Allow ggplot2 to handle survival::survfit result

fortify_survfit.R

library(survival)

library(ggplot2)
library(scales)

d.survfit <- survival::survfit(survival::Surv(time, status) ~ sex,
                               data = lung)

fortify.survfit <- function(survfit.data) {
  data.frame(time = survfit.data$time,
             n.risk = survfit.data$n.risk,
             n.event = survfit.data$n.event,
             n.censor = survfit.data$n.censor,
             surv = survfit.data$surv,
             std.err = survfit.data$std.err,
             upper = survfit.data$upper,
             lower = survfit.data$lower,
             strata = rep(names(survfit.data$strata), survfit.data$strata))
}

head(ggplot2::fortify(d.survfit))

ggplot(data = d.survfit) +
  geom_line(aes_string(x = 'time', y = 'surv', colour = 'strata')) +
  geom_ribbon(aes_string(x = 'time', ymin = 'lower', ymax = 'upper', fill = 'strata'), alpha = 0.5) + 
  scale_y_continuous(labels = scales::percent)

# plot censors
fortified <- ggplot2::fortify(d.survfit)
ggplot(data = fortified) +
  geom_line(aes_string(x = 'time', y = 'surv', colour = 'strata')) +
  geom_ribbon(aes_string(x = 'time', ymin = 'lower', ymax = 'upper', fill = 'strata'), alpha = 0.5) +
  geom_point(data = fortified[fortified$n.censor > 0, ],
             aes_string(x = 'time', y = 'surv'), shape = '+', size = 3) + 
  scale_y_continuous(labels = scales::percent)