在 ggplot 中向生存曲线添加新曲线时出错？

Question

我想在使用 ggfortify 包中的 autoplot 创建的生存分析图（Kaplan-Meier 曲线）中添加一条新线和置信带。

但是，我在使用 geom_ribbon 时收到错误消息，但在使用 geom_line 时却没有收到错误消息。下面的最小示例说明了这个问题。

# Load packages and data
library(survival)
library(ggfortify)
data(aml, package = "survival")

# Fit the Kaplan-Meier curve
fit <- survfit(Surv(time, status) ~ x, data=aml)

# Create an additional dataset to plot on top of the Kaplan-Meier curve
df <- data.frame(x = seq(1, 150, length.out=10),
                 y = seq(0, 1, length.out=10),
                 ymin = seq(0, 1, length.out=10) - 0.1,
                 ymax = seq(0, 1, length.out=10) + 0.1)

这个有效

autoplot(fit, conf.int = FALSE, censor = FALSE) +
  geom_line(data = df, mapping = aes(x=x, y=y)) +
  geom_line(data = df, mapping = aes(x=x, y=ymin)) +
  geom_line(data = df, mapping = aes(x=x, y=ymax))

这行不通

autoplot(fit, conf.int = FALSE, censor = FALSE) +
  geom_ribbon(data = df, mapping = aes(x=x, ymin=ymin, ymax=ymax))

Error in FUN(X[[i]], ...) : object 'surv' not found

Answer 1

如果您在 geom_ribbon() 中指定 inherit.aes = FALSE，则可以避免该特定错误，即

library(survival)
#install.packages("ggfortify")
library(ggfortify)
#> Warning: package 'ggfortify' was built under R version 4.1.2
#> Loading required package: ggplot2
data(aml, package = "survival")
#> Warning in data(aml, package = "survival"): data set 'aml' not found

# Fit the Kaplan-Meier curve
fit <- survfit(Surv(time, status) ~ x, data=aml)

# Create an additional dataset to plot on top of the Kaplan-Meier curve
df <- data.frame(x = seq(1, 150, length.out=10),
                 y = seq(0, 1, length.out=10),
                 ymin = seq(0, 1, length.out=10) - 0.1,
                 ymax = seq(0, 1, length.out=10) + 0.1)

autoplot(fit, conf.int = FALSE, censor = FALSE) +
  geom_line(data = df, mapping = aes(x=x, y=y)) +
  geom_line(data = df, mapping = aes(x=x, y=ymin)) +
  geom_line(data = df, mapping = aes(x=x, y=ymax))

autoplot(fit, conf.int = FALSE, censor = FALSE) +
  geom_ribbon(data = df, mapping = aes(x=x, ymin=ymin, ymax=ymax),
              inherit.aes = FALSE)

^{由 reprex package (v2.0.1)}

创建于 2022-02-21

这是否解决了您的问题？

在 ggplot 中向生存曲线添加新曲线时出错？

Error adding new curve to survival curve in ggplot?

r

ggplot2

ggfortify

这个有效

这行不通