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 <- cuminc(df$del, df$event)
# surv objet
fit_surv <- survfit(Surv(del, event_surv)~1, data=df)
# !!!! warning !!!! always use survfit with "data="You can plot with different colors, linetypes, or colors and
linetypes with the argument type_event.
Plot with different colors
Example with default colors (palette hue_pal chosen
automatically by ggcompetingrisks1).
# 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=ggcompetingrisks1(
fit,
xlab = "Time (months)", ylab="Cumulative incidence",
xlim=xlim, ylim=c(0, 1),
lwd=0.5,
title="", legend="top", legend.title="Event",
labs_event=c("event 1", "event 2"), type_event="color",
# palette=palette,
conf.int = T,
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 <- ggrisktable(
fit_surv,
data=df,
xlim=xlim,
break.time.by = break.time.by,
y.text = TRUE,
legend.labs=c(""),
fontsize=3,
tables.theme = theme_cleantable()) +
theme(plot.title = element_text(size = 11, color = "black", face = "plain" ))
icc <- ggarrange(plot.icc, num.icc, ncol = 1, nrow = 2, heights = c(0.85, 0.15), align = "v")
icc
Plot with different linetypes
# We set the xlim, break time, var_time and palette
break.time.by <- 6
var_time <- "del"
xlim <- c(0, 24)
palette <- c("grey")
plot.icc=ggcompetingrisks1(
fit,
xlab = "Time (months)", ylab="Cumulative incidence",
xlim=xlim, ylim=c(0, 1),
lwd=0.5,
title="", legend="top", legend.title="Event",
labs_event=c("event 1", "event 2"), type_event="linetype",
palette=palette,
conf.int = T,
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 <- ggrisktable(
fit_surv,
data=df,
xlim=xlim,
break.time.by = break.time.by,
# color = palette,
y.text = TRUE,
# y.text.col = palette,
legend.labs=c(""),
fontsize=3,
tables.theme = theme_cleantable()) +
theme(plot.title = element_text(size = 11, color = "black", face = "plain" ))
icc <- ggarrange(plot.icc, num.icc, ncol = 1, nrow = 2, heights = c(0.85, 0.15), align = "v")
icc
Plot with different colors and linetypes
# 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=ggcompetingrisks1(
fit,
xlab = "Time (months)", ylab="Cumulative incidence",
xlim=xlim, ylim=c(0, 1),
lwd=0.5,
title="", legend="top", legend.title="Event",
labs_event=c("event 1", "event 2"), type_event="color_linetype",
# palette=palette,
conf.int = T,
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 <- ggrisktable(
fit_surv,
data=df,
xlim=xlim,
break.time.by = break.time.by,
y.text = TRUE,
legend.labs=c(""),
fontsize=3,
tables.theme = theme_cleantable()) +
theme(plot.title = element_text(size = 11, color = "black", face = "plain" ))
icc <- ggarrange(plot.icc, num.icc, ncol = 1, nrow = 2, heights = c(0.85, 0.15), align = "v")
icc