README.md

In michaelway/ggkm: Kaplan-Meier survival curves with numbers at risk below

ggkm

Create publication quality Kaplan-Meier plots with at risk tables below.

Install

To install the ggkm package, install and run the devtools package and then run the code below in a R console:

install.packages("devtools")
library(devtools)
install_github("michaelway/ggkm")
library(ggkm)

Examples

Basic Kaplan-Meier Plot

Loading the "colon" dataset from the survival package allows us to create a survival object to plot with the ggkm() function. A basic Kaplan-Meier plot can be created and saved by running the commands below:

#Load dataset

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

#Plot the data
ggkm(fit)

#Save a PNG image using R plotting device
png("KM1.png", units='in', height=5, width=7, res = 220)
ggkm(fit)
dev.off()

Basic Kaplan-Meier plot with at-risk table

At risk tables are a handy way of demonstrating the number of individuals remaining at each time-point of a survival analysis. This can easily be added by including the parameter "table = TRUE", as below:

ggkm(fit, table = TRUE)

Customise it!

More advanced plots can be created by modifying a number of parameters. For example the title, y-strata name and lables, x-strata name can all be modified; a 95% confidence interval can be added; the dashtype can be removed or the symbol changed; and, a P-value from the survival object may also be included.

ggkm(fit, table = T, 
     main="Survival  by treatment group", 
     ystratalabs = c("Placebo", "No-drug", "Drug"),
     ystrataname = "Group",
     xlabs = "Time-to-death (days)",
     dashed=TRUE,
     pval=TRUE,
     ci=TRUE,
     shape = 4,
     linecols = "Set2")

Points

The marker points which can be modified based on the the numbering of the point symbols given in the image below.

Colours

The colours of the lines are based on colour brewer palletes. To set a pallete use a palette name shown in the image below.

Feedback

This work builds upon that of many others, predominantly Abhijit Dasgupta, Abhijit Dasgupta, Gil Tomas and Mark Crowley at https://statbandit.wordpress.com/2011/03/08/an-enhanced-kaplan-meier-plot/. I have packaged it up and extensively modified the parameters for ease of use.

I would love to hear any feedback, comments or suggestions for this package.

michaelway/ggkm documentation built on May 22, 2019, 9:52 p.m.