autoplotTen: Generate a 'ggplot' for a 'survfit' or 'ten' object

In survMisc: Miscellaneous Functions for Survival Data

Description

Generate a ggplot for a survfit or ten object

Usage

autoplot(object, ...)

## S3 method for class 'ten'
autoplot(object, ..., title = "Marks show times with censoring",
  type = c("single", "CI", "fill"), alpha = 0.05, ciLine = 10,
  censShape = 3, palette = c("Dark2", "Set2", "Accent", "Paired", "Pastel1",
  "Pastel2", "Set1", "Set3"), jitter = c("none", "noEvents", "all"),
  tabTitle = "Number at risk by time", xLab = "Time",
  timeTicks = c("major", "minor", "days", "months", "custom"), times = NULL,
  yLab = "Survival", yScale = c("perc", "frac"), legend = TRUE,
  legTitle = "Group", legLabs = NULL, legOrd = NULL, titleSize = 15,
  axisTitleSize = 15, axisLabSize = 10, survLineSize = 0.5,
  censSize = 5, legTitleSize = 10, legLabSize = 10, fillLineSize = 0.05,
  tabTitleSize = 15, tabLabSize = 5, nRiskSize = 5)

## S3 method for class 'stratTen'
autoplot(object, ..., title = NULL, type = c("single",
  "CI", "fill"), alpha = 0.05, ciLine = 10, censShape = 3,
  palette = c("Dark2", "Set2", "Accent", "Paired", "Pastel1", "Pastel2",
  "Set1", "Set3"), jitter = c("none", "noEvents", "all"),
  tabTitle = "Number at risk by time", xLab = "Time",
  timeTicks = c("major", "minor", "days", "months", "custom"), times = NULL,
  yLab = "Survival", yScale = c("perc", "frac"), legend = TRUE,
  legTitle = "Group", legLabs = NULL, legOrd = NULL, titleSize = 15,
  axisTitleSize = 15, axisLabSize = 10, survLineSize = 0.5,
  censSize = 5, legTitleSize = 10, legLabSize = 10, fillLineSize = 0.05,
  tabTitleSize = 15, tabLabSize = 5, nRiskSize = 5)

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

Arguments

object	An object of class survfit, ten or stratTen.
...	Additional arguments (not implemented).
title	Title for survival plot.
type	type="single" (the default) plots single lines. type="CI" Adds lines indicating confidence intervals (taken from upper and lower values of survfit object). Higher values of alpha (opacity) are recommended for this, e.g. alpha=0.8. type="fill" Adds filled rectangles from the survival lines to the confidence intervals above.
alpha	Opacity of lines indicating confidence intervals or filled rectangles. Should be in range 0-1. Lower = more transparent. Larger values e.g. alpha=0.7 are recommended for confidence intervals.
ciLine	Confidence interval line type. See 'line type specification' in ?graphics::par
censShape	Shape of marks to indicate censored onservations. Default is 3 which gives vertical ticks. Use censShape=10 for circular marks. See ?graphics::points
palette	Options are taken from color_brewer. palette="Dark2" (the default) is recommended for single or CI plots. palette="Set2" is recommended for type="fill" plots.
jitter	By default, jitter="none". If jitter="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 see separately. If jitter="all" add some vertical and horizontal noise to all survival lines. This can prevent overlapping of lines for censoring.
tabTitle	Table title. –Axis arguments:
xLab	Label for x axis on survival plot.
timeTicks	Numbers to mark on the x axis of the survival plot and the table. "major" (the default) only the major x-axis (time) marks from the survival plot are are labelled on the plot and table. "minor" minor axis marks are labelled instead. "days" scale is 0, 7, 14, ..., t_{max} "months" scale is 0, 12,, 24, ..., t_{max} "custom" scale is given by times below
times	Vector of custom times to use for x axis.
yLab	Label for y axis on survival plot.
yScale	Display for point on y axis: "perc" Displays as percentages. "frac" Displays as fractions e.g. 0, 0.1, 0.2, ..., 1.0. –Legend arguments:
legend	If legend=FALSE, no legends will be produced for the plot or table.
legTitle	Legend title.
legLabs	Legend labels. These can be used to replace the names of the covariate groups ('strata' in the case of a survfit object). Should be given in the same order as those strata.
legOrd	Legend order. –Size arguments: Size arguments are passed to ggplot2::element_text(size=).
titleSize	Title size for survival plot.
axisTitleSize	Title size for axes.
axisLabSize	Title size for labels on axes.
survLineSize	Survival line size.
legTitleSize	Title size for legend.
legLabSize	Legend labels width and height.
censSize	Size of marks to indicate censored onservations.
fillLineSize	Line size surrouding filled boxes.
tabTitleSize	Table title text size.
tabLabSize	Table legend text size.
nRiskSize	Number at risk - text size. –Arguments for autoplot.survfit only:
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.

Note

autoplot.survfit may be deprecated after packageVersion 0.6. Please try to use autoplot.ten instead.

Author(s)

Chris Dardis. autoplot.survfit based on existing work by R. Saccilotto, Abhijit Dasgupta, Gil Tomas and Mark Cowley.

See Also

?ggplot2::ggplot_build

Examples

## examples are slow to run; see vignette for output from these
## Not run: 
### autoplot.ten
data("kidney", package="KMsurv")
t1 <- ten(survfit(Surv(time, delta) ~ type, data=kidney))
autoplot(t1)
autoplot(t1, type="fill", survLineSize=2, jitter="all")
autoplot(t1, timeTicks="months",
 type="CI", jitter="all",
 legLabs=c("surgical", "percutaneous"),
 title="Time to infection following catheter placement \n
   by type of catheter, for dialysis patients",
 titleSize=10, censSize=2)$plot
t2 <- ten(survfit(Surv(time=time, event=delta) ~ 1, data=kidney))
autoplot(t2, legLabs="")$plot
autoplot(t2, legend=FALSE)
data("rectum.dat", package="km.ci")
t3 <- ten(survfit(Surv(time, status) ~ 1, data=rectum.dat))
## change confidence intervals to log Equal-Precision confidence bands
ci(t3, how="nair", tL=1, tU=40)
autoplot(t3, type="fill", legend=FALSE)$plot
## manually changing the output
t4 <- ten(survfit(Surv(time, delta) ~ type, data=kidney))
(a4 <- autoplot(t4, type="CI", alpha=0.8, survLineSize=2)$plot)
## change default colors
a4 + list(ggplot2::scale_color_manual(values=c("red", "blue")),
          ggplot2::scale_fill_manual(values=c("red", "blue")))
## change limits of y-axis
suppressMessages(a4 + ggplot2::scale_y_continuous(limits=c(0, 1)))

## End(Not run)
## Not run: 
data("pbc", package="survival")
t1 <- ten(Surv(time, status==2) ~ trt + strata(edema), data=pbc, abbNames=FALSE)
autoplot(t1)

## End(Not run)
### autoplot.survfit
## Not run: 
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)$plot
data(rectum.dat, package="km.ci")
s1 <- survfit(Surv(time, status) ~ 1, data=rectum.dat)
## change confidence intervals to log Equal-Precision confidence bands
if (require("km.ci")) {
 km.ci::km.ci(s1, method="logep")
 autoplot(s1, type="fill", legend=FALSE)$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))

## End(Not run)

survMisc documentation built on May 2, 2019, 5:14 p.m.