使用包“cmprsk”在 R 中自定义竞争风险图

Question

我正在尝试使用 R 和 package 定制竞争风险图cmprsk。具体来说，我想覆盖默认情况，即对于竞争事件使用颜色，对于不同组使用线型。

这是我的可重现的示例：

library(ggplot2)
library(cmprsk)
library(survminer)

# some simulated data to get started
comp.risk.data <- data.frame("tfs.days" = rweibull(n = 100, shape = 1, scale = 1)*100,
                             "status.tfs" = c(sample(c(0,1,1,1,1,2), size=50, replace=T)),
                             "Typing" = sample(c("A","B","C","D"), size=50, replace=T))

# fitting a competing risks model
CR <- cuminc(ftime = comp.risk.data$tfs.days, 
             fstatus = comp.risk.data$status.tfs, 
             cencode = 0,
             group = comp.risk.data$Typing)

# the default plot makes it impossible to identify the groups
ggcompetingrisks(fit = CR, multiple_panels = F, xlab = "Days", ylab = "Cumulative incidence of event",title = "Competing Risks Analysis")+
  scale_color_manual(name="", values=c("blue","red"), labels=c("Tumor", "Death without tumor"))

使用ggplot_build()我设法更改有关线型和颜色的默认值，但我找不到添加图例的方法。

p2 <- ggcompetingrisks(fit = CR, multiple_panels = FALSE, xlab = "Days", ylab = "Cumulative incidence of event",title = "Death by TCR", ylim = c(0, 1)) +
  scale_color_manual(name="", values=c("blue","red"), labels=c("Tumor", "Death without tumor")) 

q <- ggplot_build(p2)
q$data[[1]]$colour2 <- ifelse(q$data[[1]]$linetype=="solid","blue", ifelse(q$data[[1]]$linetype==22,"red",  ifelse(q$data[[1]]$linetype==42,"green",  ifelse(q$data[[1]]$linetype==44,"black", NA))))
q$data[[1]]$linetype <- ifelse(q$data[[1]]$colour=="blue","solid", ifelse(q$data[[1]]$colour=="red","dashed", NA))
q$data[[1]]$colour <- q$data[[1]]$colour2

q$plot <- q$plot + ggtitle("Competing Risks Analysis") + guides(col = guide_legend()) + theme(legend.position = "right")


p2 <- ggplot_gtable(q)
plot(p2)

有谁知道如何将图例添加到由 操纵的情节中ggplot_build()？或者绘制竞争风险的替代方法，例如颜色指示组和线型指示事件？

Answer 1

你不需要走这ggplot_build条路。该函数ggcompetingrisks返回一个 ggplot 对象，该对象本身包含美学映射。您可以使用以下命令覆盖它们aes：

p <- ggcompetingrisks(fit = CR, 
                 multiple_panels = F, 
                 xlab = "Days", 
                 ylab = "Cumulative incidence of event",
                 title = "Competing Risks Analysis") 

p$mapping <- aes(x = time, y = est, colour = group, linetype = event)

现在我们已经反转了线型和颜色美学映射，我们只需要交换图例标签就可以了：

p + labs(linetype = "event", colour = "group")

请注意，您还可以p像任何其他 ggplot 对象一样添加色标、主题、坐标变换。