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@nbremer
Created March 3, 2018 11:10
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Creating a Kaplan Meier plot, used in Survival Analysis, using R's ggplot2 package
#' 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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