GGally: ggsurv – R documentation

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ggsurv

Survival curves

Description

This function produces Kaplan-Meier plots using ggplot2. As a first argument it needs a survfit object, created by the survival package. Default settings differ for single stratum and multiple strata objects.

Usage

ggsurv(
  s,
  CI = "def",
  plot.cens = TRUE,
  surv.col = "gg.def",
  cens.col = "gg.def",
  lty.est = 1,
  lty.ci = 2,
  size.est = 0.5,
  size.ci = size.est,
  cens.size = 2,
  cens.shape = 3,
  back.white = FALSE,
  xlab = "Time",
  ylab = "Survival",
  main = "",
  order.legend = TRUE
)

Arguments

`s`	an object of class `survfit`
`CI`	should a confidence interval be plotted? Defaults to `TRUE` for single stratum objects and `FALSE` for multiple strata objects.
`plot.cens`	mark the censored observations?
`surv.col`	colour of the survival estimate. Defaults to black for one stratum, and to the default ggplot2 colours for multiple strata. Length of vector with colour names should be either 1 or equal to the number of strata.
`cens.col`	colour of the points that mark censored observations.
`lty.est`	linetype of the survival curve(s). Vector length should be either 1 or equal to the number of strata.
`lty.ci`	linetype of the bounds that mark the 95% CI.
`size.est`	line width of the survival curve
`size.ci`	line width of the 95% CI
`cens.size`	point size of the censoring points
`cens.shape`	shape of the points that mark censored observations.
`back.white`	if TRUE the background will not be the default grey of `ggplot2` but will be white with borders around the plot.
`xlab`	the label of the x-axis.
`ylab`	the label of the y-axis.
`main`	the plot label.
`order.legend`	boolean to determine if the legend display should be ordered by final survival time

Value

An object of class ggplot

Author(s)

Edwin Thoen

Examples

# Small function to display plots only if it's interactive
p_ <- GGally::print_if_interactive

if (require(survival) && require(scales)) {
  data(lung, package = "survival")
  sf.lung <- survival::survfit(Surv(time, status) ~ 1, data = lung)
  p_(ggsurv(sf.lung))

  # Multiple strata examples
  sf.sex <- survival::survfit(Surv(time, status) ~ sex, data = lung)
  pl.sex <- ggsurv(sf.sex)
  p_(pl.sex)

  # Adjusting the legend of the ggsurv fit
  p_(pl.sex +
    ggplot2::guides(linetype = FALSE) +
    ggplot2::scale_colour_discrete(
      name   = 'Sex',
      breaks = c(1,2),
      labels = c('Male', 'Female')
    ))

  # Multiple factors
  lung2 <- plyr::mutate(lung, older = as.factor(age > 60))
  sf.sex2 <- survival::survfit(Surv(time, status) ~ sex + older, data = lung2)
  pl.sex2 <- ggsurv(sf.sex2)
  p_(pl.sex2)

  # Change legend title
  p_(pl.sex2 + labs(color = "New Title", linetype = "New Title"))

  # We can still adjust the plot after fitting
  data(kidney, package = "survival")
  sf.kid <- survival::survfit(Surv(time, status) ~ disease, data = kidney)
  pl.kid <- ggsurv(sf.kid, plot.cens = FALSE)
  p_(pl.kid)

  # Zoom in to first 80 days
  p_(pl.kid + ggplot2::coord_cartesian(xlim = c(0, 80), ylim = c(0.45, 1)))

  # Add the diseases names to the plot and remove legend
  p_(pl.kid +
    ggplot2::annotate(
      "text",
      label  = c("PKD", "Other", "GN", "AN"),
      x      = c(90, 125, 5, 60),
      y      = c(0.8, 0.65, 0.55, 0.30),
      size   = 5,
      colour = scales::hue_pal(
        h         = c(0, 360) + 15,
        c         = 100,
        l         = 65,
        h.start   = 0,
        direction = 1
      )(4)
    ) +
    ggplot2::guides(color = FALSE, linetype = FALSE))
}

GGally

Extension to 'ggplot2'

v2.1.1

GPL (>= 2.0)

Authors

Barret Schloerke [aut, cre], Di Cook [aut, ths], Joseph Larmarange [aut], Francois Briatte [aut], Moritz Marbach [aut], Edwin Thoen [aut], Amos Elberg [aut], Ott Toomet [ctb], Jason Crowley [aut], Heike Hofmann [ths], Hadley Wickham [ths]

Initial release