ggkm: Creates a Kaplan-Meier plot with at risk tables below

In statapps/bhm: Biomarker Threshold Models

Creates a Kaplan-Meier plot with at risk tables below

Description

Creates a Kaplan-Meier plot with at risk tables below.

Based on the original packge by Michael Way(https://github.com/michaelway/ggkm), I added some minor changes that allow users to:

1) add hazards ratio (HR) and CI for HR to the plot.

2) do the incidence plot instead of KM plot.

3) plot with black and white, sometimes required by a journal.

4) change the aspect ratio of the plot.

Usage

ggkm(sfit, table = FALSE, xlabs = "Time-to-event", ylabs = "Survival (%)", xlims = c(0, max(sfit$time)), ylims = c(0, 1), ystratalabs = names(sfit$strata), ystrataname = "Strata", timeby = signif(max(sfit$time)/7, 1), main = "", pval = FALSE, pvposition = c(0.3, 0.6), marks = TRUE, shape = 3, legend = TRUE, legendposition = c(0.85, 0.8), ci = FALSE, subs = NULL, linecols = "Set1", dashed = FALSE, aspectRatio = 0.7143, black = FALSE, data = NULL, HR = FALSE, incid = FALSE, pvaltxt = NULL, hrtxt = NULL, ...)

Arguments

sfit	a survfit object
timeby	numeric: control the granularity along the time-axis; defaults to 7 time-points. Default = signif(max(sfit$time)/7, 1)
main	plot title
pval	logical: add the pvalue to the plot?
marks	logical: should censoring marks be added?
subs	= NULL,
table	logical: Create a table graphic below the K-M plot, indicating at-risk numbers?
xlabs	x-axis label
ylabs	y-axis label
xlims	numeric: list of min and max for x-axis. Default = c(0,max(sfit$time))
ylims	numeric: list of min and max for y-axis. Default = c(0,1)
ystratalabs	character list. A list of names for each strata. Default = names(sfit$strata)
ystrataname	The legend name. Default = "Strata"
shape	what shape should the censoring marks be, default is a vertical line
legend	logical. should a legend be added to the plot?
legendposition	numeric. x, y position of the legend if plotted. Default=c(0.85,0.8)
ci	logical. Should confidence intervals be plotted. Default = FALSE
linecols	Character. Colour brewer pallettes too colour lines. Default ="Set1",
dashed	logical. Should a variety of linetypes be used to identify lines. Default = FALSE
pvposition	position for the p-value, default = c(0.3, 0.6).
pvaltxt	text for the p-value, default is NULL.
aspectRatio	add aspect ratio of the plot, default is 0.7134.
black	black and white plot, default is FALSE.
data	data set for the plot, could be useful when one need HR on the plot.
incid	plot incidence curve instead of KM curve, default is FALSE.
HR	add hazards ratio to the plot, default is FALSE.
hrtxt	text for the hazards ratio, default is NULL.
...	additional arguments to be passed to the ggkm function.

Author(s)

Michael Way(https://github.com/michaelway/ggkm), heavily modified version of a script created by Abhijit Dasgupta with contributions by Gil Tomas. http://statbandit.wordpress.com/2011/03/08/an-enhanced-kaplan-meier-plot/ Michael have packaged this function, added functions to namespace and included a range of new parameters. Bingshu Chen added more options to the plot (see above) and made minor corrections of the R code and the R docments files to pass the R CMD check.

Examples

 library(survival)
 data(colon)
 fit <- survfit(Surv(time,status)~rx, data=colon)
# ggkm(fit, timeby=500)

statapps/bhm documentation built on April 5, 2024, 3:31 a.m.