library(ggplot2)

require(survival)

require(survminer)

setwd(dirname(rstudioapi::getSourceEditorContext()$path))

######## read survival data  #########

surv_data = read.csv("data/Survival_analysis_data.csv") 

######## postsurgical ctDNA #########

surv_data.postsurg = subset(surv_data,!is.na(Postsurgical_detection))

## KM plot 

# all patients ~ Fig 2a

getsurvplot("Postsurgical_detection","Postsurgical ctDNA",surv_data.postsurg)

# AD patients ~ Supplementary Fig 5a

getsurvplot("Postsurgical_detection","Postsurgical ctDNA, AD",subset(surv_data.postsurg,PathologicalType=="AD"))

# SqCC patients ~ Supplementary Fig 5b

getsurvplot("Postsurgical_detection","Postsurgical ctDNA, SqCC",subset(surv_data.postsurg,PathologicalType=="SqCC"))

## cox 

covariates <- c("Sex","Smoking","Age","PathologicalType","Stage","T_stage","N_stage","Differentiation","TP53","EGFR","Postsurgical_detection")

univ_formulas <- sapply(covariates,function(x) as.formula(paste('Surv(DFS,DFS_status)~', x)))

res.postsurg <- lapply( univ_formulas, function(x){summary(coxph(x, data = surv_data.postsurg))})

## multivariate cox regression

summary(coxph(Surv(DFS,DFS_status)~PathologicalType+TP53+T_stage+Postsurgical_detection,subset(surv_data.postsurg,AdjuvantTherapy_status==1)))

####### post-ACT ctDNA ###########

surv_data.ACT = subset(surv_data,AdjuvantTherapy_status==1& !is.na(PostACT_detection))

## KM plot

# all patients ~ Fig 2b

getsurvplot("PostACT_detection","Post-ACT ctDNA",surv_data.ACT)

# AD patients ~ Supplementary Fig 5c

getsurvplot("PostACT_detection","Post-ACT ctDNA, AD",subset(surv_data.ACT,PathologicalType=="AD"))

# SqCC patients ~ Supplementary Fig 5d

getsurvplot("PostACT_detection","Post-ACT ctDNA, SqCC",subset(surv_data.ACT,PathologicalType=="SqCC"))

## cox 

covariates <- c("Sex","Smoking","Age","PathologicalType","Stage","T_stage","N_stage","Differentiation","TP53","EGFR","PostACT_detection")

univ_formulas <- sapply(covariates,function(x) as.formula(paste('Surv(DFS,DFS_status)~', x)))

res.postsurg <- lapply( univ_formulas, function(x){summary(coxph(x, data = surv_data.ACT))})

## multivariate cox regression

summary(coxph(Surv(DFS,DFS_status)~PathologicalType+Stage+T_stage+N_stage+PostACT_detection,subset(surv_data.ACT,AdjuvantTherapy_status==1)))

######### longitudinal ctDNA ##########

surv_data.long =  subset(surv_data,! PatientID %in% c("P098","P103")) # exclude 2 patients with only pretreatment and postsurgical ctDNA

## KM plot

# all patients ~ Fig 2d

getsurvplot("Longitudinal_Detection","Post-ACT ctDNA",surv_data.long)

# AD patients ~ Supplementary Fig 5e

getsurvplot("Longitudinal_Detection","Post-ACT ctDNA, AD",subset(surv_data.long,PathologicalType=="AD"))

# SqCC patients ~ Supplementary Fig 5f

getsurvplot("Longitudinal_Detection","Post-ACT ctDNA, SqCC",subset(surv_data.long,PathologicalType=="SqCC"))

## cox 

covariates <- c("Sex","Smoking","Age","PathologicalType","Stage","T_stage","N_stage","Differentiation","TP53","EGFR","Longitudinal_Detection")

univ_formulas <- sapply(covariates,function(x) as.formula(paste('Surv(DFS,DFS_status)~', x)))

res.postsurg <- lapply( univ_formulas, function(x){summary(coxph(x, data = surv_data.long))})

## multivariate cox regression

summary(coxph(Surv(DFS,DFS_status)~PathologicalType+TP53+T_stage+Stage+Longitudinal_Detection,subset(surv_data.long,AdjuvantTherapy_status==1)))

####### postsurgical ctDNA and ACT treatment ##########

## KM plot

# all patients ~ Fig 2c

getATplot('Postsurgical ctDNA and ACT status',surv_data)

# AD patients ~ Supplementary Fig 8a

getATplot("Postsurgical ctDNA and ACT status, AD",subset(surv_data,PathologicalType=="AD"))

# SqCC patients ~ Supplementary Fig 8b

getATplot("Postsurgical ctDNA and ACT status, SqCC",subset(surv_data,PathologicalType=="SqCC"))