diff --git a/survival.R b/survival.R index 451816f..e55a243 100644 --- a/survival.R +++ b/survival.R @@ -4,6 +4,8 @@ # Jens Mathis Sauer (c) 2020 library(survival) +source("utils.R") + secmal <- read.csv2("current.csv", header=TRUE) # Setup survival object @@ -12,28 +14,52 @@ surv_asct <- Surv(time = secmal$event_time_asct, event = secmal$event_status) # plot survival after diagnosis # scaled to years -png(filename = "survival_dx.png", width = 3000, height = 3000, res = 300) -plot(survfit(surv_dx ~ 1), mark.time = TRUE, xscale = 365.25, xlab = "Years", ylab = "Survival") -title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after diagnosis") -dev.off() + +sma_plot_file("survival_dx.png", png, + list(main = "Kaplan-Meier estimate for\nsecMalASCT study", + sub = "Survival after diagnosis"), + NULL, + plot, survfit(surv_dx ~ 1), + mark.time = TRUE, + xscale = 365.25, + xlab = "Years", + ylab = "Survival") + # One graph per sex -png(filename = "survival_dx_sex.png", width = 3000, height = 3000, res = 300) -plot(survfit(surv_dx ~ sex, data = secmal), mark.time = TRUE, xscale = 365.25, xlab = "Years", ylab = "Survival", lty = 2:3) -title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after diagnosis") -legend(100, .9, c("Female", "Male"), lty = 2:3) -dev.off() +sma_plot_file("survival_dx_sex.png", png, + list(main = "Kaplan-Meier estimate for\nsecMalASCT study", + sub = "Survival after diagnosis"), + list(100, .9, c("Female", "Male"), lty = 2:3), + plot, survfit(surv_dx ~ sex, data = secmal), + mark.time = TRUE, + xscale = 365.25, + xlab = "Years", + ylab = "Survival", + lty = 2:3) + # plot survival after diagnosis # scaled to years -png(file = "survival_asct.png", width = 3000, height = 3000, res = 300) -plot(survfit(surv_asct ~ 1), mark.time = TRUE, xscale = 365.25, xlab = "Years", ylab = "Survival") -title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after transplantation") -dev.off() +sma_plot_file("survival_asct.png", png, + list(main = "Kaplan-Meier estimate for\nsecMalASCT study", + sub = "Survival after transplantation"), + NULL, + plot, survfit(surv_asct ~ 1), + mark.time = TRUE, + xscale = 365.25, + xlab = "Years", + ylab = "Survival") + # One graph per sex -png(filename = "survival_asct_sex.png", width = 3000, height = 3000, res = 300) -plot(survfit(surv_asct ~ sex, data = secmal), mark.time = TRUE, xscale = 365.25, xlab = "Years", ylab = "Survival", lty = 2:3) -title("Kaplan-Meier estimate for\nsecMalASCT study", "Survival after transplantation") -legend(100, .9, c("Female", "Male"), lty = 2:3) -dev.off() +sma_plot_file("survival_asct_sex.png", png, + list(main = "Kaplan-Meier estimate for\nsecMalASCT study", + sub = "Survival after transplantation"), + list(100, .9, c("Female", "Male"), lty = 2:3), + plot, survfit(surv_asct ~ sex, data = secmal), + mark.time = TRUE, + xscale = 365.25, + xlab = "Years", + ylab = "Survival", + lty = 2:3)