plot.survfit {survival}R Documentation

Plot Method for 'survfit'

Description

A plot of survival curves is produced, one curve for each strata. The log=T option does extra work to avoid log(0), and to try to create a pleasing result. If there are zeros, they are plotted by default at 0.8 times the smallest non-zero value on the curve(s).

If legend.text is supplied a legend is created.

Usage

## S3 method for class 'survfit':
plot(x, conf.int=, mark.time=TRUE,
 mark=3, col=1, lty=1, lwd=1, cex=1, log=FALSE, xscale=1, yscale=1, 
 firstx=0, firsty=1, xmax, ymin=0, fun,
 xlab="", ylab="", xaxs="S", bty=NULL,
legend.text=NULL,legend.pos=0,legend.bty="n",main=NULL,...)

Arguments

x an object of class survfit, usually returned by the survfit function.
conf.int determines whether confidence intervals will be plotted. The default is to do so if there is only 1 curve, i.e., no strata.
mark.time controls the labeling of the curves. If set to FALSE, no labeling is done. If TRUE, then curves are marked at each censoring time which is not also a death time. If mark.time is a numeric vector, then curves are marked at the specified time points.
mark vector of mark parameters, which will be used to label the curves. The lines help file contains examples of the possible marks. The vector is reused cyclically if it is shorter than the number of curves.
col a vector of integers specifying colors for each curve. The default value is 1.
lty a vector of integers specifying line types for each curve. The default value is 1.
lwd a vector of numeric values for line widths. The default value is 1.
cex a numeric value specifying the size of the marks. Not a vector; all marks have the same size.
log a logical value, if TRUE the y axis wll be on a log scale. Alternately, one of the standard character strings "x", "y", or "xy" can be given to specific logarithmic horizontal and/or vertical axes.
xscale scale the x-axis values before plotting. If time were in days, then a value of 365.25 will give labels in years instead of the original days.
yscale will be used to multiply the labels on the y axis. A value of 100, for instance, would be used to give a percent scale. Only the labels are changed, not the actual plot coordinates, so that adding a curve with "lines(surv.exp(...{}))", say, will perform as it did without the yscale argument.
firstx,firsty the starting point for the survival curves. If either of these is set to NA the plot will start at the first time point of the curve.
xmax the maximum horizontal plot coordinate. This can be used to shrink the range of a plot. It shortens the curve before plotting it, so that unlike using the xlim graphical parameter, warning messages about out of bounds points are not generated.
ymin lower boundary for y values. Survival curves are most often drawn in the range of 0-1, even if none of the curves approach zero. The parameter is ignored if the fun argument is present, or if it has been set to NA.
fun an arbitrary function defining a transformation of the survival curve. For example fun=log is an alternative way to draw a log-survival curve (but with the axis labeled with log(S) values), and fun=sqrt would generate a curve on square root scale. Four often used transformations can be specified with a character argument instead: "log" is the same as using the log=T option, "event" plots cumulative events (f(y) = 1-y), "cumhaz" plots the cumulative hazard function (f(y) = -log(y)), and "cloglog" creates a complimentary log-log survival plot (f(y) = log(-log(y)) along with log scale for the x-axis).
xlab label given to the x-axis.
ylab label given to the y-axis.
xaxs either "S" for a survival curve or a standard x axis style as listed in par. Survival curves are usually displayed with the curve touching the y-axis, but not touching the bounding box of the plot on the other 3 sides. Type "S" accomplishes this by manipulating the plot range and then using the "i" style internally.
bty see par
legend.pos position for the legend: a vector of length 2, or 0 to put the legend in the lower left, 1 to put it in the upper right. These may not work well with transformed curves.
legend.bty Box type, see legend
legend.text Text for legend, see legend
main Plot title
... other graphical parameters

Value

a list with components x and y, containing the coordinates of the last point on each of the curves (but not the confidence limits). This may be useful for labeling.

BUGS

Survival curve objects created from a coxph model does not include the censoring times. Therefore, specifying mark.time=T does not work. If you want to mark censoring times on the curve(s) resulting from a coxph fit, provide a vector of times as the mark.time argument in the call to plot.survfit or lines.survfit.

See Also

par, survfit, lines.survfit legend.

Examples

leukemia.surv <- survfit(Surv(time, status) ~ x, data = aml)
plot(leukemia.surv, lty = 2:3)
legend(100, .9, c("Maintenance", "No Maintenance"), lty = 2:3)
title("Kaplan-Meier Curves\nfor AML Maintenance Study")

lsurv2 <- survfit(Surv(time, status) ~ x, aml, type='fleming')
plot(lsurv2, lty=2:3, fun="cumhaz",
        xlab="Months", ylab="Cumulative Hazard")

plot(leukemia.surv,lty=1:2,legend.pos=0,col=c("Red","Blue"),legend.text=c("Maintenance",
"No Maintenance"))
if (interactive()){
cat("Click on the graphics device to place a legend\n")
plot(leukemia.surv,lty=2:3,legend.pos=locator(1),legend.text=c("Maintenance",
"No Maintenance"))
}

[Package survival version 2.31 Index]