ggkm: Kaplan-Meier Plots using ggplot

In TalhoukLab/biostatUtil: Utility Functions Used in Biostatistics Projects

Kaplan-Meier Plots using ggplot

Description

Produce nicely annotated KM plots using ggplot style.

Usage

ggkm(
  sfit,
  sfit2 = NULL,
  table = TRUE,
  returns = TRUE,
  marks = TRUE,
  CI = TRUE,
  line.pattern = NULL,
  shading.colors = NULL,
  main = "Kaplan-Meier Plot",
  xlabs = "Time",
  ylabs = "Survival Probability",
  xlims = NULL,
  ylims = NULL,
  ystratalabs = NULL,
  cox.ref.grp = NULL,
  timeby = 5,
  test = c("Log Rank", "Tarone-Ware"),
  pval = TRUE,
  bold_pval = FALSE,
  sig.level = 0.05,
  HR = TRUE,
  hide_hr_labels = FALSE,
  use.firth = 1,
  hide.border = FALSE,
  expand.scale = TRUE,
  legend = FALSE,
  legend.xy = NULL,
  legend.direction = "horizontal",
  line.y.increment = 0.05,
  size.plot = 11,
  size.summary = 3,
  size.table = 3.5,
  size.table.labels = 11,
  digits = 3,
  ...
)

Arguments

sfit	an object of class survfit containing one or more survival curves
sfit2	an (optional) second object of class survfit to compare with sfit
table	logical; if TRUE (default), the numbers at risk at each time of death is shown as a table underneath the plot
returns	logical; if TRUE the plot is returned
marks	logical; if TRUE (default), censoring marks are shown on survival curves
CI	logical; if TRUE (default), confidence bands are drawn for survival curves the using cumulative hazard, or log(survival).
line.pattern	linetype for survival curves
shading.colors	vector of colours for each survival curve
main	plot title
xlabs	horizontal axis label
ylabs	vertical axis label
xlims	horizontal limits for plot
ylims	vertical limits for plot
ystratalabs	labels for the strata being compared in survfit
cox.ref.grp	indicates reference group for the variable of interest in the cox model. this parameter will be ignored if not applicable, e.g. for continuous variable
timeby	length of time between consecutive time points spanning the entire range of follow-up. Defaults to 5.
test	type of test. Either "Log Rank" (default) or "Tarone-Ware".
pval	logical; if TRUE (default), the logrank test p-value is shown on the plot
bold_pval	logical; if TRUE, p-values are bolded if statistically significant at sig.level
sig.level	significance level; default 0.05
HR	logical; if TRUE (default), the estimated hazard ratio and its 95% confidence interval will be shown
hide_hr_labels	logical; if TRUE and there are only two strata, the strata labels are hidden from HR summary because there is only contrast being compared
use.firth	Firth's method for Cox regression is used if the percentage of censored cases exceeds use.firth. Setting use.firth = 1 (default) means Firth is never used, and use.firth = -1 means Firth is always used.
hide.border	logical; if TRUE, the upper and right plot borders are not shown.
expand.scale	logical; if TRUE (default), the scales are expanded by 5% so that the data are placed a slight distance away from the axes
legend	logical; if TRUE, the legend is overlaid on the graph (instead of on the side).
legend.xy	named vector specifying the x/y position of the legend
legend.direction	layout of items in legends ("horizontal" (default) or "vertical")
line.y.increment	how much y should be incremented for each line
size.plot	text size of main plot
size.summary	text size of numerical summaries
size.table	text size of risk table
size.table.labels	text size of risk table axis labels
digits	number of digits to round: p-values digits=number of significant digits, HR digits=number of digits after decimal point NOT significant digits
...	additional arguments to other methods

Value

A kaplan-meier plot with optional annotations for hazard ratios, log rank test p-values, and risk table counts for each stratum.

Author(s)

Samuel Leung, Derek Chiu

Examples

library(survival)
sfit <- survfit(Surv(time, status) ~ sex, lung)
ggkm(sfit, timeby = 200, main = "Survival curves by sex")

TalhoukLab/biostatUtil documentation built on April 14, 2025, 4:15 a.m.