60 lines
1.9 KiB
R
60 lines
1.9 KiB
R
# secMalASCT survival calculation
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#
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# License: GPL version 3
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# Jens Mathis Sauer (c) 2020
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library(survival)
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source("utils.R")
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secmal <- sma_load_data("current.csv")
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# Setup survival object
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surv_dx <- Surv(time = secmal$event_time_dx, event = secmal$event_status)
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surv_asct <- Surv(time = secmal$event_time_asct, event = secmal$event_status)
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# plot survival after diagnosis
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sma_plot_surv_dx <- function() {
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plot(survfit(surv_dx ~ 1), mark.time = TRUE, xscale = 365.25,
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xlab = "Years", ylab = "Survival")
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title("Kaplan-Meier estimate for\nsecMalASCT study",
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"Survival after diagnosis")
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}
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# plot survival after diagnosis per sex
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sma_plot_surv_dx_sex <- function() {
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plot(survfit(surv_dx ~ sex, data = secmal), mark.time = TRUE,
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xscale = 365.25, xlab = "Years", ylab = "Survival",
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lty = 2:3)
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title("Kaplan-Meier estimate for\nsecMalASCT study",
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"Survival after diagnosis")
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legend(100, .9, c("Female", "Male"), lty = 2:3)
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}
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# plot survival after transplantation
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sma_plot_surv_asct <- function() {
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plot(survfit(surv_asct ~ 1), mark.time = TRUE, xscale = 365.25,
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xlab = "Years", ylab = "Survival")
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title("Kaplan-Meier estimate for\nsecMalASCT study",
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"Survival after transplantation")
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}
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# plot survival after transplantation per sex
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sma_plot_surv_asct_sex <- function() {
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plot(survfit(surv_asct ~ sex, data = secmal), mark.time = TRUE,
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xscale = 365.25, xlab = "Years", ylab = "Survival",
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lty = 2:3)
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title("Kaplan-Meier estimate for\nsecMalASCT study",
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"Survival after transplantation")
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legend(100, .9, c("Female", "Male"), lty = 2:3)
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}
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#
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# Write survival plots to files
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#
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sma_plot_file_surv <- function() {
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sma_plot_file("survival_dx.png", png, sma_plot_surv_dx)
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sma_plot_file("survival_dx_sex.png", png, sma_plot_surv_dx_sex)
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sma_plot_file("survival_asct.png", png, sma_plot_surv_asct)
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sma_plot_file("survival_asct_sex.png", png, sma_plot_surv_asct_sex)
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}
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