使用R绘制生存曲线

一、加载程序包

library(survival)
library(ggplot2)
library(survminer)
library(dplyr)

二、加载数据并绘图

1	data <- read.delim('clipboard',header = T)

head(data)
       Patient Days Status Expression Group
1 TCGA-B0-5702 2172  Alive     383.07   Low
2 TCGA-B0-4696  866   Dead     810.35   Low
3 TCGA-B0-4698   42   Dead     849.64   Low
4 TCGA-CJ-4642 3205  Alive    1153.28   Low
5 TCGA-BP-5185 1132  Alive    1197.89   Low
6 TCGA-BP-4337    2   Dead    1223.26   Low

1	table(data$Status)

1 2	Alive Dead 349 173

1	table(data$Group,data$Status)

1
2
3

      Alive Dead
High   198   63
Low    151  110

1	my.surv <- Surv(data$Days,data$Status=='Dead')

1	fit <- survfit(my.surv~data$Group)

Call: survfit(formula = my.surv ~ data$Group)

                n events median 0.95LCL 0.95UCL
data$Group=High 261     63     NA    2830      NA
data$Group=Low  261    110   1980    1620    2601

绘制最基本的生存曲线

1	plot(fit,col=c("red","blue"))

优化生存曲线

plot(kmfit2,col=c("red","blue"),axes=F,xlab="Days",ylab="Survival",lwd=2,main="Kidney Renal Clear Cell Carcinoma")
axis(2,at=c(0,0.5,1),labels=c(0,0.5,1),pos=0,las=2)
axis(1,at=c(0,1000,2000,3000,4000,5000),labels=c(0,1000,2000,3000,4000,5000),pos=0)
segments(2190,0,2190,0.5,lty=2,col="red")
segments(0,0.5,3615,0.5,lty=2,col="grey")
segments(3615,0,3615,0.5,lty=2,col="blue")
text(1500,0.95,"p=0.000598",cex=0.8)
legend("topright",c("High","Low"),fill=c("red","blue"),cex=0.9,bty="n",box.lwd=0.2)