#it is essential that you load the survival package
library(survival)

# loads your survival spreadsheet
datafile <- read.csv("/Users/nsafren1/desktop/Survival_spreadsheet.csv")

#Performs cox proportional hazards and outputs statistics
coxfit <- coxph(Surv(time_death, as.logical(censored)) ~ group, data=datafile)
summary(coxfit)

# plots cumulative risk of death for each group. To save your plot click on the export button above your plot.
coxfit <- coxph(Surv(time_death, as.logical(censored)) ~ strata(group), data=datafile)
plot(survfit(coxfit), fun="cumhaz", main="Experiment Title", xlab="Time in hours", ylab="Cumulative risk of death", col=c("black","red"),lwd=c(5))
cox.zph(coxfit)
#adjust the next line to modify the legend
legend("topleft", legend=c("WT","Mutant"), col=c("black","red"), lwd=c(2), cex=.8)

# plots survival data as a Kaplan Meier Curve
kmfit <- survfit(Surv(time_death, as.logical(censored)) ~ group,
                 data=datafile)
plot(kmfit, main="Experiment Title",
     xlab="Time in hours",ylab="survival fraction", col=c("black","red"),lwd=c(5))
#adjust the next line to modify the legend
legend("bottomleft", legend=c("WT","Mutant"), col=c("black","red"), lwd=c(2), cex=.8)