Creating a Kaplan Meier plot, used in Survival Analysis, using R's ggplot2 package

KaplanMeierPlotR.R

#' Create a Kaplan-Meier plot using ggplot2
#'
#' @param sfit: a survfit object
#' @param table: logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
#' @param returns logical: if TRUE, return an arrangeGrob object
#' @param xlabs: x-axis label
#' @param ylabs: y-axis label
#' @param ystratalabs: The strata labels. Default = levels(summary(sfit)$strata)
#' @param ystrataname: The legend name. Default = "Strata"
#' @param timeby numeric: control the granularity along the time-axis
#' @param main plot title
#' @param pval logical: add the pvalue to the plot?
#' @param marks logical: should censoring marks be added?
#' @param shape: what shape should the censoring marks be, default is a vertical line
#' @param legend logical: should a legend be added to the plot?
#' 
#' @return a ggplot is made. if return=TRUE, then an arrangeGlob object
#' is returned
#' @author Abhijit Dasgupta with contributions by Gil Tomas
#' \url{http://statbandit.wordpress.com/2011/03/08/an-enhanced-kaplan-meier-plot/}
#' slight adjustment to cope with none strata calls (e.g. Surv(time,event)~1), 
#' option to remove the legend and also draw marks at censoring locations by Nadieh Bremer
#' 
#' @examples
#'  library(survival)
#'  data(colon)
#'  fit <- survfit(Surv(time,status)~rx, data=colon)
#'  ggkm(fit, timeby=500)

ggkm <- function(sfit,
                 table = TRUE,
                 returns = FALSE,
                 xlabs = "Time",
                 ylabs = "Survival Probability",
                 xlims = c(0,max(sfit$time)),
                 ylims = c(0,1),
                 ystratalabs = NULL,
                 ystrataname = NULL,
                 timeby = 100,
                 main = "Kaplan-Meier Plot",
                 pval = TRUE,
                 marks = FALSE,
                 shape = 3,
                 legend = TRUE,
                 subs = NULL,
                 ...) {
  
  #############
  # libraries #
  #############
  
  #Check if the following packages have been installed. If not, install them
  if (!"ggplot2" %in% installed.packages()) install.packages("ggplot2")
  if (!"survival" %in% installed.packages()) install.packages("survival")
  if (!"gridExtra" %in% installed.packages()) install.packages("gridExtra")
  if (!"reshape" %in% installed.packages()) install.packages("reshape")
  
  suppressPackageStartupMessages(library(ggplot2, warn.conflicts=FALSE))
  suppressPackageStartupMessages(library(survival, warn.conflicts=FALSE))
  suppressPackageStartupMessages(library(gridExtra, warn.conflicts=FALSE))
  suppressPackageStartupMessages(library(reshape, warn.conflicts=FALSE))
  
  #################################
  # sorting the use of subsetting #
  #################################
  
  times <- seq(0, max(sfit$time), by = timeby)
  
  if(is.null(subs)){
    if(length(levels(summary(sfit)$strata)) == 0) {
      subs1 <- 1
      subs2 <- 1:length(summary(sfit,censored=T)$time)
      subs3 <- 1:length(summary(sfit,times = times,extend = TRUE)$time)
    } else {
      subs1 <- 1:length(levels(summary(sfit)$strata))
      subs2 <- 1:length(summary(sfit,censored=T)$strata)
      subs3 <- 1:length(summary(sfit,times = times,extend = TRUE)$strata)
    }
  } else{
    for(i in 1:length(subs)){
      if(i==1){
        ssvar <- paste("(?=.*\\b=",subs[i],sep="")
      }
      if(i==length(subs)){
        ssvar <- paste(ssvar,"\\b)(?=.*\\b=",subs[i],"\\b)",sep="")
      }
      if(!i %in% c(1, length(subs))){
        ssvar <- paste(ssvar,"\\b)(?=.*\\b=",subs[i],sep="")
      }
      if(i==1 & i==length(subs)){
        ssvar <- paste("(?=.*\\b=",subs[i],"\\b)",sep="")
      }
    }
    subs1 <- which(regexpr(ssvar,levels(summary(sfit)$strata), perl=T)!=-1)
    subs2 <- which(regexpr(ssvar,summary(sfit,censored=T)$strata, perl=T)!=-1)
    subs3 <- which(regexpr(ssvar,summary(sfit,times = times,extend = TRUE)$strata, perl=T)!=-1)
  }
  
  if(!is.null(subs)) pval <- FALSE
  
  ##################################
  # data manipulation pre-plotting #
  ##################################
  
  if(length(levels(summary(sfit)$strata)) == 0) {
    #[subs1]
    if(is.null(ystratalabs)) ystratalabs <- as.character(sub("group=*","","All"))
  } else {
    #[subs1]
    if(is.null(ystratalabs)) ystratalabs <- as.character(sub("group=*","",names(sfit$strata)))
  }
  
  if(is.null(ystrataname)) ystrataname <- "Strata"
  m <- max(nchar(ystratalabs))
  times <- seq(0, max(sfit$time), by = timeby)
  
  if(length(levels(summary(sfit)$strata)) == 0) {
    Factor <- factor(rep("All",length(subs2)))
  } else {
    Factor <- factor(summary(sfit, censored = T)$strata[subs2])
  }
  
  #Data to be used in the survival plot
  .df <- data.frame(
    time = sfit$time[subs2],
    n.risk = sfit$n.risk[subs2],
    n.event = sfit$n.event[subs2],
    n.censor = sfit$n.censor[subs2],
    surv = sfit$surv[subs2],
    strata = Factor,
    upper = sfit$upper[subs2],
    lower = sfit$lower[subs2]
  )
  
  #Final changes to data for survival plot
  levels(.df$strata) <- ystratalabs
  zeros <- data.frame(time = 0, surv = 1,
                      strata = factor(ystratalabs, levels=levels(.df$strata)),
                      upper = 1, lower = 1)
  .df <- rbind.fill(zeros, .df)
  d <- length(levels(.df$strata))
  
  ###################################
  # specifying plot parameteres etc #
  ###################################
  
  p <- ggplot( .df, aes(time, surv)) +
    geom_step(aes(linetype = strata), size = 0.7) +
    theme_bw() +
    theme(axis.title.x = element_text(vjust = 0.5)) +
    scale_x_continuous(xlabs, breaks = times, limits = xlims) +
    scale_y_continuous(ylabs, limits = ylims) +
    theme(panel.grid.minor = element_blank()) +
    # MOVE LEGEND HERE BELOW [first is x dim, second is y dim]
    theme(legend.position = c(ifelse(m < 10, .85, .75),ifelse(d < 4, .85, .8))) +
    theme(legend.key = element_rect(colour = NA)) +
    theme(panel.border = element_blank()) +
    labs(linetype = ystrataname) +
    theme(plot.margin = unit(c(0, 1, .5,ifelse(m < 10, 1.5, 2.5)),"lines")) +
    ggtitle(main)
  
  #Removes the legend: 
  if(legend == FALSE) 
    p <- p + theme(legend.position="none")
  
  #Add censoring marks to the line:
  if(marks == TRUE)
    p <- p + geom_point(data = subset(.df, n.censor >= 1), aes(x = time, y = surv), shape = shape)
  
  ## Create a blank plot for place-holding
  blank.pic <- ggplot(.df, aes(time, surv)) +
    geom_blank() + theme_bw() +
    theme(axis.text.x = element_blank(),axis.text.y = element_blank(),
          axis.title.x = element_blank(),axis.title.y = element_blank(),
          axis.ticks = element_blank(),
          panel.grid.major = element_blank(),panel.border = element_blank())
  
  #####################
  # p-value placement #
  #####################a
  
  if(length(levels(summary(sfit)$strata)) == 0) pval <- FALSE
    
  if(pval == TRUE) {
    sdiff <- survdiff(eval(sfit$call$formula), data = eval(sfit$call$data))
    pvalue <- pchisq(sdiff$chisq,length(sdiff$n) - 1,lower.tail = FALSE)
    pvaltxt <- ifelse(pvalue < 0.0001,"p < 0.0001",paste("p =", signif(pvalue, 3)))
    # MOVE P-VALUE LEGEND HERE BELOW [set x and y]
    p <- p + annotate("text",x = 150, y = 0.1,label = pvaltxt)
  }#if
  
  ###################################################
  # Create table graphic to include at-risk numbers #
  ###################################################
  
  if(length(levels(summary(sfit)$strata)) == 0) {
    Factor <- factor(rep("All",length(subs3)))
  } else {
    Factor <- factor(summary(sfit,times = times,extend = TRUE)$strata[subs3])
  }
  
  if(table) {
    risk.data <- data.frame(
      strata = Factor,
      time = summary(sfit,times = times,extend = TRUE)$time[subs3],
      n.risk = summary(sfit,times = times,extend = TRUE)$n.risk[subs3]
    )
    risk.data$strata <- factor(risk.data$strata, levels=rev(levels(risk.data$strata)))
    
    data.table <- ggplot(risk.data,aes(x = time, y = strata, label = format(n.risk, nsmall = 0))) +
      geom_text(size = 3.5) + theme_bw() +
      scale_y_discrete(breaks = as.character(levels(risk.data$strata)),
                       labels = rev(ystratalabs)) +
      scale_x_continuous("Numbers at risk", limits = xlims) +
      theme(axis.title.x = element_text(size = 10, vjust = 1),
            panel.grid.major = element_blank(), panel.grid.minor = element_blank(),
            panel.border = element_blank(),axis.text.x = element_blank(),
            axis.ticks = element_blank(),axis.text.y = element_text(face = "bold",hjust = 1))
    
    data.table <- data.table +
      theme(legend.position = "none") + xlab(NULL) + ylab(NULL)
    
    # ADJUST POSITION OF TABLE FOR AT RISK
    data.table <- data.table +
      theme(plot.margin = unit(c(-1.5, 1, 0.1, ifelse(m < 10, 2.5, 3.5) - 0.15 * m), "lines"))
    
    #######################
    # Plotting the graphs #
    #######################

    grid.arrange(p, blank.pic, data.table, clip = FALSE, nrow = 3,
                 ncol = 1, heights = unit(c(2, .1, .25),c("null", "null", "null")))
    
    if(returns) {
      a <- arrangeGrob(p, blank.pic, data.table, clip = FALSE, nrow = 3,
                       ncol = 1, heights = unit(c(2, .1, .25), c("null", "null", "null")))
      return(a)
    }#if
  } else {
    if(returns) return(p)
  }#else
}

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