptions should be relatively short to avoid text extending outside of the plotting window.

Despite the assumptions above, any type of data may work if properly formatted and ordered according to check_river_format().

Examples

## to print a summary of the required formats
check_river_format()


## data in river format:
dd <- data.frame(
  id       = 1:5,
  dt_reg   = 1:5,
  dt_txst  = 1:5 + 1,
  dt_txend = c(10:13, 8),
  dt_prog  = c(11, 16, NA, NA, 8),
  dt_offtx = c(12, 19, NA, NA, 8),
  dt_surv  = c(12, 19, 24, 25, NA),
  surv     = c(0, 1, 0, 0, NA),
  dt_last  = c(12, 19, 24, 25, NA),
  dt_off   = c(12, 19, NA, NA, 8)
)
bd <- data.frame(
  id        = c(3, 3, 3, 3, 4, 4),
  dt_assess = c(9, 13, 17, 21, 10, 15),
  resp = factor(c('MR', 'PR', 'PR', 'CR', 'PR', 'CR'),
                levels = c('PD', 'SD', 'MR', 'PR', 'CR'))
)

## basic usage
river(dd, bd)
river(
  dd, bd, stagger = FALSE, rev = TRUE, col = 2:6,
  args.legend = list(x = 'bottom', title = 'Response', horiz = TRUE)
)


## using NA will suppress data from being plotted
river(dd, within(bd, resp <- NA))
river(within(dd, dt_txst <- NA), within(bd, resp <- NA))
river(within(dd, dt_txst <- NA), within(bd, {resp <- NA; dt_assess <- NA}))


## same data with single observations per id
bd1 <- data.frame(
  id = 3:4, dt_assesss = 9:10,
  resp = factor(c('PR','CR'), levels = c('PD','SD','MR','PR','CR'))
)

river(dd, bd1)

## id and at parameters control the positions of the timelines
river(dd, bd1, id = c(1, 2, 5, 3, 4), at = c(1:2, 4, 6:7), legend = FALSE)


## additional data for river2
tt <- data.frame(
  id       = rep(c(1, 3), times = c(1, 5)),
  dt_start = c(3, 5, 5, 8, 9, 11),
  dt_end   = c(NA, 5, NA, 10, 10, NA),
  grade    = c(1, 4, 3, 4, 1, 2),
  desc     = paste('tox', c(1, 1:5))
)

river2(dd, bd, tt, id = 3)

## multiple records per id (ie, worsening toxicities)
tt2 <- data.frame(
  id       = rep(c(1, 3), times = c(1, 8)),
  dt_start = c(3, 5, 5, 7, 15, 8, 9, 11, 14),
  dt_end   = c(NA, 5, 7, 15, NA, 10, 10, 14, NA),
  grade    = c(1, 4, 1, 2, 3, 4, 1, 2, 3),
  desc     = paste('tox', c(1, 1, 2, 2, 2, 3, 4, 5, 5))
)
                  
river2(dd, bd, tt2, id = 3)


## bar_data can also be given in river2 without additional information
river2(bar_data = tt,  id = 3)
river2(bar_data = tt2, id = 3)


## use custom axis() to change time units
river2(bar_data = tt2, id = 3, axes = FALSE)
at <- seq(0, 2, 0.5)
axis(1L, at * 7, at)
title(xlab = 'Weeks from registration', line = 2.5)

raredd/rawr documentation built on March 4, 2024, 1:36 a.m.