R/qsurvplot.R

In dewittpe/qwraps: Quick Wraps

#'KM plots
#'
#' Create Kaplan-Meier plots via ggplot2
#'
#'
#'@param fit a \code{survfit} object
#'@param show.ci logicial, show the confidence intervals for the KM fit
#'@param l.name: deprecated
#'@param labels: deprecated
#'@return ?
#' a ggplot object showing the KM curve(s)
#'@author Peter DeWitt
#'@seealso \code{\link{survfit}}
#'@references ?
#'@keywords ~kwd1 ~kwd2
#'@examples
#'
#' library(survival)
#' leukemia.surv <- survfit(Surv(time, status) ~ x, data = aml) 
#' plot(leukemia.surv, lty = 2:3)
#' qsurvplot(leukemia.surv)
#'
#' @export qsurvplot
qsurvplot <-
# function(fit, show.ci = getOption("qwraps.show.ci", TRUE), l.name = NULL, labels = NULL){
function(fit, show.ci = getOption("qwraps.show.ci", TRUE)){
  # Reassure R CMD check that the use of these variable names in ggplot
  # won't affect a global variable
  surv <- n.censor <- lower <- upper <- NULL

  n <- length(names(fit$strata))

  plot.data <- data.frame(
    time     = c(fit$time, rep(0, n)),
    n.risk   = c(fit$n.risk, rep(NA, n)),
    n.event  = c(fit$n.event, rep(NA, n)),
    n.censor = c(fit$n.censor, rep(0, n)),
    surv     = c(fit$surv, rep(1, n)),
    strata   = c(summary(fit, censored = TRUE)$strata, 1:n), 
    upper    = c(fit$upper, rep(1, n)),
    lower    = c(fit$lower, rep(1, n))) 

  plot.data$strata <- factor(plot.data$strata,
                             levels = 1:n,
                             labels = names(fit$strata))               

#   if(is.null(l.name)){
#     name <- "Strata"
#   }else{
#     name <- l.name
#   }

  g <- ggplot(plot.data, 
    aes(x = time, y = surv, colour = strata, fill = strata)) + 
    geom_step() + ylim(c(0, 1)) + ylab("Survivial") + 
    geom_point(data = subset(plot.data, n.censor > 0), shape = 3, alpha = 0.9) #+
#   if (is.null(labels)){
#     scale_colour_hue(name = name, breaks = levels(plot.data$strata))
# 	}else{
# 	  scale_colour_hue(name = name, breaks = levels(plot.data$strata),
# 	    labels = labels)
# 	}

  if (show.ci) {
    g <- g + geom_ribbon(aes(ymin = lower, ymax = upper), alpha = 0.5) 
  }

  return(g + theme(legend.position = "bottom", legend.direction = "horizontal"))
}