Question

我正在为两个不同人群绘制三种不同类型癌症的生存图。我希望每种癌症类型都有一种颜色，人口之间的差异应为线型（虚线与实线）。因此，癌症A为红色，PopA为虚线，PopB为实线，依此类推。

我似乎无法为每个癌症群体获得一种颜色，然后改变人群之间的线型。

由于受保护，因此我无法在此处发布所有数据，但这是df，surv函数和ggsurvplot：

library(tidyverse)
library(survminer)
library(survival)
library(KMsurv)
library(ggfortify)
library(ggthemes)

> srv_time_mon <- sample(0:100,200, replace = TRUE)
> cancer <- sample(1:3,200, replace = TRUE)
> alive <- sample(0:1,200, replace = TRUE)
> pop <- sample(1:2,200, replace = TRUE)
> dead <- sample(0:1,200, replace = TRUE)
> df <- data.frame(srv_time_mon,cancer, alive, pop, dead)

> head(df)
  srv_time_mon cancer alive pop dead
1           84      1     0   1    1
2           91      2     0   2    0
3           44      1     0   2    1
4           57      2     1   1    0
5           54      1     1   2    0
6           31      3     0   2    1

test <- survfit(Surv(srv_time_mon, dead)~pop+cancer, data=df)

 ggsurvplot(test, data=df, conf.int = FALSE, 
       pval = "Log-Rank p <0.001", title="Kaplan-Meier Curves", break.time.by=12,
       risk.table = TRUE, 
       pval.coord=c(156,0.60), surv.median.line = "v", 
       legend.labs=c("Pop A Cancer 1", "Pop A Cancer 2", "Pop A Cancer 3", "Pop B Cancer 1",
       "Pop B Cancer 2", "Pop B Cancer 3"), 
       legend.title="", legend = c(0.8,0.83), linetype = c("pop"), palette = "jco")+ 
       scale_linetype_discrete( name="Pop Data", labels=c("A", "B"))

Answer 1

如果您查看attachments返回的对象的class，我们将其称为ggsurvplot()，您会发现它不是p对象

ggplot

您将在此处找到class(p) #[1] "ggsurvplot" "ggsurv" "list"对象

ggplot

如果您现在运行

class(p$plot)
#[1] "gg"     "ggplot"

您会看到以下情节：

现在，如果您想要一个图例，请将p$plot + scale_linetype_discrete(name = "Pop Data", labels = c("A", "B"))调用中的linetype参数更改为ggsurvplot()，以便将两个图例组合在一起，因为现在同一变量已映射到不同的外观。

最后将"strata"和scale_linetype_manual()添加到scale_colour_manual()。

请参阅下面的完整代码。

p$plot

我假设您希望2型和3型癌症的颜色为黑色。如果您想要不同的颜色，请在下面更改代码。

p <- ggsurvplot(
  test,
  data = df,
  conf.int = FALSE,
  pval = "Log-Rank p <0.001",
  title = "Kaplan-Meier Curves",
  break.time.by = 12,
  risk.table = TRUE,
  pval.coord = c(156, 0.60),
  surv.median.line = "v",
  legend.labs = c(
    "Pop A Cancer 1",
    "Pop A Cancer 2",
    "Pop A Cancer 3",
    "Pop B Cancer 1",
    "Pop B Cancer 2",
    "Pop B Cancer 3"
  ),
  legend.title = "",
  # legend = c(0.8, 0.83), # took this out for cleaner appearance of the legend (optional)
  linetype = c("strata"), # changed from "pop" to "strata"
  palette = "jco"
)

使用patchwork package在图表下方添加风险表（另一个cols <- rep(c("red", "black"), c(2, 4)) #cols <- rep(c("red", "forestgreen", "lightblue"), 2) # example names(cols) <- paste("Pop", rep(c("A", "B"), each = 3), "Cancer", 1:3) lines <- rep(c("dashed", "solid"), each = 3) names(lines) <- paste("Pop", rep(c("A", "B"), each = 3), "Cancer", 1:3) p$plot <- p$plot + scale_linetype_manual(values = lines) + scale_colour_manual(values = cols) + theme(legend.position = "bottom")对象）。

ggplot

数据

# devtools::install_github("thomasp85/patchwork")
library(patchwork)
p$plot / p$table + plot_layout(ncol = 1, heights = c(3, 1)) + 
  theme(axis.text.y = element_text(color = rev(cols)))

生存曲线中的多个组使用不同的颜色类型和线型

1 个答案: