Data
# Libraries
library(survminer)
library(survival)
# Reformate the data table with the variables we'll use
lung <- lung[,c("time","status","sex")]lung format :
A data frame
with 228 observations on the following 10 variables :
time Survival time in days
status
Censoring status; 1=censored, 2=dead
Sex Patient sex;
Male=1 Female=2
Customized survival curves
# We set the xlim, break time and palette
break.time.by <- 250
xlim <- c(0, 1000)
palette <- c("grey")
plot.OS <-ggsurvplot(
fit,
data = lung,
xlab = "Time (months)", ylab="Survival probability",
xlim=xlim, ylim=c(0, 1),
lwd=0.5,
break.time.by = break.time.by,
title="", legend="none", legend.title="",
palette=palette,
conf.int = TRUE,
conf.int.fill = palette,
ggtheme = theme_classic(),
risk.table = T,
risk.table.y.text = FALSE,
risk.table.y.text.col = TRUE,
risk.table.fontsize=3,
tables.theme = theme_cleantable()
)
# To customize risk table
plot.OS$table <- plot.OS$table +
theme(plot.title = element_text(size = 11, color = "black", face = "plain" ))
ggarrange(plot.OS$plot, plot.OS$table, ncol = 1, nrow = 2, heights = c(0.85, 0.15), align = "v")
To change the axis origin : (0,0)
# We set the xlim, break time and palette
break.time.by <- 250
xlim <- c(0, 1000)
palette <- c("grey")
plot.OS <-ggsurvplot(
fit,
data = lung,
xlab = "Time (months)", ylab="Survival probability",
xlim=xlim, ylim=c(0, 1),
lwd=0.5,
break.time.by = break.time.by,
title="", legend="none", legend.title="",
palette=palette,
conf.int = TRUE,
conf.int.fill = palette,
ggtheme = theme_classic(),
risk.table = T,
risk.table.y.text = FALSE,
risk.table.y.text.col = TRUE,
risk.table.fontsize=3,
tables.theme = theme_cleantable()
)
plot.OS$plot <- plot.OS$plot + scale_x_continuous(expand = c(0, 0, .05, 0)) +
scale_y_continuous(expand = c(0, 0, .05, 0))
# to custemize risk table
plot.OS$table <- plot.OS$table +
theme(plot.title = element_text(size = 10, color = "black", face = "plain")) +
scale_x_continuous(expand = c(0, 0, .05, 0)) +
coord_cartesian(xlim=c(-5, 1000), clip = "off") # allows you to exit the frame with clip=off
ggarrange(plot.OS$plot, plot.OS$table, ncol = 1, nrow = 2, heights = c(0.85, 0.15), align = "v")