geom_stepribbon

The geom_stepribbon is an extension of the geom_ribbon, and is optimized for Kaplan-Meier plots with pointwise confidence intervals or a confidence band.

Usage

geom_stepribbon(mapping = NULL, data = NULL, stat = "identity",
  position = "identity", na.rm = FALSE, show.legend = NA,
  inherit.aes = TRUE, kmplot = FALSE, ...)

The additional argument

kmplot
- If TRUE, missing values are replaced by the previous values. This option is needed to make Kaplan-Meier plots if the last observation has an event, in which case the upper and lower values of the last observation are missing. This processing is optimized for results from the survfit function.

Other arguments are the same as the geom_ribbon.

Example

require("ggplot2")

## Loading required package: ggplot2

huron <- data.frame(year = 1875:1972, level = as.vector(LakeHuron))
h <- ggplot(huron, aes(year))
h + RcmdrPlugin.KMggplot2::geom_stepribbon(
      aes(ymin = level - 1, ymax = level + 1),
      fill = "grey70"
    ) +
    geom_step(aes(y = level))

## Registered S3 method overwritten by 'lme4':
##   method           from
##   na.action.merMod car

## Warning in RcmdrPlugin.KMggplot2::geom_stepribbon(aes(ymin = level - 1, :
## Ignoring unknown parameters: `orientation` and `outline.type`

h + geom_ribbon(
      aes(ymin = level - 1, ymax = level + 1),
      fill = "grey70"
    ) +
    geom_line(aes(y = level))

data(dataKm, package = "RcmdrPlugin.KMggplot2")

.df <- na.omit(data.frame(x = dataKm$time, y = dataKm$event, z = dataKm$trt))
.df <- .df[do.call(order, .df[, c("z", "x"), drop = FALSE]), , drop = FALSE]
.fit <- survival::survfit(
  survival::Surv(time = x, event = y, type = "right") ~ z, .df)
.fit <- data.frame(x = .fit$time, y = .fit$surv, nrisk = .fit$n.risk, 
  nevent = .fit$n.event, ncensor= .fit$n.censor, upper = .fit$upper,
  lower = .fit$lower)
.df <- .df[!duplicated(.df[,c("x", "z")]), ]
.df <- .fit <- data.frame(.fit, .df[, c("z"), drop = FALSE])
.df <- .fit <- rbind(unique(data.frame(x = 0, y = 1, nrisk = NA, nevent = NA,
  ncensor = NA, upper = 1, lower = 1, .df[, c("z"), drop = FALSE])), .fit)
.cens <- subset(.fit, ncensor == 1)

ggplot(data = .fit, aes(x = x, y = y, colour = z)) + 
  RcmdrPlugin.KMggplot2::geom_stepribbon(data = .fit,
    aes(x = x, ymin = lower, ymax = upper, fill = z), alpha = 0.25,
    colour = "transparent", show.legend = FALSE, kmplot = TRUE) +
  geom_step(size = 1.5) +
  geom_linerange(data = .cens, aes(x = x, ymin = y, ymax = y + 0.02),
    size = 1.5) + 
  scale_x_continuous(breaks = seq(0, 21, by = 7), limits = c(0, 21)) + 
  scale_y_continuous(limits = c(0, 1), expand = c(0.01, 0)) + 
  scale_colour_brewer(palette = "Set1") +
  scale_fill_brewer(palette = "Set1") +
  xlab("Time from entry") +
  ylab("Proportion of survival") +
  labs(colour = "trt") +
  theme_bw(base_size = 14, base_family = "sans") + 
  theme(legend.position = "right")

## Warning in RcmdrPlugin.KMggplot2::geom_stepribbon(data = .fit, aes(x = x, :
## Ignoring unknown parameters: `orientation` and `outline.type`

## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once per session.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.