We will here use the ggcompetingrisks1
function in the
Data & Functions
page.
Download
ggcompetingrisks1.R
# Libraries
library(cmprsk)
library(survminer)
library(ggplot2)
# Creation of dataset
set.seed(2)
df <- data.frame(del=rexp(100)*5,
event=sample(c(0, 1, 2),100,replace=TRUE,prob = c(0.3, 0.6, 0.1)),
group=sample(c("A", "B"),100,replace=TRUE))
df$event_surv <- ifelse(df$event==0, 0, 1)
# cuminc object
fit_gp <- cuminc(df$del, df$event, df$group)
# surv objet
fit_surv_gp <- survfit(Surv(del, event_surv)~group, data=df)
# !!!! warning !!!! always use survfit with "data="
By default, groups will be differentiated by colors and events by line types.
# We set the xlim, break time, var_time and palette
break.time.by <- 6
var_time <- "del"
xlim <- c(0, 24)
palette <- scales::hue_pal()(2)
plot.icc.gp=ggcompetingrisks1(
fit_gp,
xlab = "Time (months)",
xlim=xlim, ylim=c(0, 1),
lwd=0.5,
title="", legend="top",
legend.title="",
labs=c("Group A", "Group B"),
labs_event=c("Event 1", "Event 2"),
palette=palette,
conf.int = F, multiple_panels = F, type_group="color", type_event="linetype",
event_suppr = "",
ggtheme = theme_classic()
) + scale_x_continuous(breaks = seq(0, floor(max(df[, var_time], na.rm=T)), break.time.by))
# !!!! warning !!!! always use survfit with "data="
num.icc.gp <- ggrisktable(
fit_surv_gp,
data=df,
xlim=xlim,
break.time.by = break.time.by,
palette=palette,
# color = "group",
y.text = TRUE,
y.text.col = palette,
fontsize=3,
legend="none",
legend.labs=c("Group A", "Group B"),
tables.theme = theme_cleantable()) +
theme(plot.title = element_text(size = 11, color = "black", face = "plain" ))
icc.gp <- ggarrange(plot.icc.gp, num.icc.gp, ncol = 1, nrow = 2, heights = c(0.85, 0.15), align = "v")
icc.gp
This document is a work of the statistics team in the Biostatistics and Medical Information Department at Saint-Louis Hospital in Paris (SBIM).
Developed and updated by Noémie Bigot and Anouk Walter-Petrich
noemie.bigot@aphp.fr; anouk.walter-petrich@u-paris.fr
Based on The R Graph Gallery by Yan Holtz.