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/TJPROJ6/RNA_SH/personal_dir/liuyan/gxh/P101SC18100426-02-F003/Kaplan-Meier.R

#!/usr/bin/R /TJPROJ6/RNA_SH/software/conda/conda/envs/R-3.6.0/bin/R
library(survival)
library(ggplot2)
library(ggpubr)
#library(ggsurvplot)
library(magrittr)
library(survminer)
library(survival)
library(dplyr)

args<-commandArgs(T)
#lung <- read.table(args[1],row.names=1,header=TRUE, sep="\t", dec = ".",check.names=FALSE)
lung <- read.table(args[1],header=TRUE, sep="\t", dec = ".",check.names=FALSE)
attach(lung)

### 使用survfit()函数来拟合生存曲线
fit <- survfit(Surv(status,event) ~ Positive_Cells,data = lung)
#fit
#write.table(fit,file="fit_survfit.txt", row.names = T, quote=FALSE,sep="\t")  ## 数据的写出还是有问题
#summary(fit)
### 绘制基础曲线
pdf(file="fit_survfit.pdf",onefile=F)
ggsurvplot(fit, data = lung)
dev.off()

###  增加中位生存时间
pdf(file="fit_survfit_median_survival_time.pdf",onefile=F)
ggsurvplot(fit, data = lung,surv.median.line = "hv") # 增加中位生存时间
dev.off()

### 增加置信区间

pdf(file="fit_survfit_confidence_interval.pdf",onefile=F)
ggsurvplot(fit, data = lung,surv.median.line = "hv",conf.int = TRUE)
dev.off()

### 添加风险表

pdf(file="fit_survfit_table.pdf",onefile=F)
ggsurvplot(fit, data = lung,surv.median.line = "hv",conf.int = TRUE,risk.table = TRUE)
dev.off()

### 添加总患者生存曲线

pdf(file="fit_survfit_table_all.pdf",onefile=F)
ggsurvplot(fit, data = lung,surv.median.line = "hv",conf.int = TRUE,risk.table = TRUE,pval = TRUE,add.all = TRUE)
dev.off()