survMisc (version 0.4.6)

autoplot.survfit: Generate a ggplot for a survfit object

Description

Uses ggplot2 to render a table showing the number of subjects at risk per time period and survival curves (Kaplan-Meier plot) and to render

Usage

## S3 method for class 'survfit':
autoplot(object, ..., xLab = "Time", yLab = "Survival",
  title = "Marks show times with censoring", titleSize = 15,
  axisTitleSize = 15, axisLabSize = 10, survLineSize = 0.5,
  type = c("single", "CI", "fill"), palette = c("Dark2", "Set2", "Accent",
  "Paired", "Pastel1", "Pastel2", "Set1", "Set3"), jitter = c("none",
  "noEvents", "all"), censShape = 3, censSize = 5, legend = TRUE,
  legLabs = NULL, legTitle = "Strata", legTitleSize = 10,
  legLabSize = 10, alpha = 0.05, CIline = 10, fillLineSize = 0.05,
  pVal = FALSE, sigP = 1, pX = 0.1, pY = 0.1, timeTicks = c("major",
  "minor"), tabTitle = "Number at risk by time", tabTitleSize = 15,
  tabLabSize = 5, nRiskSize = 5)

Arguments

object

An object of class survfit

...

Additional arguments (not implemented)

xLab

Label for $x$ axis on survival plot

yLab

Label for $y$ axis on survival plot

title

Title for survival plot

titleSize

Title size for survival plot

axisTitleSize

Title size for axes

axisLabSize

Title size for label axes

survLineSize

Survival line size

type

Type of plot. The default, type="single", plots single lines.

• Iftype="CI"will add lines indicating confidence intervals (taken fromupperandlowervalues ofsurvfitobject). Highe

palette

Options are taken from http://colorbrewer2.org/{color_brewer}.

• palette="Dark2"(the default) is recommended forsingleorCIplots.
• palette="Set2"is recommended forfill

jitter

By default, jitter="none".

• Ifjitter="noEvents", adds some random, positive noise to survival lines with no events (i.e. all observations censored). This will bring them just above 1 on the y-axis, making them easier to se

legend

If legend=FALSE, no legends will be produced for the plot or table

legLabs

These can be used to replace the names of the strata from the fit. Should be given in the same order as those strata

legTitle

Title for legend

legTitleSize

Title size for legend

legLabSize

Legend labels width and height

alpha

Alpha, transparency of lines indicating confidence intervals or filled rectangles. Should be in range $0-1$. Larger values e.g. alpha=0.7 are recommended for confidence intervals

censShape

Shape of marks to indicate censored onservations. Default is 3 which gives vertical ticks. Use censShape=10 for circular marks.

censSize

Size of marks to indicate censored onservations

CIline

Confidence interval line type

fillLineSize

Line size surrouding filled boxes

pVal

If pVal=TRUE, adds $p$ value from log-rank test to plot

sigP

No. of significant digits to display in $p$ value. Typically $1$ to $3$.

pX

Location of $p$ value on $x$ axis. Should be in the range of $0 - 1$, where value is to be placed relative to the maximum observed time. E.g. pX = 0.5 will place it half-way along $x$-axis

pY

Location of $p$ value on $y$ axis. Should be in the range of $0 - 1$, as above

timeTicks

Numbers to mark on the survival plot and table.

• IftimeTicks="major"(the default) only the major$x$-axis (time) marks from the survival plot are are labelled on the plot and table.
• IftimeTicks="minor"

tabTitle

Table title

tabTitleSize

Table title text size

tabLabSize

Table legend text size

nRiskSize

Number at risk - text size

Value

• A list of ggplot objects, with elements:
• plot
  the survial plot
• table
  the table of events per time
• This list has the additional class of tableAndPlot, allowing methods from autoplot.tableAndPlot.

Examples

data(kidney, package="KMsurv")
s1 <- survfit(Surv(time, delta) ~ type, data=kidney)
autoplot(s1, type="fill", survLineSize=2)
autoplot(s1, type="CI", pVal=TRUE, pX=0.3,
 legLabs=c("surgical", "percutaneous"),
 title="Time to infection following catheter placement \n
   by type of catheter, for dialysis patients")$plot
s1 <- survfit(Surv(time=time, event=delta) ~ 1, data=kidney)
autoplot(s1, legLabs="")$plot
autoplot(s1, legend=FALSE)$plot
### load all datasets from package:km.ci
d1 <- data(package="km.ci")$results[, "Item"]
data(list=d1, package="km.ci")
(s1 <- survfit(Surv(time, status) ~ 1, data=rectum.dat))
### change confidence intervals to log Equal-Precision confidence bands
suppressWarnings(km.ci::km.ci(s1, method="logep"))
autoplot(s1, type="fill", legend=FALSE)$plot
###
### manually changing the output
###
s1 <- survfit(Surv(time, delta) ~ type, data=kidney)
g1 <- autoplot(s1, type="CI", alpha=0.8, survLineSize=2)$plot
### change default colors
g1 + ggplot2::scale_colour_manual(values=c("red", "blue")) +
    ggplot2::scale_fill_manual(values=c("red", "blue"))
### change limits of y-axis
g1 + ggplot2::scale_y_continuous(limits=c(0, 1))