mplot3_survfit: 'mplot3': Plot 'survfit' objects

In egenn/rtemis: Machine Learning and Visualization

mplot3: Plot survfit objects

Description

Plots survival step functions using mplot3_xy

Usage

mplot3_survfit(
  x,
  lty = 1,
  lwd = 1.5,
  alpha = 1,
  col = NULL,
  plot.median = FALSE,
  group.median = FALSE,
  median.lty = 3,
  median.lwd = 2,
  median.col = theme$fg,
  median.alpha = 0.5,
  censor.mark = TRUE,
  censor.col = NULL,
  censor.alpha = 0.4,
  censor.pch = "I",
  censor.cex = 0.8,
  mark.censored = FALSE,
  nrisk.table = FALSE,
  nrisk.pos = "below",
  nrisk.spacing = 0.9,
  table.font = 1,
  time.at = NULL,
  time.by = NULL,
  xlim = NULL,
  ylim = NULL,
  xlab = "Time",
  ylab = "Survival",
  main = "",
  theme = rtTheme,
  palette = rtPalette,
  plot.error = FALSE,
  error.alpha = 0.33,
  autonames = TRUE,
  group.legend = NULL,
  group.legend.type = c("legend", "mtext"),
  group.names = NULL,
  group.title = NULL,
  group.line = NULL,
  group.side = NULL,
  legend.x = NULL,
  mar = c(2.5, 3, 2, 1),
  oma = NULL,
  par.reset = TRUE,
  pdf.width = 6,
  pdf.height = 6,
  filename = NULL,
  ...
)

Arguments

x	survfit object (output of survival::survfit)
lty	Integer: Line type. See par("lty")
lwd	Float: Line width.
alpha	Float: Alpha for lines.
col	Color, vector: Color(s) to use for survival curves and annotations. If NULL, taken from palette
plot.median	Logical: If TRUE, draw lines at 50 percent median survival.
group.median	Logical: If TRUE, include median survival times with group legend
median.lty	Integer: Median survival line type
median.lwd	Float: Median line width.
median.col	Color for median survival lines
median.alpha	Float, (0, 1): Transparency for median survival lines.
censor.mark	Logical: If TRUE, mark each censored case.
censor.col	Color to mark censored cases if censor.mark = TRUE
censor.alpha	Transparency for censor.col.
censor.pch	Character: Point character for censored marks.
censor.cex	Float: Character expansion factor for censor marks.
mark.censored	Logical: This is an alternative to censor.mark which whill mark censored cases using the same color as the survival curve. It can be harder to distinguish the censoring marks from the curve itself, therefore not preferred.
nrisk.table	Logical: If TRUE, print Number at risk table.
nrisk.pos	Character: "above" or "below": where to place nrisk.table
nrisk.spacing	Float: Determines spacing between nrisk.table rows.
table.font	Integer: 1: regular font, 2: bold.
time.at	Float, vector: x-axis positions to place tickmarks and labels as well as n at risk values if nrisk.table = TRUE
time.by	Float: Divide time by this amount to determine placing of tickmarks
xlim	Float, vector, length 2: x-axis limits
ylim	Float, vector, length 2: y-axis limits
xlab	Character: x-axis label
ylab	Character: y-axis label
main	Character: main title
theme	Character: Run themes() for available themes
palette	Vector of colors, or Character defining a builtin palette - get options with rtpalette()
autonames	Logical: If TRUE, extract grouping variable names and level labels from x and use for legend. It is best to give informative level labels, like female, male instead of 0, 1 when using this.
group.legend	Logical: If TRUE, include group legend
group.names	Character, vector: Group names to use. If NULL, extracted from x
group.title	Character: Group legend title
group.line	Float, vector: Lines to print group legend using mtext
group.side	Integer: Side to print group legend. Default is determined by survival curves, to avoid overlap of legend with curves.
mar	Float, vector, length 4: Margins. See par("mar")
oma	Float, vector, length 4: Outer margins. See par("oma")
par.reset	Logical: If TRUE, reset par to initial values before exit
...	Additional arguments to pass to theme

Author(s)

E.D. Gennatas

Examples

## Not run: 
# Get the lung dataset
data(cancer, package = "survival")
sf1 <- survival::survfit(survival::Surv(time, status) ~ 1, data = lung)
mplot3_survfit(sf1)
sf2 <- survival::survfit(survival::Surv(time, status) ~ sex, data = lung)
mplot3_survfit(sf2)
# with N at risk table
mplot3_survfit(sf2, nrisk.table = TRUE)

## End(Not run)

egenn/rtemis documentation built on Oct. 28, 2024, 6:30 a.m.