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plot.survfit<- function(x, conf.int, mark.time=FALSE,
pch=3, col=1,lty=1, lwd=1,
cex=1, log=FALSE,
xscale=1, yscale=1,
xlim, ylim, xmax,
fun, xlab="", ylab="", xaxs='r',
conf.times, conf.cap=.005, conf.offset=.012,
conf.type=c("log", "log-log", "plain",
"logit", "arcsin", "none"),
mark, mark.col, noplot="(s0)", cumhaz=FALSE,
firstx, ymin, cumprob=FALSE, ...) {
dotnames <- ...names()
if (any(dotnames =='type'))
stop("The graphical argument 'type' is not allowed")
if (!missing(mark))
warning("the mark option is deprecated, use mark.time=TRUE along with pch for the character")
x <- survfit0(x, x$start.time) # align data at 0 for plotting
# decide on logarithmic axes, yes or no
if (is.logical(log)) {
ylog <- log
xlog <- FALSE
if (ylog) logax <- 'y'
else logax <- ""
}
else {
ylog <- (log=='y' || log=='xy')
xlog <- (log=='x' || log=='xy')
logax <- log
}
if (!missing(fun)) {
if (is.character(fun)) {
if (fun=='log'|| fun=='logpct') ylog <- TRUE
if (fun=='cloglog') {
xlog <- TRUE
if (ylog) logax <- 'xy'
else logax <- 'x'
}
if (fun=="cumhaz" && missing(cumhaz)) cumhaz <- TRUE
}
}
# The default for plot and lines is to add confidence limits
# if there is only one curve
if (!missing(conf.type) || is.null(x$conf.type))
conf.type <- match.arg(conf.type) # check for legal
else conf.type <- x$conf.type # use the default in the curve
if (conf.type=="none") conf.int <- FALSE
if (missing(conf.int) && missing(conf.times))
conf.int <- (!is.null(x$std.err) && prod(dim(x) ==1))
if (missing(conf.times)) conf.times <- NULL
else {
if (!is.numeric(conf.times)) stop('conf.times must be numeric')
if (missing(conf.int)) conf.int <- TRUE
}
if (!missing(conf.int)) {
if (is.numeric(conf.int)) {
conf.level <- conf.int
if (conf.level<0 || conf.level > 1)
stop("invalid value for conf.int")
if (conf.level ==0) conf.int <- FALSE
else if (conf.level != x$conf.int) {
x$upper <- x$lower <- NULL # force recomputation
}
conf.int <- TRUE
}
else conf.level = 0.95
}
# Organize data into stime, ssurv, supper, slower
stime <- x$time
std <- NULL
yzero <- FALSE #a marker that we have an "ordinary survival curve" with min 0
smat <- function(x) {
# the rest of the routine is simpler if everything is a matrix
dd <- dim(x)
if (is.null(dd)) as.matrix(x)
else if (length(dd) ==2) x
else matrix(x, nrow=dd[1])
}
if (is.numeric(cumhaz)) { # plot the cumulative hazard
if (!inherits(x, "survfitms") && any(cumhaz != 1))
stop("numeric cumhaz argument only applies to multi-state")
dd <- dim(x$cumhaz)
if (is.null(dd)) nhazard <- 1
else nhazard <- prod(dd[-1])
if (!all(cumhaz == floor(cumhaz))) stop("cumhaz argument is not integer")
if (any(cumhaz < 1 | cumhaz > nhazard)) stop("subscript out of range")
ssurv <- smat(x$cumhaz)[,cumhaz, drop=FALSE]
if (!is.null(x$std.chaz)) std <- smat(x$std.chaz)[,cumhaz, drop=FALSE]
cumhaz <- TRUE # for the rest of the code
} else if (cumhaz) {
if (is.null(x$cumhaz))
stop("survfit object does not contain a cumulative hazard")
ssurv <- smat(x$cumhaz)
if (!is.null(x$std.chaz)) std <- smat(x$std.chaz)
}
else if (inherits(x, "survfitms")) {
if (!missing(cumprob) && !(is.logical(cumprob) && !cumprob)) {
if (conf.int)
stop("confidence intervals not available when cumprob=TRUE")
dd <- dim(x)
j <- match("states", names(dd), nomatch=0)
if (j==0) stop("survfitms object with no states dimension")
# cumprob is T/F or a vector of integers
if (is.logical(cumprob)) cumprob <- 1:dd[j]
else if (!is.numeric(cumprob) || any(cumprob <1 | cumprob > dd[j])
|| any(cumprob != floor(cumprob)))
stop("cumprob contains an invalid numeric")
if (dd[j] ==1) {
# nothing to do, user subscripted to only 1 state
ssurv <- x$pstate
} else {
# reorder the states, pstate has dimension 2 or 3,
# time/strata is first, data (if present), then states
# (dd is the dimension from the user's point of view, of
# strata, data, state)
if (length(dim(x$pstate))==2) {
# drop = FALSE for the rare case of a single time point
ssurv <- t(apply(x$pstate[,cumprob, drop=FALSE],1,cumsum))
} else {
temp <- apply(x$pstate[,,cumprob, drop=FALSE],1:2, cumsum)
ssurv <- smat(aperm(temp, c(2,3,1)))
}
cumprob <- TRUE # for the lastx line
}
} else {
i <- !(x$states %in% noplot)
if (all(i) || !any(i)) {
# the !any is a failsafe, in case none are kept we ignore noplot
ssurv <- smat(x$pstate)
if (!is.null(x$std.err)) std <- smat(x$std.err)
if (!is.null(x$lower)) {
slower <- smat(x$lower)
supper <- smat(x$upper)
}
}
else {
i <- which(i) # the states to keep
# we have to be careful about subscripting
if (length(dim(x$pstate)) ==3) {
ssurv <- smat(x$pstate[,,i, drop=FALSE])
if (!is.null(x$std.err))
std <- smat(x$std.err[,,i, drop=FALSE])
if (!is.null(x$lower)) {
slower <- smat(x$lower[,,i, drop=FALSE])
supper <- smat(x$upper[,,i, drop=FALSE])
}
}
else {
ssurv <- x$pstate[,i, drop=FALSE]
if (!is.null(x$std.err)) std <- x$std.err[,i, drop=FALSE]
if (!is.null(x$lower)) {
slower <- smat(x$lower[,i, drop=FALSE])
supper <- smat(x$upper[,i, drop=FALSE])
}
}
}
}
}
else {
yzero <- TRUE
ssurv <- as.matrix(x$surv) # x$surv will have one column
if (!is.null(x$std.err)) std <- as.matrix(x$std.err)
# The fun argument usually applies to single state survfit objects
# First deal with the special case of fun='cumhaz', which is here for
# backwards compatability; people should use the cumhaz argument
if (!missing(fun) && is.character(fun) && fun=="cumhaz") {
cumhaz <- TRUE
if (!is.null(x$cumhaz)) {
ssurv <- as.matrix(x$cumhaz)
if (!is.null(x$std.chaz)) std <- as.matrix(x$std.chaz)
}
else {
ssurv <- as.matrix(-log(x$surv))
if (!is.null(x$std.err)) {
if (x$logse) std <- as.matrix(x$std.err)
else std <- as.matrix(x$std.err/x$surv)
}
}
}
}
# set up strata
if (is.null(x$strata)) {
nstrat <- 1
stemp <- rep(1, length(x$time)) # same length as stime
}
else {
nstrat <- length(x$strata)
stemp <- rep(1:nstrat, x$strata) # same length as stime
}
ncurve <- nstrat * ncol(ssurv)
if (missing(conf.type)) {
missingtype <- TRUE
conf.type <- match.arg(conf.type)
} else missingtype <- FALSE # used below for cumhaz
if (conf.type=="none") conf.int <- FALSE
if (conf.int== "none") conf.int <- FALSE
if (conf.int=="only") {
plot.surv <- FALSE
conf.int <- TRUE
}
else plot.surv <- TRUE
if (conf.int) {
if (is.null(std)) stop("object does not have standard errors, CI not possible")
if (cumhaz) {
if (missingtype) conf.type="plain"
temp <- survfit_confint(ssurv, std, logse=FALSE,
conf.type, conf.level, ulimit=FALSE)
supper <- as.matrix(temp$upper)
slower <- as.matrix(temp$lower)
}
else if (is.null(x$upper)) {
if (missing(conf.type) && !is.null(x$conf.type))
conf.type <- x$conf.type
temp <- survfit_confint(ssurv, std, logse= x$logse,
conf.type, conf.level, ulimit=FALSE)
supper <- as.matrix(temp$upper)
slower <- as.matrix(temp$lower)
}
else if (!inherits(x, "survfitms")) {
supper <- as.matrix(x$upper)
slower <- as.matrix(x$lower)
}
} else supper <- slower <- NULL
if (!missing(fun)){
if (is.character(fun)) {
if (cumhaz) {
tfun <- switch(tolower(fun),
'log' = function(x) x,
'cumhaz'=function(x) x,
'identity'= function(x) x,
stop("Invalid function argument")
)
} else if (inherits(x, "survfitms")) {
tfun <-switch(tolower(fun),
'log' = function(x) log(x),
'event'=function(x) x,
'cloglog'=function(x) log(-log(1-x)),
'cumhaz' = function(x) x,
'pct' = function(x) x*100,
'identity'= function(x) x,
stop("Invalid function argument")
)
} else {
yzero <- FALSE
tfun <- switch(tolower(fun),
'log' = function(x) x,
'event'=function(x) 1-x,
'cumhaz'=function(x) x,
'cloglog'=function(x) log(-log(x)),
'pct' = function(x) x*100,
'logpct'= function(x) 100*x, #special case further below
'identity'= function(x) x,
'f' = function(x) 1-x,
's' = function(x) x,
'surv' = function(x) x,
stop("Unrecognized function argument")
)
}
}
else if (is.function(fun)) tfun <- fun
else stop("Invalid 'fun' argument")
ssurv <- tfun(ssurv )
if (!is.null(supper)) {
supper <- tfun(supper)
slower <- tfun(slower)
}
}
# Marks are not placed on confidence bands, pch only applies to marks
if (is.numeric(mark.time) || mark.time) {
if (is.numeric(mark.time)) mark.time <- sort(mark.time)
if (missing(pch)) pch <- rep(3, ncurve)
else pch <- rep(pch, length.out=ncurve)
if (!missing(mark.col)) mark.col <- rep(mark.col, length.out=ncurve)
else if (missing(col)) mark.col <- rep(1L, ncurve)
else mark.col <- rep(col, length.out=ncurve)
}
# The actual number of curves is ncurve*3 if there are confidence bands,
# unless conf.times has been given. Colors and line types in the latter
# match the curves
# If the number of line types is 1 and lty is an integer, then use lty
# for the curve and lty+1 for the CI
# If the length(lty) <= length(ncurve), use the same color for curve and CI
# otherwise assume the user knows what they are about and has given a full
# vector of line types.
# Colors and line widths work like line types, excluding the +1 rule.
if (conf.int & is.null(conf.times)) {
if (length(lty)==1 && is.numeric(lty))
lty <- rep(c(lty, lty+1, lty+1), ncurve)
else if (length(lty) <= ncurve)
lty <- rep(rep(lty, each=3), length.out=(ncurve*3))
else lty <- rep(lty, length.out= ncurve*3)
if (length(col) <= ncurve) col <- rep(rep(col, each=3), length.out=3*ncurve)
else col <- rep(col, length.out=3*ncurve)
if (length(lwd) <= ncurve) lwd <- rep(rep(lwd, each=3), length.out=3*ncurve)
else lwd <- rep(lwd, length.out=3*ncurve)
}
else {
col <- rep(col, length.out=ncurve)
lty <- rep(lty, length.out=ncurve)
lwd <- rep(lwd, length.out=ncurve)
}
# check consistency
if (!missing(xlim)) {
if (!missing(xmax)) warning("cannot have both xlim and xmax arguments, xmax ignored")
if (!missing(firstx)) stop("cannot have both xlim and firstx arguments")
}
if (!missing(ylim)) {
if (!missing(ymin)) stop("cannot have both ylim and ymin arguments")
}
# Do axis range computations
if (!missing(xlim) && !is.null(xlim)) {
tempx <- xlim
xmax <- xlim[2]
if (xaxs == 'S') tempx[2] <- tempx[1] + diff(tempx)*1.04
}
else {
temp <- stime[is.finite(stime)]
if (!missing(xmax) && missing(xlim)) temp <- pmin(temp, xmax)
else xmax <- NULL
if (xaxs=='S') {
rtemp <- range(temp)
delta <- diff(rtemp)
#special x- axis style for survival curves
if (xlog) tempx <- c(min(rtemp[rtemp>0]), min(rtemp)+ delta*1.04)
else tempx <- c(min(rtemp), min(rtemp)+ delta*1.04)
}
else if (xlog) tempx <- range(temp[temp > 0])
else tempx <- range(temp)
}
if (!missing(xlim) || !missing(xmax))
options(plot.survfit = list(xmax=tempx[2]))
else options(plot.survfit = NULL)
if (!missing(ylim) && !is.null(ylim)) tempy <- ylim
else {
skeep <- is.finite(stime) & stime >= tempx[1] & stime <= tempx[2]
if (ylog) {
if (!is.null(supper))
tempy <- range(c(slower[is.finite(slower) & slower>0 & skeep],
supper[is.finite(supper) & skeep]))
else tempy <- range(ssurv[is.finite(ssurv)& ssurv>0 & skeep])
if (tempy[2]==1) tempy[2] <- .99 # makes for a prettier axis
if (any(c(ssurv, slower)[skeep] ==0)) {
tempy[1] <- tempy[1]*.8
ssurv[ssurv==0] <- tempy[1]
if (!is.null(slower)) slower[slower==0] <- tempy[1]
}
}
else {
if (!is.null(supper))
tempy <- range(c(supper[skeep], slower[skeep]), finite=TRUE, na.rm=TRUE)
else tempy <- range(ssurv[skeep], finite=TRUE, na.rm= TRUE)
if (yzero) tempy <- range(c(0, tempy))
}
}
if (!missing(ymin)) tempy[1] <- ymin
#
# Draw the basic box
#
temp <- if (xaxs=='S') 'i' else xaxs
plot(range(tempx, finite=TRUE, na.rm=TRUE)/xscale,
range(tempy, finite=TRUE, na.rm=TRUE)*yscale,
type='n', log=logax, xlab=xlab, ylab=ylab, xaxs=temp,...)
if(yscale != 1) {
if (ylog) par(usr =par("usr") -c(0, 0, log10(yscale), log10(yscale)))
else par(usr =par("usr")/c(1, 1, yscale, yscale))
}
if (xscale !=1) {
if (xlog) par(usr =par("usr") -c(log10(xscale), log10(xscale), 0,0))
else par(usr =par("usr")*c(xscale, xscale, 1, 1))
}
# The use of [[par(usr)]] just above is a bit sneaky. I want the
# lines and points routines to be able to add to the plot, *without*
# passing them a global parameter that determines the y-scale or forcing
# the user to repeat it.
# Create a step function, removing redundancies that sometimes occur in
# curves with lots of censoring.
dostep <- function(x,y) {
keep <- is.finite(x) & is.finite(y)
if (!any(keep)) return() #all points were infinite or NA
if (!all(keep)) {
# these won't plot anyway, so simplify (CI values are often NA)
x <- x[keep]
y <- y[keep]
}
n <- length(x)
if (n==1) list(x=x, y=y)
else if (n==2) list(x=x[c(1,2,2)], y=y[c(1,1,2)])
else {
# replace verbose horizonal sequences like
# (1, .2), (1.4, .2), (1.8, .2), (2.3, .2), (2.9, .2), (3, .1)
# with (1, .2), (.3, .2),(3, .1).
# They are slow, and can smear the looks of the line type.
temp <- rle(y)$lengths
drops <- 1 + cumsum(temp[-length(temp)]) # points where the curve drops
#create a step function
if (n %in% drops) { #the last point is a drop
xrep <- c(x[1], rep(x[drops], each=2))
yrep <- rep(y[c(1,drops)], c(rep(2, length(drops)), 1))
}
else {
xrep <- c(x[1], rep(x[drops], each=2), x[n])
yrep <- c(rep(y[c(1,drops)], each=2))
}
list(x=xrep, y=yrep)
}
}
drawmark <- function(x, y, mark.time, censor, cex, ...) {
if (!is.numeric(mark.time)) {
xx <- x[censor>0]
yy <- y[censor>0]
if (any(censor >1)) { # tied death and censor, put it on the midpoint
j <- pmax(1, which(censor>1) -1)
i <- censor[censor>0]
yy[i>1] <- (yy[i>1] + y[j])/2
}
}
else { #interpolate
xx <- mark.time
yy <- approx(x, y, xx, method="constant", f=0)$y
}
points(xx, yy, cex=cex, ...)
}
type <- 's'
c1 <- 1 # keeps track of the curve number
c2 <- 1 # keeps track of the lty, col, etc
xend <- yend <- double(ncurve)
if (length(conf.offset) ==1)
temp.offset <- (1:ncurve - (ncurve+1)/2)* conf.offset* diff(par("usr")[1:2])
else temp.offset <- rep(conf.offset, length=ncurve) * diff(par("usr")[1:2])
temp.cap <- conf.cap * diff(par("usr")[1:2])
for (j in 1:ncol(ssurv)) {
for (i in unique(stemp)) { #for each strata
who <- which(stemp==i)
# if n.censor is missing, then assume any line that does not have an
# event would not be present but for censoring, so there must have
# been censoring then
# otherwise categorize is 0= no censor, 1=censor, 2=censor and death
if (is.null(x$n.censor)) censor <- ifelse(x$n.event[who]==0, 1, 0)
else censor <- ifelse(x$n.censor[who]==0, 0, 1 + (x$n.event[who] > 0))
xx <- stime[who]
yy <- ssurv[who,j]
if (conf.int) {
ylower <- (slower[who,j])
yupper <- (supper[who,j])
}
if (!is.null(xmax) && max(xx) > xmax) { # truncate on the right
# say that there are points at 10 and 20, with xmax=15
# we want to draw the line up to time 15, so we don't want to
# toss out the point at 20, rather change its time to 15.
# But, we also need to remove the mark
xn <- min(which(xx > xmax))
xx <- xx[1:xn]
yy <- yy[1:xn]
if (xx[xn] > xmax) censor[xn] <-0 # don't draw a "+" here
xx[xn] <- xmax
yy[xn] <- yy[xn-1]
if (conf.int) {
ylower <- ylower[1:xn]
yupper <- yupper[1:xn]
ylower[xn] <- ylower[xn-1]
yupper[xn] <- yupper[xn-1]
}
}
if (plot.surv) {
if (type=='s')
lines(dostep(xx, yy), lty=lty[c2], col=col[c2], lwd=lwd[c2])
else lines(xx, yy, type=type, lty=lty[c2], col=col[c2], lwd=lwd[c2])
if (is.numeric(mark.time) || mark.time)
drawmark(xx, yy, mark.time, censor, pch=pch[c1],
col=mark.col[c1], cex=cex)
}
xend[c1] <- max(xx)
yend[c1] <- yy[length(yy)]
if (conf.int && !is.null(conf.times)) {
# add vertical bars at the specified times
x2 <- conf.times + temp.offset[c1]
templow <- approx(xx, ylower, x2,
method='constant', f=1)$y
temphigh<- approx(xx, yupper, x2,
method='constant', f=1)$y
segments(x2, templow, x2, temphigh,
lty=lty[c2], col=col[c2], lwd=lwd[c2])
if (conf.cap>0) {
segments(x2-temp.cap, templow, x2+temp.cap, templow,
lty=lty[c2], col=col[c2], lwd=lwd[c2] )
segments(x2-temp.cap, temphigh, x2+temp.cap, temphigh,
lty=lty[c2], col=col[c2], lwd=lwd[c2])
}
}
c1 <- c1 +1
c2 <- c2 +1
if (conf.int && is.null(conf.times)) {
if (type == 's') {
lines(dostep(xx, ylower), lty=lty[c2],
col=col[c2],lwd=lwd[c2])
c2 <- c2 +1
lines(dostep(xx, yupper), lty=lty[c2],
col=col[c2], lwd= lwd[c2])
c2 <- c2 + 1
}
else {
lines(xx, ylower, lty=lty[c2],
col=col[c2],lwd=lwd[c2], type=type)
c2 <- c2 +1
lines(xx, yupper, lty=lty[c2],
col=col[c2], lwd= lwd[c2], type= type)
c2 <- c2 + 1
}
}
}
}
if (cumprob) {
if (!is.null(xmax) && max(stime) > xmax) { # truncate on the right
keep <- (stime <= xmax)
lastx <- list(x = stime[keep], y= ssurv[,keep])
}
else lastx <- list(x=stime, y=ssurv)
}
else lastx <- list(x=xend, y=yend)
invisible(lastx)
}
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